SGD-Wiki - User contributions [en]

SGD Newsletter, May 2026

2026-05-27T16:38:44Z

Stacia: /* Join Us at Yeast Genetics Meeting 2026 */

'''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:Yeast26.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

2025-04-24T16:23:40Z

Stacia: /* Pathway Annotations Now Available as GO Annotations */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 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. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Summer_2025 newsletter] as well as previous newsletters, on the SGD [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Give a Gift / Support SGD: Credit Cards Now Accepted==
[[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

Thank you for your support!

==SGD's Latest Genetics Publication==
[[File:genetics_229_3cover.jpeg|link=https://academic.oup.com/genetics/article-abstract/229/3/iyae185/7895713|thumb|left|upright=.5]]
[https://www.yeastgenome.org/reference/S000377741 ''Saccharomyces'' Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements] has now been published in GENETICS and is available in the [https://academic.oup.com/genetics/issue/229/3 March 2025 issue]. Check out the most recent updates at SGD, including:
<blockquote>
* Two most recent reference genome annotation updates
* Expanded biochemical pathways representation
* Changes to SGD search and data files
* Other enhancements to the SGD website and user interface
</blockquote>
 

==Pathway Annotations Now Available as GO Annotations==
[[File:figure1GENETICS2025.jpg|thumb|left|upright=.75]]YeastPathways, the database of metabolic pathways and enzymes in the budding yeast ''Saccharomyces cerevisiae'', is manually curated and maintained by the biocuration team at SGD.

This resource is jam-packed with information, but was somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Initially, we added a new section with pathways links on the relevant gene pages (ex. [https://yeastgenome.org/locus/S000005762#pathway DFR1]). Additionally, we made the pathways available in SGD Search. Now, we have transformed the metabolic pathways and associated genes/enzymes into Gene Ontology (GO) annotations (ex. [https://yeastgenome.org/locus/S000005762/go#comp DFR1]).

Because many fundamental molecular processes and pathways are evolutionarily conserved between yeast and higher eukaryotes, including humans, the curated metabolic pathway information has great value for the transfer of knowledge to other organisms. It is for this reason that the YeastPathways data were exported in BioPAX ([https://pubmed.ncbi.nlm.nih.gov/20829833/ Demir et al. 2010]) format for import into Noctua, a tool for collaborative curation of biological pathways and gene annotations that was developed by the GO Consortium ([https://www.yeastgenome.org/reference/S000250248 Thomas et al. 2019]). BioPAX provides a standardized format for representing biological pathways, allowing researchers to integrate pathway information from different sources and databases. Noctua can import pathway data encoded in BioPAX format to populate the pathway editor with molecular interactions, biological processes, and regulatory relationships, and can utilize BioPAX files to combine pathway data from multiple datasets for pathway curation and analysis.

Pathways curated and edited in Noctua can be exported both as GO annotations for yeast and orthologous genes in other species, or as pathway annotations in BioPAX, facilitating the sharing of curated pathways with other researchers, databases, and analysis tools using a standard format, promoting data exchange, and collaboration within the scientific community.

==New Yeast Phenome Links in Phenotype Resources==
[[File:calico_life_sciences_llc_logo.jpg|link=https://www.calicolabs.com/|thumb|left|upright=.4]]

The [https://www.yeastphenome.org/ Yeast Phenome] is a collaborative project from the Baryshnikova lab at Calico Life Sciences to create a comprehensive compendium of systematic loss-of-function phenotypes for the budding yeast Saccharomyces cerevisiae.

The Yeast Phenome systematically tracks, collects, and annotates all published phenotypic screens utilizing the yeast knock-out collection. Locus-specific links to the Yeast Phenome are now available in the Resources section of the Phenotype tab and will take you directly to the corresponding page of the Yeast Phenome data library. Try it now: the SGD phenotype page for [https://yeastgenome.org/locus/S000001171/phenotype#resources ARP1], and the linked [https://www.yeastphenome.org/genes/1096/ ARP1] page at Yeast Phenome.

==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 [https://pubmed.ncbi.nlm.nih.gov PubMed] and [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].

Consider [https://www.micropublication.org/journals/biology/species/s-cerevisiae microPubublications] when you have a result that doesn't necessarily fit into a larger story, but will be of value to others.

Latest [https://www.micropublication.org/journals/biology/species/s-cerevisiae yeast microPublications]:

*[https://www.yeastgenome.org/reference/S100000138 Pfliegler WP, Imre A, Biotechnology BSc Class Of UOD, Pócsi I (2025)] PCR-fingerprinting of culturable yeasts from commercially obtained beers: a simple and engaging applied microbiological laboratory exercise. MicroPubl Biol 2025

*[https://www.yeastgenome.org/reference/S100000262 Andrade Latino A, Biggins S (2025)] Analysis of a cancer-associated mutation in the budding yeast Nuf2 kinetochore protein. MicroPubl Biol 2025

*[https://www.yeastgenome.org/reference/S100000150 Thota K, Fredette-Roman JD, Sharp NP (2025)] Yeast mutation rates in alternative carbon sources reflect the influence of reactive oxygen species. MicroPubl Biol 2025

*[https://www.yeastgenome.org/reference/S100000243 Butcher C, VanderVen K, Li J (2025)] Proteasome condensates repeatedly "contact and release" at the nuclear periphery during dissolution. MicroPubl Biol 2025

*[https://www.yeastgenome.org/reference/S100000338 James M, Klain GK, Brito SO, Trejo L, Okello TMA, Segarra VA (2025)] Autophagy-deficient budding yeast cells are sensitive to freeze-thaw stress. MicroPubl Biol 2025

*[https://www.yeastgenome.org/reference/S100000186 Eftimie A, Meyer D (2025)] Transcription Regulatory Protein ''SIN3'' (YOL004W) Influences Mutation Rates in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025

All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD].

==Alliance of Genome Resources - Latest Release 8.0.0==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]

The 8.0.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.

Pathway Viewer Update:

* Redesign of the legend corrects issues with casual relationship representation; interface visuals have been refined; all defined causal relationships are now depicted using standardized glyphs with a matching color legend.

There is now an Event Calendar with the schedule of upcoming Alliance office hours and webinars: https://www.alliancegenome.org/event-calendar

==Upcoming Conferences & Courses==
*[https://geneontology.org/ Gene Ontology Consortium Spring 2025 Meeting]
**May 5-8, 2025
**Geneva, Switzerland
**''SGD will be attending''

*[https://www.csh-asia.org/?content/2721 CSH Asia: Yeast and Life Sciences]
**June 02 to June 06, 2025 -
**Suzhou, China

*[https://www.pnwyc.net/ PNWYC 2025: Pacific Northwest Yeast Club]
**June 20, 2025
**Vancouver, Canada

*[https://premc.org/yeast2025/about-paris/ Yeast2025: 32nd International Conference on Yeast Genetics and Molecular Biology ICYGMB32]
**July 21 to July 24, 2025
**Sorbonne University, Paris, France
**''SGD will be attending''

*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS Yeast Genetics & Genomics]
**July 22 to August 12, 2025
**Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
**''SGD will be attending''

*[https://issy38.com.pl/ 38th International Specialized Symposium on Yeasts (ISSY38)]
**September 01 to September 05, 2025 -
**Warsaw University, Warsaw, Poland

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

2024-06-18T20:38:56Z

Stacia: /* microPublications - latest yeast papers */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2024 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. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Summer_2024 newsletter] as well as previous newsletters, on the SGD [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Give a Gift / Support SGD==
[[Image:gift.png |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 will help us to continue providing essential information for your research and teaching efforts.

To contribute, please make checks payable to Stanford University, noting that "the funds should be used to support the Saccharomyces Genome Database project, under the direction of Drs. Sherlock and Cherry in the Department of Genetics, Stanford University. Account : GHJKO, Genetics : WAZC."

Thank you for your support!

''Kindly send by mail to:''

Development Services 
PO Box 20466 
Stanford, CA 94309

[mailto:sgd-helpdesk@lists.stanford.edu CONTACT US]: sgd-helpdesk@lists.stanford.edu

==Reference genome update R64.5==
[[File:SuperYeast.jpg|thumb|right|upright=.5]]
The ''S. cerevisiae'' strain S288C reference genome annotation has been updated to include previously unannotated features. The new genome annotation is release R64.5.1, dated 2024-05-29. Note that the underlying genome sequence itself was not altered; the chromosome sequences remain stable and unchanged.

The R64.5.1 update included:
*Six new open reading frames (ORFs): [https://www.yeastgenome.org/locus/YDL204W-A YDL204W-A], [https://www.yeastgenome.org/locus/YFR035W-A YFR035W-A], [https://www.yeastgenome.org/locus/YGR016C-A YGR016C-A], [https://www.yeastgenome.org/locus/YMR106W-A YMR106W-A], [https://www.yeastgenome.org/locus/YNL040C-A YNL040C-A], [https://www.yeastgenome.org/locus/YNL155C-A YNL155C-A]
*New uORFs for 4 ORFs: [https://www.yeastgenome.org/locus/ATG12 ATG12/YBR217W], [https://www.yeastgenome.org/locus/ATG19 ATG19/YOL082W], [https://www.yeastgenome.org/locus/ATG5 ATG5/YPL149W], [https://www.yeastgenome.org/locus/ATG13 ATG13/YPR185W]
**A uORF is a small upstream open reading frame that precedes, and regulates downstream translation of, the major ORF.
*Move start downstream: [https://www.yeastgenome.org/locus/EFM4 EFM4/YIL064W]
*ORF upgraded from Dubious to Verified: [https://www.yeastgenome.org/locus/YIL059C YIL059C]

Various sequence and annotation files are available on SGD’s [http://sgd-archive.yeastgenome.org Downloads] site. You can find more update details on the [https://wiki.yeastgenome.org/index.php/Details_of_2024_Reference_Genome_Annotation_Update_R64.5#R64.5_Annotation_update_summary Details of 2024 Reference Genome Annotation Update R64.5] SGD Wiki page.

==Extend gene coordinates in GFF==
The saccharomyces_cerevisiae.gff contains sequence features of ''Saccharomyces cerevisiae'' and related information such as Locus descriptions and GO annotations. The saccharomyces_cerevisiae.gff is fully compatible with [http://gmod.org/wiki/GFF3 Generic Feature Format Version 3], and is [http://sgd-archive.yeastgenome.org/curation/chromosomal_feature/ updated weekly].

After November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used.

''Old version: BDH2/YAL061W with rows for longest transcripts expressed in GAL and in YPD.''
[[File:yal061w_w2transcripts.jpg]]

Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023).

''After February 2024: BDH2/YAL061W with expanded start/stop coordinates for 'gene', still with rows for longest transcripts expressed in GAL, YPD.''
[[File:yal061w_extendedgene.jpg]]

This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.

==Updates to SGD search==
[[File:sgd maintenanceguy.jpeg|thumb|right|upright=.5]]
SGD is jam-packed with information, with new data being added every day. It's a lot to keep up with, and with so much info, some inevitably ends up hidden from view. To make the various data types in SGD more readily accessible, we have made various improvements to the [https://www.yeastgenome.org/search?q=&is_quick=true SGD search]:

*New category for [https://www.yeastgenome.org/search?q=&category=dataset datasets]. Over 3700 yeast datasets are accessible. Search by reference, keyword, assay, and lab.
*Macromolecular [https://www.yeastgenome.org/search?q=&category=complex complexes] can now be searched with aliases. Further refine by reference, subunit, function, process, and location.
*Search for [https://www.yeastgenome.org/search?q=&category=allele alleles] via their descriptions and SGDIDs. Drill down based on reference, allele type, gene, and phenotype.
*RNA products can now be searched using RNAcentral IDs.

==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 [https://pubmed.ncbi.nlm.nih.gov PubMed] and [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].

Consider [https://www.micropublication.org/journals/biology/species/s-cerevisiae microPubublications] when you have a result that doesn't necessarily fit into a larger story, but will be of value to others.

Latest [https://www.micropublication.org/journals/biology/species/s-cerevisiae yeast microPublications]:

*[https://www.yeastgenome.org/reference/S000349401 Caligaris M, De Virgilio C (2024)] Proxies introduce bias in decoding TORC1 activity. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000349402 Fromont-Racine M, Khanna V, Jacquier A, Badis G (2024)] YLR419W is the homolog of the mammalian translation initiation factor DHX29. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348700 Greenlaw A, Dell R, Tsukiyama T (2024)] Initial acidic media promotes quiescence entry in Saccharomyces cerevisiae. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348494 Harmer ZP, Hohener TC, Landolt AE, Mitchell C, McClean M (2024)] Enhancing high-throughput optogenetics: Integration of LITOS with Lustro enables simultaneous light stimulation and shaking. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000347552 Karpel JE (2024) Caenorhabditis elegans ddx-15 helicase fails to complement loss of Prp43p in Saccharomyces cerevisiae. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000347382 Medina-Suarez S, Machin F (2024)] The CRISPR/Cas9 system forms a condensate in the yeast nucleus. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348904 Putnam CD (2024)] Loss of mitochondrial DNA is associated with reduced DNA content variability in Saccharomyces cerevisiae. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348874 Rosenbaum JC, Carlson AE (2024)] The SARS coronavirus accessory protein ORF3a rescues potassium conductance in yeast. MicroPubl Biol 2024.

All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD].

==Alliance of Genome Resources - Latest Release 7.2==
[[Image:alliance_logo.png|link=https://www.micropublication.org|thumb|right|upright=.725]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort between SGD and other model organism databases (MODs), released [https://www.alliancegenome.org/release-notes version 7.2] in June 2024.

The 7.2.0 release updates the Disease pages’ Associated Alleles table and the Associated Models table:

*Each table has a new column, Disease Qualifier, with a working filter. The qualifier describes whether an allele or model may be, for example, implicated in the onset of a disease or a model for the severity of a disease, respectively
*In addition to the Disease Qualifier, the Associated Models table now has new columns for Condition Modifier and Genetic Modifier
*The “Annotation Details” pop-up has expanded to include more information.
**Alleles table: Association, Genetic Modifiers, Genetic Sex, Notes, and Annotation Type
**Models table: Genetic Sex, Notes, and Annotation Type
*The Associated Models table now has working filters for the Experimental Condition, Condition Modifier, and Genetic Modifier columns, including the ability to filter on relationship (e.g. induced by) as well as content (e.g. “copper”)
*The Download files from the disease page Associated Alleles table and Associated Models table now include additional information as well.
**New columns and information for the Associated Alleles table include: Allele Association, Genetic Entity Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Genetic Sex, Notes, Annotation Type, Source URL, and Date.
**New columns and information for the Associated Models table include: Model Type, Model Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Condition Modifiers, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Genetic Sex, Notes, Annotation Type, Source URL, and Date.

==Upcoming conferences and courses==
*[https://www.yeastorfanproject.com/summer-workshops/ RCN-UBE: Yeast ORFan Gene Project] - Summer Workshop - Gene Expression Analysis
**June 20 to June 21, 2024
**Virtual
*[https://events.faseb.org/event/f0c82874-ec6f-4b41-98e4-fe34d1646b74/summary FASEB Yeast Chromosome Biology and Cell Cycle]
**June 23 to June 27, 2024
**Fort Garry Hotel, Winnipeg, Manitoba, Canada
*[https://www.biologists.com/meetings/jcsevocellbio24/ JCS2024: Diversity and Evolution in Cell Biology]
**June 24 to June 27, 2024
**Montanya Hotel & Lodge, Catalonia, Spain
*[https://www.pnwyc.net Pacific Northwest Yeast Club]
**July 26, 2024
**Fred Hutchinson Cancer Center, Seattle, WA
*[https://web.cvent.com/event/4f188521-d6e8-4bd4-b0b5-b923ef8b3e5f/summary 39th Small Meeting of Yeast Transporters and Energetics (SMYTE)]
**August 28 to September 01, 2024
**University of York, York, United Kingdom
*[https://easternsun.eventsair.com/2024-16th-international-congress-on-yeasts ICY2024: 16th International Congress on Yeasts]
**September 29 to October 03, 2024
**Cape Town International Convention Centre, Cape Town, South Africa
*[https://premc.org/yeast2025/about-paris/ Yeast2025: 32nd International Conference on Yeast Genetics and Molecular Biology ICYGMB32]
**July 21 to July 24, 2025
**Sorbonne University, Paris, France

SGD Newsletter, Summer 2024

2024-06-18T20:38:42Z

Stacia: /* Alliance of Genome Resources - Latest Release 7.2 */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2024 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. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Summer_2024 newsletter] as well as previous newsletters, on the SGD [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Give a Gift / Support SGD==
[[Image:gift.png |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 will help us to continue providing essential information for your research and teaching efforts.

To contribute, please make checks payable to Stanford University, noting that "the funds should be used to support the Saccharomyces Genome Database project, under the direction of Drs. Sherlock and Cherry in the Department of Genetics, Stanford University. Account : GHJKO, Genetics : WAZC."

Thank you for your support!

''Kindly send by mail to:''

Development Services 
PO Box 20466 
Stanford, CA 94309

[mailto:sgd-helpdesk@lists.stanford.edu CONTACT US]: sgd-helpdesk@lists.stanford.edu

==Reference genome update R64.5==
[[File:SuperYeast.jpg|thumb|right|upright=.5]]
The ''S. cerevisiae'' strain S288C reference genome annotation has been updated to include previously unannotated features. The new genome annotation is release R64.5.1, dated 2024-05-29. Note that the underlying genome sequence itself was not altered; the chromosome sequences remain stable and unchanged.

The R64.5.1 update included:
*Six new open reading frames (ORFs): [https://www.yeastgenome.org/locus/YDL204W-A YDL204W-A], [https://www.yeastgenome.org/locus/YFR035W-A YFR035W-A], [https://www.yeastgenome.org/locus/YGR016C-A YGR016C-A], [https://www.yeastgenome.org/locus/YMR106W-A YMR106W-A], [https://www.yeastgenome.org/locus/YNL040C-A YNL040C-A], [https://www.yeastgenome.org/locus/YNL155C-A YNL155C-A]
*New uORFs for 4 ORFs: [https://www.yeastgenome.org/locus/ATG12 ATG12/YBR217W], [https://www.yeastgenome.org/locus/ATG19 ATG19/YOL082W], [https://www.yeastgenome.org/locus/ATG5 ATG5/YPL149W], [https://www.yeastgenome.org/locus/ATG13 ATG13/YPR185W]
**A uORF is a small upstream open reading frame that precedes, and regulates downstream translation of, the major ORF.
*Move start downstream: [https://www.yeastgenome.org/locus/EFM4 EFM4/YIL064W]
*ORF upgraded from Dubious to Verified: [https://www.yeastgenome.org/locus/YIL059C YIL059C]

Various sequence and annotation files are available on SGD’s [http://sgd-archive.yeastgenome.org Downloads] site. You can find more update details on the [https://wiki.yeastgenome.org/index.php/Details_of_2024_Reference_Genome_Annotation_Update_R64.5#R64.5_Annotation_update_summary Details of 2024 Reference Genome Annotation Update R64.5] SGD Wiki page.

==Extend gene coordinates in GFF==
The saccharomyces_cerevisiae.gff contains sequence features of ''Saccharomyces cerevisiae'' and related information such as Locus descriptions and GO annotations. The saccharomyces_cerevisiae.gff is fully compatible with [http://gmod.org/wiki/GFF3 Generic Feature Format Version 3], and is [http://sgd-archive.yeastgenome.org/curation/chromosomal_feature/ updated weekly].

After November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used.

''Old version: BDH2/YAL061W with rows for longest transcripts expressed in GAL and in YPD.''
[[File:yal061w_w2transcripts.jpg]]

Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023).

''After February 2024: BDH2/YAL061W with expanded start/stop coordinates for 'gene', still with rows for longest transcripts expressed in GAL, YPD.''
[[File:yal061w_extendedgene.jpg]]

This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.

==Updates to SGD search==
[[File:sgd maintenanceguy.jpeg|thumb|right|upright=.5]]
SGD is jam-packed with information, with new data being added every day. It's a lot to keep up with, and with so much info, some inevitably ends up hidden from view. To make the various data types in SGD more readily accessible, we have made various improvements to the [https://www.yeastgenome.org/search?q=&is_quick=true SGD search]:

*New category for [https://www.yeastgenome.org/search?q=&category=dataset datasets]. Over 3700 yeast datasets are accessible. Search by reference, keyword, assay, and lab.
*Macromolecular [https://www.yeastgenome.org/search?q=&category=complex complexes] can now be searched with aliases. Further refine by reference, subunit, function, process, and location.
*Search for [https://www.yeastgenome.org/search?q=&category=allele alleles] via their descriptions and SGDIDs. Drill down based on reference, allele type, gene, and phenotype.
*RNA products can now be searched using RNAcentral IDs.

==microPublications - latest yeast papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|https://www.micropublication.org|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 [https://pubmed.ncbi.nlm.nih.gov PubMed] and [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].

Consider [https://www.micropublication.org/journals/biology/species/s-cerevisiae microPubublications] when you have a result that doesn't necessarily fit into a larger story, but will be of value to others.

Latest [https://www.micropublication.org/journals/biology/species/s-cerevisiae yeast microPublications]:

*[https://www.yeastgenome.org/reference/S000349401 Caligaris M, De Virgilio C (2024)] Proxies introduce bias in decoding TORC1 activity. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000349402 Fromont-Racine M, Khanna V, Jacquier A, Badis G (2024)] YLR419W is the homolog of the mammalian translation initiation factor DHX29. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348700 Greenlaw A, Dell R, Tsukiyama T (2024)] Initial acidic media promotes quiescence entry in Saccharomyces cerevisiae. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348494 Harmer ZP, Hohener TC, Landolt AE, Mitchell C, McClean M (2024)] Enhancing high-throughput optogenetics: Integration of LITOS with Lustro enables simultaneous light stimulation and shaking. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000347552 Karpel JE (2024) Caenorhabditis elegans ddx-15 helicase fails to complement loss of Prp43p in Saccharomyces cerevisiae. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000347382 Medina-Suarez S, Machin F (2024)] The CRISPR/Cas9 system forms a condensate in the yeast nucleus. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348904 Putnam CD (2024)] Loss of mitochondrial DNA is associated with reduced DNA content variability in Saccharomyces cerevisiae. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348874 Rosenbaum JC, Carlson AE (2024)] The SARS coronavirus accessory protein ORF3a rescues potassium conductance in yeast. MicroPubl Biol 2024.

All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD].

==Alliance of Genome Resources - Latest Release 7.2==
[[Image:alliance_logo.png|link=https://www.micropublication.org|thumb|right|upright=.725]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort between SGD and other model organism databases (MODs), released [https://www.alliancegenome.org/release-notes version 7.2] in June 2024.

The 7.2.0 release updates the Disease pages’ Associated Alleles table and the Associated Models table:

*Each table has a new column, Disease Qualifier, with a working filter. The qualifier describes whether an allele or model may be, for example, implicated in the onset of a disease or a model for the severity of a disease, respectively
*In addition to the Disease Qualifier, the Associated Models table now has new columns for Condition Modifier and Genetic Modifier
*The “Annotation Details” pop-up has expanded to include more information.
**Alleles table: Association, Genetic Modifiers, Genetic Sex, Notes, and Annotation Type
**Models table: Genetic Sex, Notes, and Annotation Type
*The Associated Models table now has working filters for the Experimental Condition, Condition Modifier, and Genetic Modifier columns, including the ability to filter on relationship (e.g. induced by) as well as content (e.g. “copper”)
*The Download files from the disease page Associated Alleles table and Associated Models table now include additional information as well.
**New columns and information for the Associated Alleles table include: Allele Association, Genetic Entity Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Genetic Sex, Notes, Annotation Type, Source URL, and Date.
**New columns and information for the Associated Models table include: Model Type, Model Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Condition Modifiers, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Genetic Sex, Notes, Annotation Type, Source URL, and Date.

==Upcoming conferences and courses==
*[https://www.yeastorfanproject.com/summer-workshops/ RCN-UBE: Yeast ORFan Gene Project] - Summer Workshop - Gene Expression Analysis
**June 20 to June 21, 2024
**Virtual
*[https://events.faseb.org/event/f0c82874-ec6f-4b41-98e4-fe34d1646b74/summary FASEB Yeast Chromosome Biology and Cell Cycle]
**June 23 to June 27, 2024
**Fort Garry Hotel, Winnipeg, Manitoba, Canada
*[https://www.biologists.com/meetings/jcsevocellbio24/ JCS2024: Diversity and Evolution in Cell Biology]
**June 24 to June 27, 2024
**Montanya Hotel & Lodge, Catalonia, Spain
*[https://www.pnwyc.net Pacific Northwest Yeast Club]
**July 26, 2024
**Fred Hutchinson Cancer Center, Seattle, WA
*[https://web.cvent.com/event/4f188521-d6e8-4bd4-b0b5-b923ef8b3e5f/summary 39th Small Meeting of Yeast Transporters and Energetics (SMYTE)]
**August 28 to September 01, 2024
**University of York, York, United Kingdom
*[https://easternsun.eventsair.com/2024-16th-international-congress-on-yeasts ICY2024: 16th International Congress on Yeasts]
**September 29 to October 03, 2024
**Cape Town International Convention Centre, Cape Town, South Africa
*[https://premc.org/yeast2025/about-paris/ Yeast2025: 32nd International Conference on Yeast Genetics and Molecular Biology ICYGMB32]
**July 21 to July 24, 2025
**Sorbonne University, Paris, France

SGD Newsletter, Summer 2024

2024-06-18T20:35:28Z

Stacia: /* Alliance of Genome Resources - Latest Release 7.2 */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2024 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. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Summer_2024 newsletter] as well as previous newsletters, on the SGD [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Give a Gift / Support SGD==
[[Image:gift.png |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 will help us to continue providing essential information for your research and teaching efforts.

To contribute, please make checks payable to Stanford University, noting that "the funds should be used to support the Saccharomyces Genome Database project, under the direction of Drs. Sherlock and Cherry in the Department of Genetics, Stanford University. Account : GHJKO, Genetics : WAZC."

Thank you for your support!

''Kindly send by mail to:''

Development Services 
PO Box 20466 
Stanford, CA 94309

[mailto:sgd-helpdesk@lists.stanford.edu CONTACT US]: sgd-helpdesk@lists.stanford.edu

==Reference genome update R64.5==
[[File:SuperYeast.jpg|thumb|right|upright=.5]]
The ''S. cerevisiae'' strain S288C reference genome annotation has been updated to include previously unannotated features. The new genome annotation is release R64.5.1, dated 2024-05-29. Note that the underlying genome sequence itself was not altered; the chromosome sequences remain stable and unchanged.

The R64.5.1 update included:
*Six new open reading frames (ORFs): [https://www.yeastgenome.org/locus/YDL204W-A YDL204W-A], [https://www.yeastgenome.org/locus/YFR035W-A YFR035W-A], [https://www.yeastgenome.org/locus/YGR016C-A YGR016C-A], [https://www.yeastgenome.org/locus/YMR106W-A YMR106W-A], [https://www.yeastgenome.org/locus/YNL040C-A YNL040C-A], [https://www.yeastgenome.org/locus/YNL155C-A YNL155C-A]
*New uORFs for 4 ORFs: [https://www.yeastgenome.org/locus/ATG12 ATG12/YBR217W], [https://www.yeastgenome.org/locus/ATG19 ATG19/YOL082W], [https://www.yeastgenome.org/locus/ATG5 ATG5/YPL149W], [https://www.yeastgenome.org/locus/ATG13 ATG13/YPR185W]
**A uORF is a small upstream open reading frame that precedes, and regulates downstream translation of, the major ORF.
*Move start downstream: [https://www.yeastgenome.org/locus/EFM4 EFM4/YIL064W]
*ORF upgraded from Dubious to Verified: [https://www.yeastgenome.org/locus/YIL059C YIL059C]

Various sequence and annotation files are available on SGD’s [http://sgd-archive.yeastgenome.org Downloads] site. You can find more update details on the [https://wiki.yeastgenome.org/index.php/Details_of_2024_Reference_Genome_Annotation_Update_R64.5#R64.5_Annotation_update_summary Details of 2024 Reference Genome Annotation Update R64.5] SGD Wiki page.

==Extend gene coordinates in GFF==
The saccharomyces_cerevisiae.gff contains sequence features of ''Saccharomyces cerevisiae'' and related information such as Locus descriptions and GO annotations. The saccharomyces_cerevisiae.gff is fully compatible with [http://gmod.org/wiki/GFF3 Generic Feature Format Version 3], and is [http://sgd-archive.yeastgenome.org/curation/chromosomal_feature/ updated weekly].

After November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used.

''Old version: BDH2/YAL061W with rows for longest transcripts expressed in GAL and in YPD.''
[[File:yal061w_w2transcripts.jpg]]

Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023).

''After February 2024: BDH2/YAL061W with expanded start/stop coordinates for 'gene', still with rows for longest transcripts expressed in GAL, YPD.''
[[File:yal061w_extendedgene.jpg]]

This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.

==Updates to SGD search==
[[File:sgd maintenanceguy.jpeg|thumb|right|upright=.5]]
SGD is jam-packed with information, with new data being added every day. It's a lot to keep up with, and with so much info, some inevitably ends up hidden from view. To make the various data types in SGD more readily accessible, we have made various improvements to the [https://www.yeastgenome.org/search?q=&is_quick=true SGD search]:

*New category for [https://www.yeastgenome.org/search?q=&category=dataset datasets]. Over 3700 yeast datasets are accessible. Search by reference, keyword, assay, and lab.
*Macromolecular [https://www.yeastgenome.org/search?q=&category=complex complexes] can now be searched with aliases. Further refine by reference, subunit, function, process, and location.
*Search for [https://www.yeastgenome.org/search?q=&category=allele alleles] via their descriptions and SGDIDs. Drill down based on reference, allele type, gene, and phenotype.
*RNA products can now be searched using RNAcentral IDs.

==microPublications - latest yeast papers==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|https://www.micropublication.org|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 [https://pubmed.ncbi.nlm.nih.gov PubMed] and [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].

Consider [https://www.micropublication.org/journals/biology/species/s-cerevisiae microPubublications] when you have a result that doesn't necessarily fit into a larger story, but will be of value to others.

Latest [https://www.micropublication.org/journals/biology/species/s-cerevisiae yeast microPublications]:

*[https://www.yeastgenome.org/reference/S000349401 Caligaris M, De Virgilio C (2024)] Proxies introduce bias in decoding TORC1 activity. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000349402 Fromont-Racine M, Khanna V, Jacquier A, Badis G (2024)] YLR419W is the homolog of the mammalian translation initiation factor DHX29. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348700 Greenlaw A, Dell R, Tsukiyama T (2024)] Initial acidic media promotes quiescence entry in Saccharomyces cerevisiae. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348494 Harmer ZP, Hohener TC, Landolt AE, Mitchell C, McClean M (2024)] Enhancing high-throughput optogenetics: Integration of LITOS with Lustro enables simultaneous light stimulation and shaking. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000347552 Karpel JE (2024) Caenorhabditis elegans ddx-15 helicase fails to complement loss of Prp43p in Saccharomyces cerevisiae. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000347382 Medina-Suarez S, Machin F (2024)] The CRISPR/Cas9 system forms a condensate in the yeast nucleus. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348904 Putnam CD (2024)] Loss of mitochondrial DNA is associated with reduced DNA content variability in Saccharomyces cerevisiae. MicroPubl Biol 2024.
*[https://www.yeastgenome.org/reference/S000348874 Rosenbaum JC, Carlson AE (2024)] The SARS coronavirus accessory protein ORF3a rescues potassium conductance in yeast. MicroPubl Biol 2024.

All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD].

==Alliance of Genome Resources - Latest Release 7.2==
[[Image:alliance_logo.png|thumb|right|upright=.725]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort between SGD and other model organism databases (MODs), released [https://www.alliancegenome.org/release-notes version 7.2] in June 2024.

The 7.2.0 release updates the Disease pages’ Associated Alleles table and the Associated Models table:

*Each table has a new column, Disease Qualifier, with a working filter. The qualifier describes whether an allele or model may be, for example, implicated in the onset of a disease or a model for the severity of a disease, respectively
*In addition to the Disease Qualifier, the Associated Models table now has new columns for Condition Modifier and Genetic Modifier
*The “Annotation Details” pop-up has expanded to include more information.
**Alleles table: Association, Genetic Modifiers, Genetic Sex, Notes, and Annotation Type
**Models table: Genetic Sex, Notes, and Annotation Type
*The Associated Models table now has working filters for the Experimental Condition, Condition Modifier, and Genetic Modifier columns, including the ability to filter on relationship (e.g. induced by) as well as content (e.g. “copper”)
*The Download files from the disease page Associated Alleles table and Associated Models table now include additional information as well.
**New columns and information for the Associated Alleles table include: Allele Association, Genetic Entity Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Genetic Sex, Notes, Annotation Type, Source URL, and Date.
**New columns and information for the Associated Models table include: Model Type, Model Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Condition Modifiers, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Genetic Sex, Notes, Annotation Type, Source URL, and Date.

==Upcoming conferences and courses==
*[https://www.yeastorfanproject.com/summer-workshops/ RCN-UBE: Yeast ORFan Gene Project] - Summer Workshop - Gene Expression Analysis
**June 20 to June 21, 2024
**Virtual
*[https://events.faseb.org/event/f0c82874-ec6f-4b41-98e4-fe34d1646b74/summary FASEB Yeast Chromosome Biology and Cell Cycle]
**June 23 to June 27, 2024
**Fort Garry Hotel, Winnipeg, Manitoba, Canada
*[https://www.biologists.com/meetings/jcsevocellbio24/ JCS2024: Diversity and Evolution in Cell Biology]
**June 24 to June 27, 2024
**Montanya Hotel & Lodge, Catalonia, Spain
*[https://www.pnwyc.net Pacific Northwest Yeast Club]
**July 26, 2024
**Fred Hutchinson Cancer Center, Seattle, WA
*[https://web.cvent.com/event/4f188521-d6e8-4bd4-b0b5-b923ef8b3e5f/summary 39th Small Meeting of Yeast Transporters and Energetics (SMYTE)]
**August 28 to September 01, 2024
**University of York, York, United Kingdom
*[https://easternsun.eventsair.com/2024-16th-international-congress-on-yeasts ICY2024: 16th International Congress on Yeasts]
**September 29 to October 03, 2024
**Cape Town International Convention Centre, Cape Town, South Africa
*[https://premc.org/yeast2025/about-paris/ Yeast2025: 32nd International Conference on Yeast Genetics and Molecular Biology ICYGMB32]
**July 21 to July 24, 2025
**Sorbonne University, Paris, France