SGD-Wiki - User contributions [en]

SGD Newsletter, May 2026

2026-05-22T01:59:16Z

Suzia: /* Textpresso Literature Search: New Login System */

'''About this newsletter:''' 
This is the May 2026 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

== Contents ==

* [[#ygm2026|Join Us at Yeast Genetics Meeting 2026]]
* [[#blast|Introducing BLAST Search for SGD at the Alliance of Genome Resources]]
* [[#textpressosearch|Textpresso Literature Search: New Login System]]
* [[#naming|Naming Your Newly Characterized Yeast Gene: A Guide to SGD Gene Nomenclature]]
* [[#alliancenews|Alliance of Genome Resources News]]
* [[#latestmicropubs|microPublications – Latest Yeast Papers]]
* [[#upcoming|Upcoming Conferences & Courses]]
* [[#pombase|The End of PomBase?]]
* [[#davidbotstein|In Memoriam: David Botstein]]

== Join Us at Yeast Genetics Meeting 2026 ==


The [https://genetics-gsa.org/yeast-2026/ Yeast Genetics Meeting] is the premier meeting for people studying various aspects of eukaryotic biology in yeast, the major model organism for understanding human cell biology and human disease mechanisms. This international meeting has a [https://genetics-gsa.org/yeast/ 40-year history] and is held every two years in North America.

The SGD team will be at this year's Yeast Genetics Meeting at Asilomar, and we'd love to connect with you! We're hosting a workshop and will have a table and posters throughout the conference.

'''Workshop: Unlocking Yeast Biology with SGD: Tools, Data, and Discovery''' 
Monday, June 15, 2026 | 3:30 p.m. - 5:30 p.m.

Learn how to leverage the ''Saccharomyces'' Genome Database (SGD) to accelerate your research. This workshop will highlight key tools, curated datasets, and practical strategies for exploring gene function, pathways, and genomic data in ''Saccharomyces cerevisiae''. Whether you're a longtime SGD user or new to the resource, you'll discover ways to make the most of SGD's comprehensive data and analysis tools.

Stop by our table and posters during the meeting to chat with the SGD team, share your feedback, ask questions, or learn about the latest updates to SGD and the Alliance of Genome Resources. We look forward to seeing you there!

[[File:hotel-and-travel-e28093-yeast-genetics-meeting-2026-1.png]]

== Introducing BLAST Search for SGD at the Alliance of Genome Resources ==


[[File:Blast results.png|thumb|right]]

We're excited to announce the launch of a new BLAST service for ''Saccharomyces'' Genome Database (SGD) data, [https://www.alliancegenome.org/blastservice now available at the Alliance of Genome Resources]. This release marks another significant milestone in our ongoing effort to migrate SGD services and data to the Alliance platform, ensuring continued access to essential yeast genomics tools within an integrated, multi-organism framework.

'''What's New'''

The Alliance BLAST service provides researchers with powerful sequence similarity search capabilities against SGD datasets, maintaining the functionality that the yeast research community has relied on for years while benefiting from the Alliance's modern infrastructure and cross-species integration.

'''Key Features'''

* '''Comprehensive SGD datasets:''' Search against the complete ''S. cerevisiae'' genome, including coding sequences, proteins, and genomic DNA
* '''Familiar BLAST functionality:''' All standard BLAST algorithms (BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX) are supported
* '''Enhanced performance:''' Leveraging the Alliance's updated infrastructure for faster search results
* '''Cross-species exploration:''' Seamlessly explore homologs across other Alliance member databases

'''Part of a Broader Migration'''

This BLAST service is part of our comprehensive strategy to transition SGD resources to the Alliance of Genome Resources. This migration ensures that:

* SGD data remains accessible and well-maintained for the research community
* Users benefit from integration with data from other model organisms
* Resources are consolidated on a sustainable, collaborative platform
* The yeast community gains access to enhanced comparative genomics tools

Visit the Alliance of Genome Resources to access the new services for [https://www.alliancegenome.org/blast/SGD/R64-5-1m SGD BLAST] and [https://www.alliancegenome.org/blast/SGD/R64-5-1m Fungal BLAST]. The datasets will be familiar to longtime SGD users.

We remain committed to supporting the yeast research community through this transition. Additional SGD tools and features will continue to migrate to the Alliance platform in the coming months. Stay tuned for updates, and as always, we welcome your feedback.

== Textpresso Literature Search: New Login System ==


[[File:textpresso_logo.png|thumb|left|378px]]

Textpresso is a specialized literature search tool provided by SGD that allows users to search through full-text scientific articles using keywords.

It's particularly useful for finding specific mentions of genes, phenotypes, or experimental details that might not appear in article abstracts.

Textpresso has implemented a new authentication system using Amazon Cognito as part of the ongoing migration to the Alliance of Genome Resources infrastructure. Previously, Textpresso could be used without logging in, but going forward, all users will need to create a free account through a simple self-signup process. The new system provides secure authentication while maintaining the powerful literature search capabilities researchers depend on. When you next visit [https://sgd-textpresso.alliancegenome.org/tpc/search Textpresso], you'll be prompted to create an account using your email address. You'll receive a verification code to complete the setup, and then you'll be ready to search. Your existing Textpresso bookmarks will continue to work, you'll just need to log in first. More information: http://textmining.textpresso.org/new-login-system/

== Naming Your Newly Characterized Yeast Gene: A Guide to SGD Gene Nomenclature ==


Have you discovered the function of a previously uncharacterized ''Saccharomyces cerevisiae'' gene? Here's everything you need to know about giving it an official standard name.

'''Understanding Yeast Gene Nomenclature'''

SGD maintains the ''S. cerevisiae'' nomenclature according to guidelines established by the yeast research community. These conventions ensure consistency and clarity across the field, making it easier for researchers worldwide to communicate about genes and their functions.

'''The Naming Rules'''

Valid standard names for ''S. cerevisiae'' ORFs follow a simple but important format:

* Three letters followed by a number (for example, COX2 or CDC28)
* Must be unique, not previously used to describe another yeast gene
* Should ideally reflect function when possible

This naming convention has served the yeast community well for decades, creating an intuitive system where gene names often provide immediate clues about biological roles.

[[File:AI-gen_buddingwithpencil.png|thumb|right|AI-generated cartoon yeast cell and bud holding a pencil]]

'''How to Reserve Your Gene Name'''

If you're preparing to publish work on a gene that currently has only a systematic name (like YAL037W), reserve a standard name through SGD before publication. Here's how:

'''The Reservation Process'''

# '''Submit early:''' Reserve your gene name before you publish. A gene name reservation is valid for twelve months, which is typically enough time to write, submit, and publish your manuscript.
# '''Access the reservation form:''' Visit https://www.yeastgenome.org/reserved_name/new, or navigate from any SGD page using the purple toolbar at the top: Community > Nomenclature > Submit a Gene Registration.
# '''Publication makes it official:''' Your reserved gene name will become the standard gene name upon publication.

'''Best Practices for Publication'''

When you're ready to publish, we recommend:

✓ Double-check the literature to ensure your chosen name is still unique 
✓ Include both the ORF name and gene name in your abstract – this helps SGD and other databases find and curate your paper efficiently 
✓ Verify your reservation is still active if your publication timeline will extend beyond the initial twelve-month period

'''Need More Information?'''

You can review the [https://sites.google.com/view/yeastgenome-help/community-help/nomenclature-conventions nomenclature conventions for yeast] on our Help pages. The complete gene naming process is described in detail in our [https://sites.google.com/view/yeastgenome-help/community-help/gene-registry Gene Naming Guidelines].

'''Questions?'''

The SGD team is here to help! If you have questions about the gene name reservation process or nomenclature guidelines, please don't hesitate to contact us.

== Alliance of Genome Resources News ==


=== Alliance of Genome Resources – Latest Releases 9.0.0 & 8.3.0 ===

==== 9.0.0 Release '''– May 13, 2026''' ====

[[File:alliance_logo.png|220px|left|link=https://www.alliancegenome.org/]]

The [https://www.alliancegenome.org/release-notes 9.0.0 release] includes data refreshes from each of the model organism source databases as well as various backend improvements.

Updates and improvements have been made to the following pages:

* Non-gene genome features, e.g. enhancers, TF binding sites, etc., are now represented on their own respective "Gene" pages labeled as "GENOME FEATURE". Examples include [https://www.alliancegenome.org/gene/MGI:5000540 this enhancer page] and [https://www.alliancegenome.org/gene/MGI:6835783 this TF binding site page]
* The gene page Alleles and Variants table now has fully functional filtering for Allele symbol and Variant name
* Allele page Genomic Variant Information and (high-throughput) Variant page Summary widgets now display the relevant genome assembly, thousand comma separators for genomic coordinates (for ease of reading), and symbol hyperlinks to JBrowse for the respective variant
* Note that rs IDs for variants are no longer used to construct URLs for high-throughput variants matching the rs IDs because a single rs ID can represent multiple individual variants for which we would like to render a Variant page. Instead, HGVS.g names are used as unique identifiers in URLs to point to distinct and individual variants in a more robust manner. An example of an rs ID use on the 8.3.0 release and prior is rs864303764 which enabled a single URL in those prior releases but did not adequately represent all three individual variants that the rs ID represents. These are now represented by URLs constructed based on the full HGVS.g name for each variant: NC_000085.7:g.3684464A>C, NC_000085.7:g.3684464A>G, and NC_000085.7:g.3684464A>T (example URL: https://www.alliancegenome.org/variant/NC_000085.7:g.3684464A>C)
* Many high throughput variant insertions, deletions and indels had been mistakenly omitted from the Alliance variant data set, but have now been included for the 9.0.0 release
* This release makes available a large increase in the number of ''C. elegans'' alleles (~12K to ~1.9M) due to shifting data sources on our back end resources
* Gene page Summary widgets now display, where applicable, a gene systematic name (for fly, worm, and yeast genes) and UniProt Gene Centric Reference Proteome (GCRP) IDs, distinct from other UniProtKB IDs
* A number of significant backend changes have removed or modified existing Alliance public API endpoints. See [https://www.alliancegenome.org/release-notes release notes for examples].
** All "Cache Search" endpoints have been removed. See [https://www.alliancegenome.org/release-notes release notes for examples].
** All "Homology" endpoints have been removed (homology data can be extracted from the Orthology file on the Downloads page and endpoints for gene/orthologs and gene/paralogs). See [https://www.alliancegenome.org/release-notes release notes for examples].
** Other select endpoints have been removed, replaced by the updated endpoints. See [https://www.alliancegenome.org/release-notes release notes for examples].
** Modified endpoints are now compliant with [https://alliance-genome.github.io/agr_curation_schema/ our LinkML data model] and deliver a different JSON format from previous releases. See [https://www.alliancegenome.org/release-notes release notes for examples].

==== 8.3.0 Release '''– December 17, 2025''' ====

The [https://www.alliancegenome.org/release-notes 8.3.0 release] includes data refreshes from each of the model organism source databases as well as various backend improvements.

Updates and improvements have been made to the following pages:

* The News page https://www.alliancegenome.org/news now includes a feed for the Alliance Mastodon account.

* The Alliance BLAST Service page https://www.alliancegenome.org/blastservice has been updated to include fly, worm, yeast, fungal, and rat BLAST services. This BLAST service allows researchers to search genomic sequences using the Basic Local Alignment Search Tool (BLAST). By entering a sequence or query, users can find regions of similarity to various genomes within the Alliance. This service supports separate environments for each of the Model Organism Databases (MODs) as well as a unified environment for the Alliance. Results provide detailed alignments and annotations to aid in your research.
* Gene page [https://www.alliancegenome.org/gene/WB:WBGene00000912#transgenic-alleles transgenic alleles tables] have been updated with improved filter and sort options, and now include alleles where the focus gene plays a regulatory role in transgenic constructs.
* Gene page [https://www.alliancegenome.org/gene/MGI:109583#expression expression data] now features enhanced sorting capabilities and clearer formatting in downloadable files.

== microPublications – Latest Yeast Papers ==


[[File:MicroPub.png|120px|left|link=https://www.micropublication.org/]]

[https://www.micropublication.org/ microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral. Consider microPubublications when you have a result that doesn't necessarily fit into a larger story, but will be of value to others. [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= Latest yeast microPublications]:

* [https://www.yeastgenome.org/reference/S100003293 Wang TK, et al. (2026)] A cross-species rescue by mating method to interrogate gene essentiality across the ''Saccharomyces'' genus. MicroPubl Biol. 2026 Mar 27;2026:10.17912/micropub.biology.002022. doi: 10.17912/micropub.biology.002022. eCollection 2026.
* [https://www.yeastgenome.org/reference/S100002193 Brown K, Singuluri H, Perkins F, Kuchin S (2026)] The N-terminal α helix domain of the mitochondrial VDAC protein Por2 is dispensable for promoting the nuclear localization of yeast AMPK. MicroPubl Biol. 2026 Feb 23:2026:10.17912/micropub.biology.001040. doi: 10.17912/micropub.biology.001040. eCollection 2026.
* [https://yeastgenome.org/reference/S100002125 Ackermann LM, Ro A, Dunn B, Moore R, Doss G, Armstrong JO, Dunham MJ (2026)] Using Experimental Evolution to Correct Mother-Daughter Separation Defects in Brewing Yeast. MicroPubl

SGD Newsletter, May 2026

2026-05-21T23:20:52Z

Suzia:

'''About this newsletter:''' 
This is the May 2026 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

== Contents ==

* [[#ygm2026|Join Us at Yeast Genetics Meeting 2026]]
* [[#blast|Introducing BLAST Search for SGD at the Alliance of Genome Resources]]
* [[#textpressosearch|Textpresso Literature Search: New Login System]]
* [[#naming|Naming Your Newly Characterized Yeast Gene: A Guide to SGD Gene Nomenclature]]
* [[#alliancenews|Alliance of Genome Resources News]]
* [[#latestmicropubs|microPublications – Latest Yeast Papers]]
* [[#upcoming|Upcoming Conferences & Courses]]
* [[#pombase|The End of PomBase?]]
* [[#davidbotstein|In Memoriam: David Botstein]]

== Join Us at Yeast Genetics Meeting 2026 ==


The [https://genetics-gsa.org/yeast-2026/ Yeast Genetics Meeting] is the premier meeting for people studying various aspects of eukaryotic biology in yeast, the major model organism for understanding human cell biology and human disease mechanisms. This international meeting has a [https://genetics-gsa.org/yeast/ 40-year history] and is held every two years in North America.

The SGD team will be at this year's Yeast Genetics Meeting at Asilomar, and we'd love to connect with you! We're hosting a workshop and will have a table and posters throughout the conference.

'''Workshop: Unlocking Yeast Biology with SGD: Tools, Data, and Discovery''' 
Monday, June 15, 2026 | 3:30 p.m. - 5:30 p.m.

Learn how to leverage the ''Saccharomyces'' Genome Database (SGD) to accelerate your research. This workshop will highlight key tools, curated datasets, and practical strategies for exploring gene function, pathways, and genomic data in ''Saccharomyces cerevisiae''. Whether you're a longtime SGD user or new to the resource, you'll discover ways to make the most of SGD's comprehensive data and analysis tools.

Stop by our table and posters during the meeting to chat with the SGD team, share your feedback, ask questions, or learn about the latest updates to SGD and the Alliance of Genome Resources. We look forward to seeing you there!

[[File:hotel-and-travel-e28093-yeast-genetics-meeting-2026-1.png]]

== Introducing BLAST Search for SGD at the Alliance of Genome Resources ==


[[File:Blast results.png|thumb|right]]

We're excited to announce the launch of a new BLAST service for ''Saccharomyces'' Genome Database (SGD) data, [https://www.alliancegenome.org/blastservice now available at the Alliance of Genome Resources]. This release marks another significant milestone in our ongoing effort to migrate SGD services and data to the Alliance platform, ensuring continued access to essential yeast genomics tools within an integrated, multi-organism framework.

'''What's New'''

The Alliance BLAST service provides researchers with powerful sequence similarity search capabilities against SGD datasets, maintaining the functionality that the yeast research community has relied on for years while benefiting from the Alliance's modern infrastructure and cross-species integration.

'''Key Features'''

* '''Comprehensive SGD datasets:''' Search against the complete ''S. cerevisiae'' genome, including coding sequences, proteins, and genomic DNA
* '''Familiar BLAST functionality:''' All standard BLAST algorithms (BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX) are supported
* '''Enhanced performance:''' Leveraging the Alliance's updated infrastructure for faster search results
* '''Cross-species exploration:''' Seamlessly explore homologs across other Alliance member databases

'''Part of a Broader Migration'''

This BLAST service is part of our comprehensive strategy to transition SGD resources to the Alliance of Genome Resources. This migration ensures that:

* SGD data remains accessible and well-maintained for the research community
* Users benefit from integration with data from other model organisms
* Resources are consolidated on a sustainable, collaborative platform
* The yeast community gains access to enhanced comparative genomics tools

Visit the Alliance of Genome Resources to access the new services for [https://www.alliancegenome.org/blast/SGD/R64-5-1m SGD BLAST] and [https://www.alliancegenome.org/blast/SGD/R64-5-1m Fungal BLAST]. The datasets will be familiar to longtime SGD users.

We remain committed to supporting the yeast research community through this transition. Additional SGD tools and features will continue to migrate to the Alliance platform in the coming months. Stay tuned for updates, and as always, we welcome your feedback.

== Textpresso Literature Search: New Login System ==


[[File:textpresso_logo.png|thumb|right|378px]]

Textpresso is a specialized literature search tool provided by SGD that allows users to search through full-text scientific articles using keywords.

It's particularly useful for finding specific mentions of genes, phenotypes, or experimental details that might not appear in article abstracts.

Textpresso has implemented a new authentication system using Amazon Cognito as part of the ongoing migration to the Alliance of Genome Resources infrastructure. Previously, Textpresso could be used without logging in, but going forward, all users will need to create a free account through a simple self-signup process. The new system provides secure authentication while maintaining the powerful literature search capabilities researchers depend on. When you next visit [https://sgd-textpresso.alliancegenome.org/tpc/search Textpresso], you'll be prompted to create an account using your email address. You'll receive a verification code to complete the setup, and then you'll be ready to search. Your existing Textpresso bookmarks will continue to work, you'll just need to log in first. More information: http://textmining.textpresso.org/new-login-system/

== Naming Your Newly Characterized Yeast Gene: A Guide to SGD Gene Nomenclature ==


Have you discovered the function of a previously uncharacterized ''Saccharomyces cerevisiae'' gene? Here's everything you need to know about giving it an official standard name.

'''Understanding Yeast Gene Nomenclature'''

SGD maintains the ''S. cerevisiae'' nomenclature according to guidelines established by the yeast research community. These conventions ensure consistency and clarity across the field, making it easier for researchers worldwide to communicate about genes and their functions.

'''The Naming Rules'''

Valid standard names for ''S. cerevisiae'' ORFs follow a simple but important format:

* Three letters followed by a number (for example, COX2 or CDC28)
* Must be unique, not previously used to describe another yeast gene
* Should ideally reflect function when possible

This naming convention has served the yeast community well for decades, creating an intuitive system where gene names often provide immediate clues about biological roles.

[[File:AI-gen_buddingwithpencil.png|thumb|right|AI-generated cartoon yeast cell and bud holding a pencil]]

'''How to Reserve Your Gene Name'''

If you're preparing to publish work on a gene that currently has only a systematic name (like YAL037W), reserve a standard name through SGD before publication. Here's how:

'''The Reservation Process'''

# '''Submit early:''' Reserve your gene name before you publish. A gene name reservation is valid for twelve months, which is typically enough time to write, submit, and publish your manuscript.
# '''Access the reservation form:''' Visit https://www.yeastgenome.org/reserved_name/new, or navigate from any SGD page using the purple toolbar at the top: Community > Nomenclature > Submit a Gene Registration.
# '''Publication makes it official:''' Your reserved gene name will become the standard gene name upon publication.

'''Best Practices for Publication'''

When you're ready to publish, we recommend:

✓ Double-check the literature to ensure your chosen name is still unique 
✓ Include both the ORF name and gene name in your abstract – this helps SGD and other databases find and curate your paper efficiently 
✓ Verify your reservation is still active if your publication timeline will extend beyond the initial twelve-month period

'''Need More Information?'''

You can review the [https://sites.google.com/view/yeastgenome-help/community-help/nomenclature-conventions nomenclature conventions for yeast] on our Help pages. The complete gene naming process is described in detail in our [https://sites.google.com/view/yeastgenome-help/community-help/gene-registry Gene Naming Guidelines].

'''Questions?'''

The SGD team is here to help! If you have questions about the gene name reservation process or nomenclature guidelines, please don't hesitate to contact us.

== Alliance of Genome Resources News ==


=== Alliance of Genome Resources – Latest Releases 9.0.0 & 8.3.0 ===

==== 9.0.0 Release '''– May 13, 2026''' ====

[[File:alliance_logo.png|220px|left|link=https://www.alliancegenome.org/]]

The [https://www.alliancegenome.org/release-notes 9.0.0 release] includes data refreshes from each of the model organism source databases as well as various backend improvements.

Updates and improvements have been made to the following pages:

* Non-gene genome features, e.g. enhancers, TF binding sites, etc., are now represented on their own respective "Gene" pages labeled as "GENOME FEATURE". Examples include [https://www.alliancegenome.org/gene/MGI:5000540 this enhancer page] and [https://www.alliancegenome.org/gene/MGI:6835783 this TF binding site page]
* The gene page Alleles and Variants table now has fully functional filtering for Allele symbol and Variant name
* Allele page Genomic Variant Information and (high-throughput) Variant page Summary widgets now display the relevant genome assembly, thousand comma separators for genomic coordinates (for ease of reading), and symbol hyperlinks to JBrowse for the respective variant
* Note that rs IDs for variants are no longer used to construct URLs for high-throughput variants matching the rs IDs because a single rs ID can represent multiple individual variants for which we would like to render a Variant page. Instead, HGVS.g names are used as unique identifiers in URLs to point to distinct and individual variants in a more robust manner. An example of an rs ID use on the 8.3.0 release and prior is rs864303764 which enabled a single URL in those prior releases but did not adequately represent all three individual variants that the rs ID represents. These are now represented by URLs constructed based on the full HGVS.g name for each variant: NC_000085.7:g.3684464A>C, NC_000085.7:g.3684464A>G, and NC_000085.7:g.3684464A>T (example URL: https://www.alliancegenome.org/variant/NC_000085.7:g.3684464A>C)
* Many high throughput variant insertions, deletions and indels had been mistakenly omitted from the Alliance variant data set, but have now been included for the 9.0.0 release
* This release makes available a large increase in the number of ''C. elegans'' alleles (~12K to ~1.9M) due to shifting data sources on our back end resources
* Gene page Summary widgets now display, where applicable, a gene systematic name (for fly, worm, and yeast genes) and UniProt Gene Centric Reference Proteome (GCRP) IDs, distinct from other UniProtKB IDs
* A number of significant backend changes have removed or modified existing Alliance public API endpoints. See [https://www.alliancegenome.org/release-notes release notes for examples].
** All "Cache Search" endpoints have been removed. See [https://www.alliancegenome.org/release-notes release notes for examples].
** All "Homology" endpoints have been removed (homology data can be extracted from the Orthology file on the Downloads page and endpoints for gene/orthologs and gene/paralogs). See [https://www.alliancegenome.org/release-notes release notes for examples].
** Other select endpoints have been removed, replaced by the updated endpoints. See [https://www.alliancegenome.org/release-notes release notes for examples].
** Modified endpoints are now compliant with [https://alliance-genome.github.io/agr_curation_schema/ our LinkML data model] and deliver a different JSON format from previous releases. See [https://www.alliancegenome.org/release-notes release notes for examples].

==== 8.3.0 Release '''– December 17, 2025''' ====

The [https://www.alliancegenome.org/release-notes 8.3.0 release] includes data refreshes from each of the model organism source databases as well as various backend improvements.

Updates and improvements have been made to the following pages:

* The News page https://www.alliancegenome.org/news now includes a feed for the Alliance Mastodon account.

* The Alliance BLAST Service page https://www.alliancegenome.org/blastservice has been updated to include fly, worm, yeast, fungal, and rat BLAST services. This BLAST service allows researchers to search genomic sequences using the Basic Local Alignment Search Tool (BLAST). By entering a sequence or query, users can find regions of similarity to various genomes within the Alliance. This service supports separate environments for each of the Model Organism Databases (MODs) as well as a unified environment for the Alliance. Results provide detailed alignments and annotations to aid in your research.
* Gene page [https://www.alliancegenome.org/gene/WB:WBGene00000912#transgenic-alleles transgenic alleles tables] have been updated with improved filter and sort options, and now include alleles where the focus gene plays a regulatory role in transgenic constructs.
* Gene page [https://www.alliancegenome.org/gene/MGI:109583#expression expression data] now features enhanced sorting capabilities and clearer formatting in downloadable files.

== microPublications – Latest Yeast Papers ==


[[File:MicroPub.png|120px|left|link=https://www.micropublication.org/]]

[https://www.micropublication.org/ microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral. Consider microPubublications when you have a result that doesn't necessarily fit into a larger story, but will be of value to others. [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= Latest yeast microPublications]:

* [https://www.yeastgenome.org/reference/S100003293 Wang TK, et al. (2026)] A cross-species rescue by mating method to interrogate gene essentiality across the ''Saccharomyces'' genus. MicroPubl Biol. 2026 Mar 27;2026:10.17912/micropub.biology.002022. doi: 10.17912/micropub.biology.002022. eCollection 2026.
* [https://www.yeastgenome.org/reference/S100002193 Brown K, Singuluri H, Perkins F, Kuchin S (2026)] The N-terminal α helix domain of the mitochondrial VDAC protein Por2 is dispensable for promoting the nuclear localization of yeast AMPK. MicroPubl Biol. 2026 Feb 23:2026:10.17912/micropub.biology.001040. doi: 10.17912/micropub.biology.001040. eCollection 2026.
* [https://yeastgenome.org/reference/S100002125 Ackermann LM, Ro A, Dunn B, Moore R, Doss G, Armstrong JO, Dunham MJ (2026)] Using Experimental Evolution to Correct Mother-Daughter Separation Defects in Brewing Yeast. MicroPubl

File:AI-gen buddingwithpencil.png

2026-05-21T23:17:00Z

Suzia:

File:textpresso logo.png

2026-05-21T20:44:30Z

Suzia:

File:Blast results.png

2026-05-21T20:42:51Z

Suzia:

File:hotel-and-travel-e28093-yeast-genetics-meeting-2026-1.png

2026-05-21T20:41:19Z

Suzia:

SGD Newsletter, May 2026

2026-05-21T15:55:32Z

Suzia: Created page with "'''About this newsletter:''' This is the May 2026 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster c..."

'''About this newsletter:''' 
This is the May 2026 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

== Contents ==

* [[#ygm2026|Join Us at Yeast Genetics Meeting 2026]]
* [[#blast|Introducing BLAST Search for SGD at the Alliance of Genome Resources]]
* [[#textpressosearch|Textpresso Literature Search: New Login System]]
* [[#naming|Naming Your Newly Characterized Yeast Gene: A Guide to SGD Gene Nomenclature]]
* [[#alliancenews|Alliance of Genome Resources News]]
* [[#latestmicropubs|microPublications – Latest Yeast Papers]]
* [[#upcoming|Upcoming Conferences & Courses]]
* [[#pombase|The End of PomBase?]]
* [[#davidbotstein|In Memoriam: David Botstein]]

== Join Us at Yeast Genetics Meeting 2026 ==


The [https://genetics-gsa.org/yeast-2026/ Yeast Genetics Meeting] is the premier meeting for people studying various aspects of eukaryotic biology in yeast, the major model organism for understanding human cell biology and human disease mechanisms. This international meeting has a [https://genetics-gsa.org/yeast/ 40-year history] and is held every two years in North America.

The SGD team will be at this year's Yeast Genetics Meeting at Asilomar, and we'd love to connect with you! We're hosting a workshop and will have a table and posters throughout the conference.

'''Workshop: Unlocking Yeast Biology with SGD: Tools, Data, and Discovery''' 
Monday, June 15, 2026 | 3:30 p.m. - 5:30 p.m.

Learn how to leverage the ''Saccharomyces'' Genome Database (SGD) to accelerate your research. This workshop will highlight key tools, curated datasets, and practical strategies for exploring gene function, pathways, and genomic data in ''Saccharomyces cerevisiae''. Whether you're a longtime SGD user or new to the resource, you'll discover ways to make the most of SGD's comprehensive data and analysis tools.

Stop by our table and posters during the meeting to chat with the SGD team, share your feedback, ask questions, or learn about the latest updates to SGD and the Alliance of Genome Resources. We look forward to seeing you there!

[[File:screenshot-2026-04-30-at-22-01-41-hotel-and-travel-e28093-yeast-genetics-meeting-2026-1.png]]

== Introducing BLAST Search for SGD at the Alliance of Genome Resources ==


[[File:screenshot-2026-02-17-at-15.39.05-3.png|thumb|right]]

We're excited to announce the launch of a new BLAST service for ''Saccharomyces'' Genome Database (SGD) data, [https://www.alliancegenome.org/blastservice now available at the Alliance of Genome Resources]. This release marks another significant milestone in our ongoing effort to migrate SGD services and data to the Alliance platform, ensuring continued access to essential yeast genomics tools within an integrated, multi-organism framework.

'''What's New'''

The Alliance BLAST service provides researchers with powerful sequence similarity search capabilities against SGD datasets, maintaining the functionality that the yeast research community has relied on for years while benefiting from the Alliance's modern infrastructure and cross-species integration.

'''Key Features'''

* '''Comprehensive SGD datasets:''' Search against the complete ''S. cerevisiae'' genome, including coding sequences, proteins, and genomic DNA
* '''Familiar BLAST functionality:''' All standard BLAST algorithms (BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX) are supported
* '''Enhanced performance:''' Leveraging the Alliance's updated infrastructure for faster search results
* '''Cross-species exploration:''' Seamlessly explore homologs across other Alliance member databases

'''Part of a Broader Migration'''

This BLAST service is part of our comprehensive strategy to transition SGD resources to the Alliance of Genome Resources. This migration ensures that:

* SGD data remains accessible and well-maintained for the research community
* Users benefit from integration with data from other model organisms
* Resources are consolidated on a sustainable, collaborative platform
* The yeast community gains access to enhanced comparative genomics tools

Visit the Alliance of Genome Resources to access the new services for [https://www.alliancegenome.org/blast/SGD/R64-5-1m SGD BLAST] and [https://www.alliancegenome.org/blast/SGD/R64-5-1m Fungal BLAST]. The datasets will be familiar to longtime SGD users.

We remain committed to supporting the yeast research community through this transition. Additional SGD tools and features will continue to migrate to the Alliance platform in the coming months. Stay tuned for updates, and as always, we welcome your feedback.

== Textpresso Literature Search: New Login System ==


[[File:screenshot-2026-05-01-at-14-01-02-sgd-newsletter-may-2026-google-docs.png|thumb|right|378px]]

Textpresso is a specialized literature search tool provided by SGD that allows users to search through full-text scientific articles using keywords.

It's particularly useful for finding specific mentions of genes, phenotypes, or experimental details that might not appear in article abstracts.

Textpresso has implemented a new authentication system using Amazon Cognito as part of the ongoing migration to the Alliance of Genome Resources infrastructure. Previously, Textpresso could be used without logging in, but going forward, all users will need to create a free account through a simple self-signup process. The new system provides secure authentication while maintaining the powerful literature search capabilities researchers depend on. When you next visit [https://sgd-textpresso.alliancegenome.org/tpc/search Textpresso], you'll be prompted to create an account using your email address. You'll receive a verification code to complete the setup, and then you'll be ready to search. Your existing Textpresso bookmarks will continue to work, you'll just need to log in first. More information: http://textmining.textpresso.org/new-login-system/

== Naming Your Newly Characterized Yeast Gene: A Guide to SGD Gene Nomenclature ==


Have you discovered the function of a previously uncharacterized ''Saccharomyces cerevisiae'' gene? Here's everything you need to know about giving it an official standard name.

'''Understanding Yeast Gene Nomenclature'''

SGD maintains the ''S. cerevisiae'' nomenclature according to guidelines established by the yeast research community. These conventions ensure consistency and clarity across the field, making it easier for researchers worldwide to communicate about genes and their functions.

'''The Naming Rules'''

Valid standard names for ''S. cerevisiae'' ORFs follow a simple but important format:

* Three letters followed by a number (for example, COX2 or CDC28)
* Must be unique, not previously used to describe another yeast gene
* Should ideally reflect function when possible

This naming convention has served the yeast community well for decades, creating an intuitive system where gene names often provide immediate clues about biological roles.

[[File:sgd-blog-6a04d03390eb1.png|thumb|right|AI-generated cartoon yeast cell and bud holding a pencil]]

'''How to Reserve Your Gene Name'''

If you're preparing to publish work on a gene that currently has only a systematic name (like YAL037W), reserve a standard name through SGD before publication. Here's how:

'''The Reservation Process'''

# '''Submit early:''' Reserve your gene name before you publish. A gene name reservation is valid for twelve months, which is typically enough time to write, submit, and publish your manuscript.
# '''Access the reservation form:''' Visit https://www.yeastgenome.org/reserved_name/new, or navigate from any SGD page using the purple toolbar at the top: Community > Nomenclature > Submit a Gene Registration.
# '''Publication makes it official:''' Your reserved gene name will become the standard gene name upon publication.

'''Best Practices for Publication'''

When you're ready to publish, we recommend:

✓ Double-check the literature to ensure your chosen name is still unique 
✓ Include both the ORF name and gene name in your abstract – this helps SGD and other databases find and curate your paper efficiently 
✓ Verify your reservation is still active if your publication timeline will extend beyond the initial twelve-month period

'''Need More Information?'''

You can review the [https://sites.google.com/view/yeastgenome-help/community-help/nomenclature-conventions nomenclature conventions for yeast] on our Help pages. The complete gene naming process is described in detail in our [https://sites.google.com/view/yeastgenome-help/community-help/gene-registry Gene Naming Guidelines].

'''Questions?'''

The SGD team is here to help! If you have questions about the gene name reservation process or nomenclature guidelines, please don't hesitate to contact us.

== Alliance of Genome Resources News ==


=== Alliance of Genome Resources – Latest Releases 9.0.0 & 8.3.0 ===

==== 9.0.0 Release '''– May 13, 2026''' ====

[[File:alliance_logo.png|220px|left|link=https://www.alliancegenome.org/]]

The [https://www.alliancegenome.org/release-notes 9.0.0 release] includes data refreshes from each of the model organism source databases as well as various backend improvements.

Updates and improvements have been made to the following pages:

* Non-gene genome features, e.g. enhancers, TF binding sites, etc., are now represented on their own respective "Gene" pages labeled as "GENOME FEATURE". Examples include [https://www.alliancegenome.org/gene/MGI:5000540 this enhancer page] and [https://www.alliancegenome.org/gene/MGI:6835783 this TF binding site page]
* The gene page Alleles and Variants table now has fully functional filtering for Allele symbol and Variant name
* Allele page Genomic Variant Information and (high-throughput) Variant page Summary widgets now display the relevant genome assembly, thousand comma separators for genomic coordinates (for ease of reading), and symbol hyperlinks to JBrowse for the respective variant
* Note that rs IDs for variants are no longer used to construct URLs for high-throughput variants matching the rs IDs because a single rs ID can represent multiple individual variants for which we would like to render a Variant page. Instead, HGVS.g names are used as unique identifiers in URLs to point to distinct and individual variants in a more robust manner. An example of an rs ID use on the 8.3.0 release and prior is rs864303764 which enabled a single URL in those prior releases but did not adequately represent all three individual variants that the rs ID represents. These are now represented by URLs constructed based on the full HGVS.g name for each variant: NC_000085.7:g.3684464A>C, NC_000085.7:g.3684464A>G, and NC_000085.7:g.3684464A>T (example URL: https://www.alliancegenome.org/variant/NC_000085.7:g.3684464A>C)
* Many high throughput variant insertions, deletions and indels had been mistakenly omitted from the Alliance variant data set, but have now been included for the 9.0.0 release
* This release makes available a large increase in the number of ''C. elegans'' alleles (~12K to ~1.9M) due to shifting data sources on our back end resources
* Gene page Summary widgets now display, where applicable, a gene systematic name (for fly, worm, and yeast genes) and UniProt Gene Centric Reference Proteome (GCRP) IDs, distinct from other UniProtKB IDs
* A number of significant backend changes have removed or modified existing Alliance public API endpoints. See [https://www.alliancegenome.org/release-notes release notes for examples].
** All "Cache Search" endpoints have been removed. See [https://www.alliancegenome.org/release-notes release notes for examples].
** All "Homology" endpoints have been removed (homology data can be extracted from the Orthology file on the Downloads page and endpoints for gene/orthologs and gene/paralogs). See [https://www.alliancegenome.org/release-notes release notes for examples].
** Other select endpoints have been removed, replaced by the updated endpoints. See [https://www.alliancegenome.org/release-notes release notes for examples].
** Modified endpoints are now compliant with [https://alliance-genome.github.io/agr_curation_schema/ our LinkML data model] and deliver a different JSON format from previous releases. See [https://www.alliancegenome.org/release-notes release notes for examples].

==== 8.3.0 Release '''– December 17, 2025''' ====

The [https://www.alliancegenome.org/release-notes 8.3.0 release] includes data refreshes from each of the model organism source databases as well as various backend improvements.

Updates and improvements have been made to the following pages:

* The News page https://www.alliancegenome.org/news now includes a feed for the Alliance Mastodon account.

* The Alliance BLAST Service page https://www.alliancegenome.org/blastservice has been updated to include fly, worm, yeast, fungal, and rat BLAST services. This BLAST service allows researchers to search genomic sequences using the Basic Local Alignment Search Tool (BLAST). By entering a sequence or query, users can find regions of similarity to various genomes within the Alliance. This service supports separate environments for each of the Model Organism Databases (MODs) as well as a unified environment for the Alliance. Results provide detailed alignments and annotations to aid in your research.
* Gene page [https://www.alliancegenome.org/gene/WB:WBGene00000912#transgenic-alleles transgenic alleles tables] have been updated with improved filter and sort options, and now include alleles where the focus gene plays a regulatory role in transgenic constructs.
* Gene page [https://www.alliancegenome.org/gene/MGI:109583#expression expression data] now features enhanced sorting capabilities and clearer formatting in downloadable files.

== microPublications – Latest Yeast Papers ==


[[File:MicroPub.png|120px|left|link=https://www.micropublication.org/]]

[https://www.micropublication.org/ microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral. Consider microPubublications when you have a result that doesn't necessarily fit into a larger story, but will be of value to others. [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= Latest yeast microPublications]:

* [https://www.yeastgenome.org/reference/S100003293 Wang TK, et al. (2026)] A cross-species rescue by mating method to interrogate gene essentiality across the ''Saccharomyces'' genus. MicroPubl Biol. 2026 Mar 27;2026:10.17912/micropub.biology.002022. doi: 10.17912/micropub.biology.002022. eCollection 2026.
* [https://www.yeastgenome.org/reference/S100002193 Brown K, Singuluri H, Perkins F, Kuchin S (2026)] The N-terminal α helix domain of the mitochondrial VDAC protein Por2 is dispensable for promoting the nuclear localization of yeast AMPK. MicroPubl Biol. 2026 Feb 23:2026:10.17912/micropub.biology.001040. doi: 10.17912/micropub.biology.001040. eCollection 2026.
* [https://yeastgenome.org/reference/S100002125 Ackermann LM, Ro A, Dunn B, Moore R, Doss G, Armstrong JO, Dunham MJ (2026)] Using Experimental Evolution to Correct Mother-Daughter Separation Defects in Brewing Yeast. MicroPubl

SGD Newsletter Archives

2026-05-02T00:04:43Z

Suzia:

[[Category:Newsletter]]
SGD periodically publishes a community newsletters. This page contains links to the SGD Newsletters that have been released, listed in chronological order. Click on a date to see the newsletter published on that date.

{| width="50%" border="1"
|-
| '''2026'''
|
|
|
|
|-bgcolor="E6E6FA"
| '''2025'''
|
|[[SGD_Newsletter,_Spring_2025 | 2025-04-24]]
|
|[[SGD_Newsletter,_December_2025 | 2025-12-11]]
|-
| '''2024'''
|
|[[SGD_Newsletter,_Summer_2024 | 2024-06-19]]
|
|[[SGD_Newsletter,_Winter_2024 | 2024-12-12]]
|-bgcolor="E6E6FA"

| '''2023'''
|
|[[SGD_Newsletter,_Summer_2023 | 2023-06-22]]
|
|[[SGD_Newsletter,_December_2023 | 2023-12-13]]
|-
| '''2022'''
|
|
|[[SGD_Newsletter,_Summer_2022 | 2022-08-01]]
|
|-
|-bgcolor="E6E6FA"
| '''2021'''
|
|[[SGD_Newsletter,_Spring_2021 | 2021-05-27]]
|
|[[SGD_Newsletter,_Fall_2021 | 2021-12-14]]
|-
| '''2020'''
|
|[[SGD_Newsletter,_Summer_2020 | 2020-06-08]]
|
|[[SGD_Newsletter,_Fall 2020 | 2020-12-08]]
|-bgcolor="E6E6FA"
| '''2019'''
|
|[[SGD_Newsletter,_Spring_2019 | 2019-05-29]]
|
|[[SGD_Newsletter,_Fall_2019 | 2019-12-05]]
|-
|'''2018'''
|
|[[SGD_Newsletter,_April_2018 | 2018-04-30]]
|[[SGD_Newsletter,_Fall_2018 | 2018-10-05]]
|
|-bgcolor="E6E6FA"
|'''2017'''
|
|
|
| [[SGD_Newsletter,_December_2017 | 2017-12-20]]
|-
|'''2016'''
| [[SGD_Newsletter,_March_2016 | 2016-03-14]]
|
| [[SGD_Newsletter,_August_2016|2016-08-29]]
| [[SGD_Newsletter,_December_2016 | 2016-12-20]]
|- bgcolor="E6E6FA"
| '''2015'''
| [[SGD_Quarterly_Newsletter,_Spring_2015| 2015-02-26]]
|
| [[SGD_Quarterly_Newsletter,_Summer_2015 | 2015-08-28]]
| [[SGD_Newsletter,_December_2015 | 2015-12-18]]
|-
| '''2014'''
|
| [[SGD_Quarterly_Newsletter,_Spring_2014| 2014-04-17]]
| [[SGD_Quarterly_Newsletter,_Summer_2014| 2014-07-23]]
| [[SGD_Quarterly_Newsletter,_Fall_2014|2014-10-15]]
|- bgcolor="E6E6FA"
| '''2013'''
|
| [[SGD_Quarterly_Newsletter,_Summer_2013| 2013-06-10]]
|
| [[SGD_Quarterly_Newsletter,_Winter_2013| 2013-12-16]]
|-
| '''2012'''
| [[SGD_Quarterly_Newsletter,_Winter_2012| 2012-01-27]]
| [[SGD_Quarterly_Newsletter,_Spring_2012| 2012-04-28]]
| [[SGD_Quarterly_Newsletter,_Summer_2012| 2012-08-22]]
| [[SGD_Quarterly_Newsletter,_Fall_2012| 2012-12-13]]
|- bgcolor="E6E6FA"
| '''2011'''
| [[SGD_Quarterly_Newsletter,_Winter_2011| 2011-02-18]]
| [[SGD_Quarterly_Newsletter,_Spring_2011| 2011-05-05]]
| [[SGD_Quarterly_Newsletter,_Summer_2011| 2011-08-11]]
|
|-
| '''2010'''
| [[SGD_Quarterly_Newsletter,_Winter_2010| 2010-01-29]]
| [[SGD_Quarterly_Newsletter,_Spring_2010| 2010-04-29]]
| [[SGD_Quarterly_Newsletter,_Summer_2010| 2010-07-22]]
| [[SGD_Quarterly_Newsletter,_Fall_2010| 2010-11-01]]
|- bgcolor="E6E6FA"
| '''2009'''
| [[SGD_Quarterly_Newsletter,_Winter_2009| 2009-02-03]]
| [[SGD_Quarterly_Newsletter,_Spring_2009| 2009-05-01]]
| [[SGD_Quarterly_Newsletter,_Summer_2009| 2009-08-04]]
| [[SGD_Quarterly_Newsletter,_Fall_2009| 2009-11-06]]
|-
| '''2008'''
| [[SGD_Quarterly_Newsletter,_Winter_2008| 2008-01-31]]
| [[SGD_Quarterly_Newsletter,_Spring_2008| 2008-04-30]]
| [[SGD_Quarterly_Newsletter,_Summer_2008| 2008-07-31]]
| [[SGD_Quarterly_Newsletter,_Fall_2008| 2008-11-03]]
|- bgcolor="E6E6FA"
| '''2007'''
| [[SGD_Quarterly_Newsletter,_Winter_2007| 2007-01-29]]
| [[SGD_Quarterly_Newsletter,_Spring_2007| 2007-05-07]]
| [[SGD_Quarterly_Newsletter,_Summer_2007| 2007-07-30]]
| [[SGD_Quarterly_Newsletter,_Fall_2007| 2007-11-08]]
|-
| '''2006'''
| [[SGD_Quarterly_Newsletter,_Winter_2006| 2006-02-02]]
| [[SGD_Quarterly_Newsletter,_Spring_2006| 2006-05-01]]
| [[SGD_Quarterly_Newsletter,_Summer_2006| 2006-07-20]]
| [[SGD_Quarterly_Newsletter,_Fall_2006| 2006-11-01]]
|- bgcolor="E6E6FA"
| '''2005'''
| [[SGD_Quarterly_Newsletter,_Winter_2005| 2005-01-31]]
| [[SGD_Quarterly_Newsletter,_Spring_2005| 2005-04-28]]
| [[SGD_Quarterly_Newsletter,_Summer_2005| 2005-07-29]]
| [[SGD_Quarterly_Newsletter,_Fall_2005| 2005-10-24]]
|-
| '''2004'''
| [[SGD_Quarterly_Newsletter,_Winter_2004| 2004-01-30]]
| [[SGD_Quarterly_Newsletter,_Spring_2004| 2004-04-26]]
| [[SGD_Quarterly_Newsletter,_Summer_2004| 2004-07-23]]
| [[SGD_Quarterly_Newsletter,_Fall_2004| 2004-11-18]]
|- bgcolor="E6E6FA"
| '''2003'''
| [[SGD_Quarterly_Newsletter,_Winter_2003| 2003-01-31]]
| [[SGD_Quarterly_Newsletter,_Spring_2003| 2003-04-28]]
| [[SGD_Quarterly_Newsletter,_Summer_2003| 2003-08-04]]
| [[SGD_Quarterly_Newsletter,_Fall_2003| 2003-10-31]]
|-
|}

SGD Newsletter Archives

2026-05-02T00:03:15Z

Suzia:

[[Category:Newsletter]]
SGD periodically publishes a community newsletters. This page contains links to the SGD Newsletters that have been released, listed in chronological order. Click on a date to see the newsletter published on that date.

{| width="50%" border="1"
|-bgcolor="E6E6FA"
| '''2026'''
|
|
|
|
|-
| '''2025'''
|
|[[SGD_Newsletter,_Spring_2025 | 2025-04-24]]
|
|[[SGD_Newsletter,_December_2025 | 2025-12-11]]
|-
| '''2024'''
|
|[[SGD_Newsletter,_Summer_2024 | 2024-06-19]]
|
|[[SGD_Newsletter,_Winter_2024 | 2024-12-12]]
|-

| '''2023'''
|
|[[SGD_Newsletter,_Summer_2023 | 2023-06-22]]
|
|[[SGD_Newsletter,_December_2023 | 2023-12-13]]
|-
| '''2022'''
|
|
|[[SGD_Newsletter,_Summer_2022 | 2022-08-01]]
|
|-
|-bgcolor="E6E6FA"
| '''2021'''
|
|[[SGD_Newsletter,_Spring_2021 | 2021-05-27]]
|
|[[SGD_Newsletter,_Fall_2021 | 2021-12-14]]
|-
| '''2020'''
|
|[[SGD_Newsletter,_Summer_2020 | 2020-06-08]]
|
|[[SGD_Newsletter,_Fall 2020 | 2020-12-08]]
|-bgcolor="E6E6FA"
| '''2019'''
|
|[[SGD_Newsletter,_Spring_2019 | 2019-05-29]]
|
|[[SGD_Newsletter,_Fall_2019 | 2019-12-05]]
|-
|'''2018'''
|
|[[SGD_Newsletter,_April_2018 | 2018-04-30]]
|[[SGD_Newsletter,_Fall_2018 | 2018-10-05]]
|
|-bgcolor="E6E6FA"
|'''2017'''
|
|
|
| [[SGD_Newsletter,_December_2017 | 2017-12-20]]
|-
|'''2016'''
| [[SGD_Newsletter,_March_2016 | 2016-03-14]]
|
| [[SGD_Newsletter,_August_2016|2016-08-29]]
| [[SGD_Newsletter,_December_2016 | 2016-12-20]]
|- bgcolor="E6E6FA"
| '''2015'''
| [[SGD_Quarterly_Newsletter,_Spring_2015| 2015-02-26]]
|
| [[SGD_Quarterly_Newsletter,_Summer_2015 | 2015-08-28]]
| [[SGD_Newsletter,_December_2015 | 2015-12-18]]
|-
| '''2014'''
|
| [[SGD_Quarterly_Newsletter,_Spring_2014| 2014-04-17]]
| [[SGD_Quarterly_Newsletter,_Summer_2014| 2014-07-23]]
| [[SGD_Quarterly_Newsletter,_Fall_2014|2014-10-15]]
|- bgcolor="E6E6FA"
| '''2013'''
|
| [[SGD_Quarterly_Newsletter,_Summer_2013| 2013-06-10]]
|
| [[SGD_Quarterly_Newsletter,_Winter_2013| 2013-12-16]]
|-
| '''2012'''
| [[SGD_Quarterly_Newsletter,_Winter_2012| 2012-01-27]]
| [[SGD_Quarterly_Newsletter,_Spring_2012| 2012-04-28]]
| [[SGD_Quarterly_Newsletter,_Summer_2012| 2012-08-22]]
| [[SGD_Quarterly_Newsletter,_Fall_2012| 2012-12-13]]
|- bgcolor="E6E6FA"
| '''2011'''
| [[SGD_Quarterly_Newsletter,_Winter_2011| 2011-02-18]]
| [[SGD_Quarterly_Newsletter,_Spring_2011| 2011-05-05]]
| [[SGD_Quarterly_Newsletter,_Summer_2011| 2011-08-11]]
|
|-
| '''2010'''
| [[SGD_Quarterly_Newsletter,_Winter_2010| 2010-01-29]]
| [[SGD_Quarterly_Newsletter,_Spring_2010| 2010-04-29]]
| [[SGD_Quarterly_Newsletter,_Summer_2010| 2010-07-22]]
| [[SGD_Quarterly_Newsletter,_Fall_2010| 2010-11-01]]
|- bgcolor="E6E6FA"
| '''2009'''
| [[SGD_Quarterly_Newsletter,_Winter_2009| 2009-02-03]]
| [[SGD_Quarterly_Newsletter,_Spring_2009| 2009-05-01]]
| [[SGD_Quarterly_Newsletter,_Summer_2009| 2009-08-04]]
| [[SGD_Quarterly_Newsletter,_Fall_2009| 2009-11-06]]
|-
| '''2008'''
| [[SGD_Quarterly_Newsletter,_Winter_2008| 2008-01-31]]
| [[SGD_Quarterly_Newsletter,_Spring_2008| 2008-04-30]]
| [[SGD_Quarterly_Newsletter,_Summer_2008| 2008-07-31]]
| [[SGD_Quarterly_Newsletter,_Fall_2008| 2008-11-03]]
|- bgcolor="E6E6FA"
| '''2007'''
| [[SGD_Quarterly_Newsletter,_Winter_2007| 2007-01-29]]
| [[SGD_Quarterly_Newsletter,_Spring_2007| 2007-05-07]]
| [[SGD_Quarterly_Newsletter,_Summer_2007| 2007-07-30]]
| [[SGD_Quarterly_Newsletter,_Fall_2007| 2007-11-08]]
|-
| '''2006'''
| [[SGD_Quarterly_Newsletter,_Winter_2006| 2006-02-02]]
| [[SGD_Quarterly_Newsletter,_Spring_2006| 2006-05-01]]
| [[SGD_Quarterly_Newsletter,_Summer_2006| 2006-07-20]]
| [[SGD_Quarterly_Newsletter,_Fall_2006| 2006-11-01]]
|- bgcolor="E6E6FA"
| '''2005'''
| [[SGD_Quarterly_Newsletter,_Winter_2005| 2005-01-31]]
| [[SGD_Quarterly_Newsletter,_Spring_2005| 2005-04-28]]
| [[SGD_Quarterly_Newsletter,_Summer_2005| 2005-07-29]]
| [[SGD_Quarterly_Newsletter,_Fall_2005| 2005-10-24]]
|-
| '''2004'''
| [[SGD_Quarterly_Newsletter,_Winter_2004| 2004-01-30]]
| [[SGD_Quarterly_Newsletter,_Spring_2004| 2004-04-26]]
| [[SGD_Quarterly_Newsletter,_Summer_2004| 2004-07-23]]
| [[SGD_Quarterly_Newsletter,_Fall_2004| 2004-11-18]]
|- bgcolor="E6E6FA"
| '''2003'''
| [[SGD_Quarterly_Newsletter,_Winter_2003| 2003-01-31]]
| [[SGD_Quarterly_Newsletter,_Spring_2003| 2003-04-28]]
| [[SGD_Quarterly_Newsletter,_Summer_2003| 2003-08-04]]
| [[SGD_Quarterly_Newsletter,_Fall_2003| 2003-10-31]]
|-
|}

SGD Newsletter Archives

2026-05-01T18:52:39Z

Suzia:

[[Category:Newsletter]]
SGD periodically publishes a community newsletters. This page contains links to the SGD Newsletters that have been released, listed in chronological order. Click on a date to see the newsletter published on that date.

{| width="50%" border="1"
|-bgcolor="E6E6FA"
| '''2025'''
|
|[[SGD_Newsletter,_Spring_2025 | 2025-04-24]]
|
|[[SGD_Newsletter,_December_2025 | 2025-12-11]]
|-
| '''2024'''
|
|[[SGD_Newsletter,_Summer_2024 | 2024-06-19]]
|
|[[SGD_Newsletter,_Winter_2024 | 2024-12-12]]
|-

| '''2023'''
|
|[[SGD_Newsletter,_Summer_2023 | 2023-06-22]]
|
|[[SGD_Newsletter,_December_2023 | 2023-12-13]]
|-
| '''2022'''
|
|
|[[SGD_Newsletter,_Summer_2022 | 2022-08-01]]
|
|-
|-bgcolor="E6E6FA"
| '''2021'''
|
|[[SGD_Newsletter,_Spring_2021 | 2021-05-27]]
|
|[[SGD_Newsletter,_Fall_2021 | 2021-12-14]]
|-
| '''2020'''
|
|[[SGD_Newsletter,_Summer_2020 | 2020-06-08]]
|
|[[SGD_Newsletter,_Fall 2020 | 2020-12-08]]
|-bgcolor="E6E6FA"
| '''2019'''
|
|[[SGD_Newsletter,_Spring_2019 | 2019-05-29]]
|
|[[SGD_Newsletter,_Fall_2019 | 2019-12-05]]
|-
|'''2018'''
|
|[[SGD_Newsletter,_April_2018 | 2018-04-30]]
|[[SGD_Newsletter,_Fall_2018 | 2018-10-05]]
|
|-bgcolor="E6E6FA"
|'''2017'''
|
|
|
| [[SGD_Newsletter,_December_2017 | 2017-12-20]]
|-
|'''2016'''
| [[SGD_Newsletter,_March_2016 | 2016-03-14]]
|
| [[SGD_Newsletter,_August_2016|2016-08-29]]
| [[SGD_Newsletter,_December_2016 | 2016-12-20]]
|- bgcolor="E6E6FA"
| '''2015'''
| [[SGD_Quarterly_Newsletter,_Spring_2015| 2015-02-26]]
|
| [[SGD_Quarterly_Newsletter,_Summer_2015 | 2015-08-28]]
| [[SGD_Newsletter,_December_2015 | 2015-12-18]]
|-
| '''2014'''
|
| [[SGD_Quarterly_Newsletter,_Spring_2014| 2014-04-17]]
| [[SGD_Quarterly_Newsletter,_Summer_2014| 2014-07-23]]
| [[SGD_Quarterly_Newsletter,_Fall_2014|2014-10-15]]
|- bgcolor="E6E6FA"
| '''2013'''
|
| [[SGD_Quarterly_Newsletter,_Summer_2013| 2013-06-10]]
|
| [[SGD_Quarterly_Newsletter,_Winter_2013| 2013-12-16]]
|-
| '''2012'''
| [[SGD_Quarterly_Newsletter,_Winter_2012| 2012-01-27]]
| [[SGD_Quarterly_Newsletter,_Spring_2012| 2012-04-28]]
| [[SGD_Quarterly_Newsletter,_Summer_2012| 2012-08-22]]
| [[SGD_Quarterly_Newsletter,_Fall_2012| 2012-12-13]]
|- bgcolor="E6E6FA"
| '''2011'''
| [[SGD_Quarterly_Newsletter,_Winter_2011| 2011-02-18]]
| [[SGD_Quarterly_Newsletter,_Spring_2011| 2011-05-05]]
| [[SGD_Quarterly_Newsletter,_Summer_2011| 2011-08-11]]
|
|-
| '''2010'''
| [[SGD_Quarterly_Newsletter,_Winter_2010| 2010-01-29]]
| [[SGD_Quarterly_Newsletter,_Spring_2010| 2010-04-29]]
| [[SGD_Quarterly_Newsletter,_Summer_2010| 2010-07-22]]
| [[SGD_Quarterly_Newsletter,_Fall_2010| 2010-11-01]]
|- bgcolor="E6E6FA"
| '''2009'''
| [[SGD_Quarterly_Newsletter,_Winter_2009| 2009-02-03]]
| [[SGD_Quarterly_Newsletter,_Spring_2009| 2009-05-01]]
| [[SGD_Quarterly_Newsletter,_Summer_2009| 2009-08-04]]
| [[SGD_Quarterly_Newsletter,_Fall_2009| 2009-11-06]]
|-
| '''2008'''
| [[SGD_Quarterly_Newsletter,_Winter_2008| 2008-01-31]]
| [[SGD_Quarterly_Newsletter,_Spring_2008| 2008-04-30]]
| [[SGD_Quarterly_Newsletter,_Summer_2008| 2008-07-31]]
| [[SGD_Quarterly_Newsletter,_Fall_2008| 2008-11-03]]
|- bgcolor="E6E6FA"
| '''2007'''
| [[SGD_Quarterly_Newsletter,_Winter_2007| 2007-01-29]]
| [[SGD_Quarterly_Newsletter,_Spring_2007| 2007-05-07]]
| [[SGD_Quarterly_Newsletter,_Summer_2007| 2007-07-30]]
| [[SGD_Quarterly_Newsletter,_Fall_2007| 2007-11-08]]
|-
| '''2006'''
| [[SGD_Quarterly_Newsletter,_Winter_2006| 2006-02-02]]
| [[SGD_Quarterly_Newsletter,_Spring_2006| 2006-05-01]]
| [[SGD_Quarterly_Newsletter,_Summer_2006| 2006-07-20]]
| [[SGD_Quarterly_Newsletter,_Fall_2006| 2006-11-01]]
|- bgcolor="E6E6FA"
| '''2005'''
| [[SGD_Quarterly_Newsletter,_Winter_2005| 2005-01-31]]
| [[SGD_Quarterly_Newsletter,_Spring_2005| 2005-04-28]]
| [[SGD_Quarterly_Newsletter,_Summer_2005| 2005-07-29]]
| [[SGD_Quarterly_Newsletter,_Fall_2005| 2005-10-24]]
|-
| '''2004'''
| [[SGD_Quarterly_Newsletter,_Winter_2004| 2004-01-30]]
| [[SGD_Quarterly_Newsletter,_Spring_2004| 2004-04-26]]
| [[SGD_Quarterly_Newsletter,_Summer_2004| 2004-07-23]]
| [[SGD_Quarterly_Newsletter,_Fall_2004| 2004-11-18]]
|- bgcolor="E6E6FA"
| '''2003'''
| [[SGD_Quarterly_Newsletter,_Winter_2003| 2003-01-31]]
| [[SGD_Quarterly_Newsletter,_Spring_2003| 2003-04-28]]
| [[SGD_Quarterly_Newsletter,_Summer_2003| 2003-08-04]]
| [[SGD_Quarterly_Newsletter,_Fall_2003| 2003-10-31]]
|-
|}

File:LibrarYeast.jpeg

2025-12-11T21:29:03Z

Suzia: Suzia uploaded a new version of File:LibrarYeast.jpeg

File:LibrarYeast.jpeg

2025-12-11T21:28:25Z

Suzia: Suzia uploaded a new version of File:LibrarYeast.jpeg

SGD Newsletter, December 2025

2025-12-11T21:17:09Z

Suzia: /* New at SGD: Links to a Comprehensive Overview of Yeast Libraries */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_gavin.jpeg|400px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_r_party.jpeg|550px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===

On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars. View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T21:10:17Z

Suzia: /* Retirement of Mike Cherry */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_gavin.jpeg|400px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_r_party.jpeg|550px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===

On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars. View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T20:39:51Z

Suzia: /* Alliance of Genome Resources News */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|550px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|400px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===

On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars. View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:44:54Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|550px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|400px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:43:01Z

Suzia: /* Retirement of Mike Cherry */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|550px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|400px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:42:45Z

Suzia: /* Retirement of Mike Cherry */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|600px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|400px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:40:08Z

Suzia: /* Retirement of Mike Cherry */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|500px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|500px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

File:mike r party.jpeg

2025-12-11T19:39:31Z

Suzia: Suzia uploaded a new version of File:mike r party.jpeg

File:mike gavin.jpeg

2025-12-11T19:31:55Z

Suzia: Suzia uploaded a new version of File:mike gavin.jpeg

SGD Newsletter, December 2025

2025-12-11T19:29:42Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:29:34Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:29:25Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:29:16Z

Suzia: /* FlyBase End of Funding */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:29:00Z

Suzia: /* Alliance of Genome Resources – Latest Release 8.2.0 */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:28:08Z

Suzia: /* Alliance of Genome Resources – Latest Release 8.2.0 */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:27:45Z

Suzia: /* Alliance of Genome Resources – Latest Release 8.2.0 */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:27:30Z

Suzia: /* Alliance of Genome Resources – Latest Release 8.2.0 */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten]. Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:27:03Z

Suzia: /* Alliance of Genome Resources News */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: [https://youtu.be/RFXXu-4nc2E Introduction to MicroPublication Biology]
On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:19:03Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:18:53Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:18:33Z

Suzia: /* Alliance of Genome Resources – Latest Release 8.2.0 */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example [https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants mouse gene Pten] and [https://www.alliancegenome.org/allele/MGI:6781825 mouse allele for Pten). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.

===Alliance Webinars: MicroPublication Biology===
View the video of the latest Alliance of Genome Resources webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the [https://www.micropublication.org/ MicroPublication] journal which publishes brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March. See the [https://www.alliancegenome.org/event-calendar Event Calendar] for the schedule of upcoming Alliance office hours and webinars.

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:01:59Z

Suzia: /* Support SGD this Holiday Season */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “''Saccharomyces'' Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T19:00:29Z

Suzia: /* microPublications – Latest Yeast Papers */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* [https://www.yeastgenome.org/reference/S100000835 King A, Emery TM, Reese K, Tinsley HN (2025)] Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001052 Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025)] Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001492 Nnabuenyi N, Sands MA, Camlin NJ (2025)] Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001226 Sasahara M, Matsumoto S, Tamura Y (2025)] Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001127 Dutca LM, Freed EF, Baserga SJ (2025)] Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001171 Schiemann AH, Sarwar M, Sattlegger E (2025)] Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000597 Torvi JR, Wong J, Drubin DG, Barnes G (2025)] Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000625 VanderVen K, Butcher C, Fokine R, Li J (2025)] Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100001518 Tang L, AlKaabi A, Meyer D (2025)] Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000660 Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025)] Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* [https://www.yeastgenome.org/reference/S100000639 Takesue H, Okada S, Ito T (2025)] Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T18:07:58Z

Suzia: /* microPublications – Latest Yeast Papers */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
[https://www.micropublication.org microPublication Biology] is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T18:05:41Z

Suzia: /* Retirement of Mike Cherry */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter.

Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T18:05:20Z

Suzia: /* Retirement of Mike Cherry */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]

This year, we celebrate and thank J. Michael “Mike” Cherry as he retires after decades of visionary leadership of the ''Saccharomyces'' Genome Database. From the earliest days of the yeast genome to today’s multi‑omic era, Mike helped shape SGD into the trusted, rigorously curated resource at the heart of the yeast community. His commitment to high‑quality data, interoperability, and open science empowered discoveries around the world, and his mentorship nurtured generations of curators, developers, and collaborators. Mike’s steady guidance, big‑picture thinking, and relentless focus on serving researchers have left a lasting legacy that will continue to guide SGD’s mission.

On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone who attended, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is SGD's new PI, and he is hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

On behalf of the SGD team and the global yeast community, we extend our deepest gratitude to Mike and wish him joy and fulfillment in the next chapter. Thank you, Mike, for everything.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T18:00:40Z

Suzia: /* Retirement of Mike Cherry */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: [https://www.yeastgenome.org/reference/S000060071 Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence].

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:57:21Z

Suzia: /* FlyBase End of Funding */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase wiki]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:57:10Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase website]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:56:56Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase website]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:56:16Z

Suzia: /* FlyBase End of Funding */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters. For more information on how to support FlyBase, see the [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase FlyBase website]:

*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:52:30Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there will no longer be updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new data for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters:
*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups
*For more information on how to support FlyBase: [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase Contribute to FlyBase]
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:50:52Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will continue provide access to this archived WS298 release of WormBase, and the content hosted there is no longer being updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new releases for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current Worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters:
*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups
*For more information on how to support FlyBase: [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase Contribute to FlyBase]
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:49:51Z

Suzia: /* FlyBase End of Funding */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will only provide access to this archived WS298 release of WormBase, and the content hosted there is no longer being updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new releases for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current Worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters:
*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups
*For more information on how to support FlyBase: [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase Contribute to FlyBase]
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:49:45Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will only provide access to this archived WS298 release of WormBase, and the content hosted there is no longer being updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new releases for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current Worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters:
*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups
*For more information on how to support FlyBase: [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase Contribute to FlyBase]
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:49:38Z

Suzia: /* Final Release of WormBase */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announced their final release, WS298, on November 27, 2025. The existing [https://wormbase.org WormBase] website will only provide access to this archived WS298 release of WormBase, and the content hosted there is no longer being updated except for essential maintenance to ensure continued availability. Ongoing curation, annotation, data updates, and new releases for ''Caenorhabditis elegans'' will now be managed through the Alliance of Genome Resources. Users should refer to the Alliance for the most current Worm datasets and continued resource development. Read more on the [https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/ WormBase blog].
 
 
 
 
 

===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters:
*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups
*For more information on how to support FlyBase: [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase Contribute to FlyBase]
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:41:45Z

Suzia: /* FlyBase End of Funding */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announces the schedule for its final major update, WS298, in October 2025. This will mark the end of new WormBase releases and the shift to focus on integrating existing data into the Alliance of Genome Resources, ensuring vital C. elegans datasets remain accessible. This transition promises new tools and long-term access to curated data that scientists rely on. Stay tuned for more updates.
Read more: https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/
 
 
 
 
 
===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters:
*European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
*U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups
*For more information on how to support FlyBase: [https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase Contribute to FlyBase]
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

SGD Newsletter, December 2025

2025-12-11T17:39:24Z

Suzia: /* Alliance of Genome Resources News */

[[Category: Newsletter]]
'''About this newsletter:''' This is the December 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

==Support SGD this Holiday Season==
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. '''Donations are now critical for our work to continue'''. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu].

* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
* In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
* Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

We thank you in advance for your support!

==New at SGD: Links to a Comprehensive Overview of Yeast Libraries==

[[File:LibrarYeast paper border.jpeg|700px|link=https://www.yeastgenome.org/reference/S100001554]]
 
Baruch et al. have compiled and published [https://www.yeastgenome.org/reference/S100001554 A comprehensive overview of yeast libraries and their role in advancing cell biology], which describes a comprehensive list of genome-wide collections of ''Saccharomyces cerevisiae''. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on [https://mayaschuldiner.wixsite.com/schuldinerlab/libraryeast LibrarYeast]. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

[[File:LibrarYeast.jpeg|500px|link=https://www.yeastgenome.org/locus/S000000747/phenotype#resources]]

==Retirement of Mike Cherry==
[[File:mike_r_party.jpeg|700px|right]]
After 32 years at SGD, our longtime PI Mike Cherry is leaving SGD to explore the world outside of the lab. On November 14th, many past and current Cherry lab members gathered at Stanford to celebrate Mike’s career. Thank you to everyone that came, and especially to everyone that shared stories or memories from the past 3 decades of SGD.
Gavin Sherlock is the new PI, and he’s hardly a stranger to SGD! Mike and Gavin published their first article together about SGD in Science all the way back in 1998: Chervitz et al., Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence.

[[File:mike_gavin.jpeg|700px]]

==Reminder: Submit Data Form==

If you're itching for something to do over the winter break, have you checked your newly published data at SGD lately? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD's simple “Submit Data" form ([https://www.yeastgenome.org/submitData https://www.yeastgenome.org/submitData]).
 
[[File:submit_data_2025.jpeg|700px|link=https://www.yeastgenome.org/submitData]]

==Alliance of Genome Resources News==

===Alliance of Genome Resources – Latest Release 8.2.0===
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
The sequence viewers on the gene and allele pages have been restored; On gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example https://www.alliancegenome.org/gene/MGI:109583#alleles-and-variants and https://www.alliancegenome.org/allele/MGI:6781825). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored.
Website infrastructure is upgraded to React 19 and migrated to Vite.
Alliance Webinars: MicroPublication Biology
View the video of the next Alliance of Genome Resources webinar:
Webinar: Introduction to MicroPublication Biology
Presented on November 20, 2025
Tim Schedl, microPublication Biology Editorial Board member, will give an overview of the MicroPublication journal which published brief scholarly reports of research findings based on data presented in a single figure.
Webinars are also planned for 2026, in January, February, and March.See the Event Calendar with the schedule of upcoming Alliance office hours and webinars: Alliance of Genome Resources

===Final Release of WormBase===
[[Image:alliance_logo_wormbase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

WormBase announces the schedule for its final major update, WS298, in October 2025. This will mark the end of new WormBase releases and the shift to focus on integrating existing data into the Alliance of Genome Resources, ensuring vital C. elegans datasets remain accessible. This transition promises new tools and long-term access to curated data that scientists rely on. Stay tuned for more updates.
Read more: https://blog.wormbase.org/2025/07/23/announcing-the-final-release-of-wormbase/
 
 
 
 
 
===FlyBase End of Funding===
[[Image:alliance_logo_flybase.png|link=https://www.alliancegenome.org|thumb|left|upright=.3]]

FlyBase Update – October 2025
The termination of the NIH/NHGRI FlyBase grant has placed the long-term sustainability of FlyBase at risk. However, thanks to the generous support of several key individuals and institutions, FlyBase has announced that they will remain operational through the coming year. Looking ahead, ensuring FlyBase’s sustainability beyond the next year – and successfully integrating with the Alliance – will require new funding sources. FlyBase, like SGD, is asking for continued donations from any and all Fly supporters:
European labs: Please consider contributing to the Cambridge, U.K. FlyBase group
U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups
For more information on how to support FlyBase: Contribute to FlyBase
 
 

==microPublications – Latest Yeast Papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:

* King A, Emery TM, Reese K, Tinsley HN (2025) Yeast gene of unknown function YGL081W is involved in DNA damage response. MicroPubl Biol 2025
* Avogo EW, Burlingame NA, Badenahalli Narasimhaiah S, Delorme-Axford E (2025) Bioinformatics analysis identifies Mot2 protein as a potential regulator of autophagy in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Nnabuenyi N, Sands MA, Camlin NJ (2025) Specific auxin and medium combinations alter ''Saccharomyces cerevisiae'' growth. MicroPubl Biol 2025
* Sasahara M, Matsumoto S, Tamura Y (2025) Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. MicroPubl Biol 2025
* Dutca LM, Freed EF, Baserga SJ (2025) Yeast pre-rRNA is processed at the A' site. MicroPubl Biol 2025
* Schiemann AH, Sarwar M, Sattlegger E (2025) Functional Analysis of the Yeast Counterpart to the Human GCN2 p.Glu738_Asp739insArgArg Variant. MicroPubl Biol 2025
* Torvi JR, Wong J, Drubin DG, Barnes G (2025) Stu2 is required for plus-end directed chromosome transport along microtubules during metaphase in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* VanderVen K, Butcher C, Fokine R, Li J (2025) Pep12 is important for proteasome microautophagy under low glucose conditions. MicroPubl Biol 2025
* Tang L, AlKaabi A, Meyer D (2025) Copper Homeostasis is influenced by Ics3 in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
* Taguchi S, Matsuzawa R, Suda Y, Irie K, Ozaki H (2025) Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. MicroPubl Biol 2025
* Takesue H, Okada S, Ito T (2025) Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. MicroPubl Biol 2025

==Upcoming Conferences & Courses==

*[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference]
**March 17 to March 22, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting 2026]
**June 13 to June 17, 2026 -
**Asilomar Conference Grounds, Pacific Grove, CA

*[https://www.issy39.org/html/?pmode=welcome 39th International Specialized Symposium on Yeasts (ISSY39)]
**Nov 8 - 12, 2026
**Jeongdong 1928 Art Center, Seoul, KR

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.25|link=http://www.yeastgenome.org]]
We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.