SGD-Wiki - User contributions [en]

SGD Newsletter, Spring 2025

2025-04-23T16:07:36Z

Edith: /* New Yeast Phenome Links in Phenotype Resources */

[[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'' and are greatly appreciated..

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>
* the 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==
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 (ex. [https://yeastgenome.org/locus/S000001171/phenotype#resources ARP1]), and will take you directly to the corresponding page of the Yeast Phenome data library.

==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

SGD Newsletter, Spring 2025

2025-04-23T15:48:35Z

Edith: /* 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'' and are greatly appreciated..

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>
* the 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==
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.

==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

SGD Newsletter, Spring 2025

2025-04-23T15:47:31Z

Edith: /* 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'' and are greatly appreciated..

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>
* the 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==
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, which facilitates the sharing of curated pathways with other researchers, databases, and pathway 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.

==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

SGD Newsletter, Spring 2025

2025-04-23T15:44:13Z

Edith: /* 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'' and are greatly appreciated..

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>
* the 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==
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 somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Some time ago we added a new section with pathways links on the relevant gene pages (ex. [https://yeastgenome.org/locus/S000005762#pathway DFR1]). We also 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, which facilitates the sharing of curated pathways with other researchers, databases, and pathway 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.

==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

SGD Newsletter, Spring 2025

2025-04-23T15:43:57Z

Edith: /* 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'' and are greatly appreciated..

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>
* the 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==
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 somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Some time ago we added a new section with pathways links on the relevant gene pages (ex. [https://yeastgenome.org/locus/S000005762#pathway DFR1). We also 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, which facilitates the sharing of curated pathways with other researchers, databases, and pathway 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.

==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

SGD Newsletter, Spring 2025

2025-04-23T15:41:06Z

Edith: /* 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'' and are greatly appreciated..

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>
* the 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==
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 somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Some time ago we added a new section with pathways links on the relevant gene pages (ex. DFR1). We also made the pathways available in SGD Search. Now we have transformed the metabolic pathways and associated genes/enzymes into Gene Ontology (GO) annotations (ex. 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, which facilitates the sharing of curated pathways with other researchers, databases, and pathway 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.

==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

SGD Newsletter, Spring 2025

2025-04-23T15:40:36Z

Edith: /* 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'' and are greatly appreciated..

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>
* the 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==
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 somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Some time ago we added a new section with pathways links on the relevant gene pages (ex. DFR1). We also made the pathways available in SGD Search. Now we have transformed the metabolic pathways and associated genes/enzymes into Gene Ontology (GO) annotations (ex. 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, which facilitates the sharing of curated pathways with other researchers, databases, and pathway 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.

==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

SGD Newsletter, Spring 2025

2025-04-23T15:38:08Z

Edith: /* 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'' and are greatly appreciated..

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>
* the 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==
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 somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Some time ago we added a new section with pathways links on the relevant gene pages (ex. DFR1). We also made the pathways available in SGD Search. Now we have transformed the metabolic pathways and associated genes/enzymes into Gene Ontology (GO) annotations (ex. 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 (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, which facilitates the sharing of curated pathways with other researchers, databases, and pathway 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.

==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

SGD Newsletter, Spring 2025

2025-04-23T15:30:43Z

Edith: /* SGD's Latest Genetics Publication */

[[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'' and are greatly appreciated..

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>
* the 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==
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 somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Some time ago we added a new section with pathways links on the relevant gene pages (ex. DFR1). We also made the pathways available in SGD Search. Now we have transformed the metabolic pathways and associated genes/enzymes into Gene Ontology (GO) annotations (ex. 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 (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 (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, which facilitates the sharing of curated pathways with other researchers, databases, and pathway 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.

==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

SGD Newsletter, Spring 2025

2025-04-23T15:27:49Z

Edith: /* SGD's Latest Genetics Publication */

[[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'' and are greatly appreciated..

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:
* the 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
 

==Pathway Annotations Now Available as GO Annotations==
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 somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Some time ago we added a new section with pathways links on the relevant gene pages (ex. DFR1). We also made the pathways available in SGD Search. Now we have transformed the metabolic pathways and associated genes/enzymes into Gene Ontology (GO) annotations (ex. 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 (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 (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, which facilitates the sharing of curated pathways with other researchers, databases, and pathway 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.

==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

SGD Newsletter, Summer 2024

2024-06-18T20:52:06Z

Edith: /* Extend gene coordinates in GFF */

[[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|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 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|link=https://www.yeastgenome.org|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.

==Extended 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|link=https://www.yeastgenome.org/search?q=&is_quick=true|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.alliancegenome.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 Associated Alleles and Associated Models tables on Disease pages:

*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

Systematic Sequencing Table

2024-04-11T19:18:51Z

Edith: /* Saccharomyces cerevisiae chromosome statistics and retrieval options */

== ''Saccharomyces cerevisiae'' chromosome statistics and retrieval options ==
{| border="1" style="border-collapse:collapse; width:90%" cellpadding="4"
|-
! style="background: #D8D8D8" | Chromosome Region & Reference
! style="background: #D8D8D8" | DNA Coordinator
! style="background: #D8D8D8" | Total Length
! style="background: #D8D8D8" | S288c sub-strain(s)
! style="background: #D8D8D8" | Retrieve
|-
|
[https://www.yeastgenome.org/contig/Chromosome_I I]
 [https://www.yeastgenome.org/reference/S000039624 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/?term=7731988 PubMed], [[media:Bussey_chr_I.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Howard_Bussey_741 H. Bussey], Montreal, Canada
| 230,218
| [[Commonly_used_strains#AB972 | AB972]]
|
[https://jbrowse.yeastgenome.org/?loc=chrI%3A1..230218&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=1&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr01.fsa Download FASTA]
|-
|
[https://www.yeastgenome.org/contig/Chromosome_II II]
 [https://www.yeastgenome.org/reference/S000057497 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/7813418 PubMed], [[media:Feldmann_chr_II.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Horst_Feldmann_1721 H. Feldmann], Muenchen, Germany
| 813,184
| genuine strain [[Commonly_used_strains#S288C | S288C]]
|
[https://jbrowse.yeastgenome.org/?loc=chrII%3A1..813184&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=2&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr02.fsa Download FASTA]
|-
|
[https://www.yeastgenome.org/contig/Chromosome_III III]
 [https://www.yeastgenome.org/reference/S000060078 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/1574125 PubMed], [[media:Oliver_chr_III.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Stephen_G._Oliver_4376 S.G. Oliver], Manchester, England
| 316,620
| [[Commonly_used_strains#XJ24-24a | XJ24-24a]], [[Commonly_used_strains#AB972 | AB972]], [[Commonly_used_strains#A364A | A364A]], [[Commonly_used_strains#DC5 | DC5]]
|
[https://jbrowse.yeastgenome.org/?loc=chrIII%3A1..316620&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=3&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr03.fsa Download FASTA]
|-
|
[https://www.yeastgenome.org/contig/Chromosome_IV IV]
 [https://www.yeastgenome.org/reference/S000060079 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/9169867 PubMed], [[media:Jacq_chr_IV.pdf | PDF]]
|
''Telo to Cen'': [https://www-aws.yeastgenome.org/colleague/Jacq_Claude_8573 C. Jacq], Paris, France
 ''Cen to 960K'': [https://www-aws.yeastgenome.org/colleague/Barclay_G._Barrell_296 B. Barrell], Cambridge, England
 ''960K to 1110K'': [https://www-aws.yeastgenome.org/colleague/Mark_Johnston_2827 M. Johnston], St. Louis, Missouri, USA
 ''1110K to Telo'': [https://www-aws.yeastgenome.org/colleague/Ronald_W._Davis_1262 R. Davis], Stanford, California, USA
| 1,531,933
| [[Commonly_used_strains#AB972 | AB972]]
|
[https://jbrowse.yeastgenome.org/?loc=chrIV%3A1..1531933&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=4&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr04.fsa Download FASTA]
|-
|
[https://www.yeastgenome.org/contig/Chromosome_V V]
 [https://www.yeastgenome.org/reference/S000058121 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/9169868 PubMed], [[media:Dietrich_chr_V.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Ronald_W._Davis_1262 R. Davis], Stanford, California, USA
| 576,874
| [[Commonly_used_strains#AB972 | AB972]]
|
[https://jbrowse.yeastgenome.org/?loc=chrV%3A1..576874&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=5&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr05.fsa Download FASTA]
|-
|
[https://www.yeastgenome.org/contig/Chromosome_VI VI]
 [https://www.yeastgenome.org/reference/S000057428 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/7670463 PubMed], [[media:Murakami_chr_VI.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Yasufumi_Murakami_4124 Y. Murakami], Tokyo, Japan
| 270,161
| [[Commonly_used_strains#AB972 | AB972]]
|
[https://jbrowse.yeastgenome.org/?loc=chrVI%3A1..270161&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=6&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr06.fsa Download FASTA]
|-
|
[https://www.yeastgenome.org/contig/Chromosome_VII VII]
 [https://www.yeastgenome.org/reference/S000060080 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/9169869 PubMed], [[media:Tettelin_chr_VII.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Herve_Tettelin_9854 H. Tettelin], Louvain-la-Neuve, Belgium
| 1,090,940
| [[Commonly_used_strains#FY1679 | FY1679]]
|
[https://jbrowse.yeastgenome.org/?loc=chrVII%3A1..1090940&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=7&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr07.fsa Download FASTA]
|-
|
[https://www.yeastgenome.org/contig/Chromosome_VIII VIII]
 [https://www.yeastgenome.org/reference/S000057599 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/8091229 PubMed], [[media:Johnston_chr_VIII.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Mark_Johnston_2827 M. Johnston], St. Louis, Missouri, USA
| 562,643
| [[Commonly_used_strains#AB972 | AB972]]
|
[https://jbrowse.yeastgenome.org/?loc=chrVII%3A1..562764&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=8&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr08.fsa Download FASTA]
|-
|
[https://www.yeastgenome.org/contig/Chromosome_IX IX]
 [https://www.yeastgenome.org/reference/S000060081 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/9169870 PubMed], [[media:Barrell_chr_IX.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Barclay_G._Barrell_296 B. Barrell], Cambridge, England
| 439,888
| [[Commonly_used_strains#AB972 | AB972]]
|
[https://jbrowse.yeastgenome.org/?loc=chrIX%3A1..439888&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=9&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr09.fsa Download FASTA]
|-
|
[https://www.yeastgenome.org/contig/Chromosome_X X]
 [https://www.yeastgenome.org/reference/S000060082 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/8641269 PubMed], [[media:Galibert_chr_X.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Francis_Galibert_1906 F. Galibert], Rouen, France
| 745,751
| [[Commonly_used_strains#FY1679 | FY1679]]
|
[https://jbrowse.yeastgenome.org/?loc=chrX%3A1..745751&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=10&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr10.fsa Download FASTA]
|-
|
[https://www.yeastgenome.org/contig/Chromosome_XI XI]
 [https://www.yeastgenome.org/reference/S000057636 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/8196765 PubMed], [[media:Dujon_chr_XI.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Bernard_Dujon_1514 B. Dujon], Paris, France
| 666,816
| [[Commonly_used_strains#FY1679 | FY1679]]
|
[https://jbrowse.yeastgenome.org/?loc=chrXI%3A1..666816&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=11&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr11.fsa Download FASTA]
|-
| [https://www.yeastgenome.org/contig/Chromosome_XII XII]
[https://www.yeastgenome.org/reference/S000060083 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/9169871 PubMed], [[media:Johnston_chr_XII.pdf | PDF]]
|
''Left'': [https://www-aws.yeastgenome.org/colleague/Jorg_D._Hoheisel_2528 J. Hoheisel], Heidelberg, Germany
 ''Right'': [https://www-aws.yeastgenome.org/colleague/Mark_Johnston_2827 M. Johnston], St. Louis, Missouri, USA
| 1,078,177
| [[Commonly_used_strains#AB972 | AB972]]
|
[https://jbrowse.yeastgenome.org/?loc=chrXII%3A1..1078177&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CDoube_strand_break_hotspots%2CXrn1-sensitive_unstable%20transcripts_XUTs%2CScGlycerolMedia%2C3'UTRs%2CPolII_occupancy_WT&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=12&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr12.fsa Download FASTA]
|-
|[https://www.yeastgenome.org/contig/Chromosome_XIII XIII]
[https://www.yeastgenome.org/reference/S000060084 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/9169872 PubMed], [[media:Barrell_chr_XIII.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Barclay_G._Barrell_296 B. Barrell], Cambridge, England
| 924,431
| [[Commonly_used_strains#AB972 | AB972]]
|
[https://jbrowse.yeastgenome.org/?loc=chrXIII%3A1..924431&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CDoube_strand_break_hotspots%2CXrn1-sensitive_unstable%20transcripts_XUTs%2CScGlycerolMedia%2C3'UTRs%2CPolII_occupancy_WT&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=13&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr13.fsa Download FASTA]
|-
| [https://www.yeastgenome.org/contig/Chromosome_XIV XIV]
[https://www.yeastgenome.org/reference/S000060085 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/9169873 PubMed], [[media:Philippsen_chr_XIV.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Peter_Philippsen_4609 P. Philippsen, Basel], Switzerland
| 784,333
| [[Commonly_used_strains#FY1679 | FY1679]], [[Commonly_used_strains#AB972 | AB972]]
|
[https://jbrowse.yeastgenome.org/?loc=chrXIV%3A1..784333&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CDoube_strand_break_hotspots%2CXrn1-sensitive_unstable%20transcripts_XUTs%2CScGlycerolMedia%2C3'UTRs%2CPolII_occupancy_WT&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=14&start=&end=&submit2=Submit+Form Gene/SequenceResources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr14.fsa Download FASTA]
|-
| [https://www.yeastgenome.org/contig/Chromosome_XV XV]
[https://www.yeastgenome.org/reference/S000060298 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/9169874 PubMed], [[media:Dujon_chr_XV.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Bernard_Dujon_1514 B. Dujon], Paris, France
| 1,091,291
| [[Commonly_used_strains#FY1679 | FY1679]]
|
[https://jbrowse.yeastgenome.org/?loc=chrXV%3A1..1091291&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CDoube_strand_break_hotspots%2CXrn1-sensitive_unstable%20transcripts_XUTs%2CScGlycerolMedia%2C3'UTRs%2CPolII_occupancy_WT&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=15&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr15.fsa Download FASTA]
|-
| [https://www.yeastgenome.org/contig/Chromosome_XVI XVI]
[https://www.yeastgenome.org/reference/S000045447 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/9169875 PubMed], [[media:Bussey_chr_XVI.pdf | PDF]]
|
''Left 1'': [https://www-aws.yeastgenome.org/colleague/Andre_Goffeau_2067 A. Goffeau], Louvain-la-Neuve, Belgium
 ''Left 2'': [https://www-aws.yeastgenome.org/colleague/Howard_Bussey_741 H. Bussey], Montreal, Canada
 ''Left 2a'': [https://www-aws.yeastgenome.org/colleague/Ronald_W._Davis_1262 R. Davis], Stanford, California, USA
 ''Right 1'': [https://www-aws.yeastgenome.org/colleague/Barclay_G._Barrell_296 B. Barrell], Cambridge, England
 ''Right 2'': [https://www-aws.yeastgenome.org/colleague/Mark_Johnston_2827 M. Johnston], St. Louis, Missouri, USA
| 948,066
| [[Commonly_used_strains#AB972 | AB972]]
|
[https://jbrowse.yeastgenome.org/?loc=chrXVI%3A1..948066&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CDoube_strand_break_hotspots%2CXrn1-sensitive_unstable%20transcripts_XUTs%2CScGlycerolMedia%2C3'UTRs%2CPolII_occupancy_WT&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=16&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chr16.fsa Download FASTA]
|-
| [https://www.yeastgenome.org/contig/Chromosome_mito Mitochondrial]
[https://www.yeastgenome.org/reference/S000058438 SGD], [https://www.ncbi.nlm.nih.gov/pubmed/9872396 PubMed], [[media:Foury_chr_mito.pdf | PDF]]
| [https://www-aws.yeastgenome.org/colleague/Francoise_Foury_1817 Foury, Francoise], Unite de Biochimie Physiologique
| 85,779
| [[Commonly_used_strains#FY1679 | FY1679]]
|
[https://jbrowse.yeastgenome.org/?loc=chrmt%3A1..85779&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CDoube_strand_break_hotspots%2CXrn1-sensitive_unstable%20transcripts_XUTs%2CScGlycerolMedia%2C3'UTRs%2CPolII_occupancy_WT&highlight= JBrowse Viewer]
 [https://www.yeastgenome.org/seqTools?chr=17&start=&end=&submit2=Submit+Form Gene/Sequence Resources]
 [http://downloads.yeastgenome.org/sequence/S288C_reference/NCBI_genome_source/chrmt.fsa Download FASTA]
|-

SGD Newsletter, December 2023

2023-12-11T23:44:21Z

Edith:

[[Category: Newsletter]]
'''About this newsletter:''' This is the Winter 2023 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_2023 newsletter] as well as previous newsletters, on the SGD [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].
==Reference Genome Annotation Update R64.4==

==Textpresso updated==

==Biochemical Pathways now in SGD Search==

==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. We are seeing a strong set of microPublications come through the database and are glad for this venue to publish 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 [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 yeast microPublications:

*[https://www.yeastgenome.org/reference/S000345614 Bennett SA, Cobos SN, Son E, Segal R, Mathew S, Yousuf H, Torrente MP (2023)] Impaired RNA Binding Does Not Prevent Histone Modification Changes in a FUS ALS/FTD Yeast Model. MicroPubl Biol 2023

*[https://www.yeastgenome.org/reference/S000346184 Chang S, Joyson M, Kelly A, Tang L, Iannotta J, Rich A, Castilho Coelho N, Carvunis AR (2023)] Unannotated Open Reading Frame in Saccharomyces cerevisiae Encodes Protein Localizing to the Endoplasmic Reticulum. MicroPubl Biol 2023

*[https://www.yeastgenome.org/reference/S000345122 Chen A, Gibney PA (2023)] Disruption of GRR1 in Saccharomyces cerevisiae rescues tps1Δ growth on fermentable carbon sources. MicroPubl Biol 2023

*[https://www.yeastgenome.org/reference/S000345620 Courtin B, Namane A, Gomard M, Meyer L, Jacquier A, Fromont-Racine M (2023)] Xrn1 biochemically associates with eisosome proteins after the post diauxic shift in yeast. MicroPubl Biol 2023

*[https://www.yeastgenome.org/reference/S000345449 Delorme-Axford E, Tasmi TA, Klionsky DJ (2023)] The Pho23-Rpd3 histone deacetylase complex regulates the yeast metabolic transcription factor Stb5. MicroPubl Biol 2023

*[https://www.yeastgenome.org/reference/S000345142 Garcia B, Riley KJ (2023)] Saccharomyces cerevisiae NRE1 and IRC24 Encode Paralogous Benzil Oxidoreductases. MicroPubl Biol 2023

*[https://www.yeastgenome.org/reference/S000344979 Kowaleski SJ, Hurmis CS, Coleman CN, Philips KD, Najor NA (2023)] SHE9 deletion mutants display fitness defects during diauxic shift in Saccharomyces cerevisiae . MicroPubl Biol 2023

*[https://www.yeastgenome.org/reference/S000346642 Runnebohm AM, Indovina CJ, Turk SM, Bailey CG, Orchard CJ, Wade L, Overton DL, Snow BJ, Rubenstein EM (2023)] Methionine Restriction Impairs Degradation of a Protein that Aberrantly Engages the Endoplasmic Reticulum Translocon. MicroPubl Biol 2023

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

 

==Allele SGDIDs added to YeastMine==

==Downloads files added to YeastMine==

==Chemical structures now on Chemical pages in SGD==

==Alliance of Genome Resources - Release 6.0==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.725]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort between SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 6.0] in September 2023.

'''Version 6.0''' adds new features to gene pages:

*New Paralogy section. Similar to Orthology, the Paralogy data are sourced from the DRSC’s [https://fgr.hms.harvard.edu/diopt DIOPT] tool, which lets you view predictions from several tools at one time. Each table is ranked based on similarity, identity, alignment length, and a count of algorithms (methods) used to predict a paralogous match. See human HSPA1A gene page for an example.
*New Sequence Detail section. For different transcripts of the gene, you can choose to view the sequence for the gene, or its CDS, cDNA, protein, gene with collapsed introns, or genomic sequence with or without 500 bp up and downstream.
*Disease Qualifier. The qualifier describes whether a gene may be, for example, a marker_for the onset of a disease, or implicated_in the severity of a disease.
*Disease “Annotation details”. The pop-up for individual table rows has expanded to include Association, Additional Implicated Genes, Genetic Modifiers, Strain Background, Genetic Sex, Notes, and Annotation Type.
*The Download file from the gene page disease table now includes fields for Additional Implicated Gene ID, Additional Implicated Gene Symbol, Gene Association, Genetic Entity Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Strain Background ID, Strain Background Name, Genetic Sex, Notes, Annotation Type, and Source URL.
*The Source column entries now link back to their respective resource webpages.

 

==Upcoming Conferences and Courses==
*[https://genetics-gsa.org/tagc/ TAGC2024 The Allied Genetics Conference]
**National Harbor | Washington DC Metro Area
**March 05 to March 10, 2024

*[https://genetics-gsa.org/fungal/ 32nd Fungal Genetics Conference]
**Asilomar Conference Grounds, Pacific Grove, CA
**March 12 to March 17, 2024

*[http://www.yeastlipidconference.com/next-meetings-2024-and-beyond.html 16th Yeast Lipid Conference]
**May 29 to May 31, 2024 -
**Saarland University, Homburg, Germany

*[https://www.biologists.com/meetings/jcsevocellbio24/ JCS2024: Diversity and Evolution in Cell Biology]
**June 24 to June 27, 2024 -
**Montanya Hotel & Lodge, Catalonia, Spain

*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]
**Cape Town International Convention Centre, Cape Town, South Africa
**September 29 to October 03, 2024

Software

2023-07-31T18:12:37Z

Edith:

*[[MochiView]] Desktop genome browsing and motif analysis software (with easy import of S. cerevisiae genome/genes/motif libraries)
*[[EGAN]] Downstream/pathway/gene set enrichment/visualization tool for exploring results of -omics experiments
*[[REVIGO]] A Web server that summarizes and visualizes long lists of Gene Ontology terms
*[[Primers-4-Yeast]] Design primers for gene targeting of PCR-based transformation cassettes into S. cerevisiae, and for validation of correct insertion.
*[[MyLabStocks]] Manage molecular biology stocks of your lab (primers, strains, plasmids and more...)
*[[GRSandPRIMED|GRS]]: Retrieve custom sequences from any annotated genome
*[[Yeastriction]] A web based tool to select targets for CRISPR editing of the genome.
*[[Genome Compiler]] is a free all-in-one software platform for DNA design and visualization, data management, lab collaboration and seamless DNA ordering.
*[[YeaZ]] is a Python-based graphical user interface and web application that applies a convolutional neural network, based on a training set, to aid in the visualization of yeast images by segmentation.
*[https://github.com/irahorecka/sgd-rest sgd-rest] is a Python-based wrapper for the SGD REST API.

Positions in yeast labs

2023-04-05T17:41:37Z

Edith:

=='''Post-doctoral position in ''S. cerevisiae'' research (posted 5 April 2023)'''==
De Wulf lab, University of Trento, Italy

'''Description''': The De Wulf lab at the Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy, is looking for an outstanding, highly motivated post-doctoral scientist to study the biological activity of oncogenic kinetochore kinase Rio1. The research will aim to understand how this kinase regulates the chromatin at centromeres and pericentromeres to ensure correct levels of centromeric RNAs, required for faithful centromeric nucleosome formation and kinetochore recruitment/activity.

Candidates with expertise in yeast genetics, biochemistry, cell and molecular biology are encouraged to apply. Experience with live-cell fluorescence imaging is greatly appreciated. For publications related to the topic: Bock LJ et al (2012) Nature Cell Biology, Iacovella MG et al (2015) Nature Communications, Iacovella MG et al (2018) Nucleic Acids Research, Berto G et al (2019) Current Genetics. More details of the project itself (Smurova K et al. (2023) Nature Communications, in press) will be provided upon request. A video call via Zoom can surely be arranged.

'''Position overview''': : The candidate should hold a recent PhD degree and a good publication record (at least one first-author publication in a reputable peer-reviewed journal). S/he must be motivated to excel in science, be curious, open-minded, and pro-active.

The lab is located in the city of Trento (150K inhabitants), near lakes and mountains, and lies close to Bolzano, Verona, Venice, and Milan.

Trento University is top-ranked in Italy, and CIBIO is the nr. 1 department of biology in Italy. State-of-the art equipment and facilities are available in our lab and in the department. Please visit our website for more information on our group, research interests and publications: http://www.cibio.unitn.it/510/chromosome-segregation-biology

'''How to apply''': Please send a detailed CV with publications, and the names + emails of 2-3 referees to Peter De Wulf (peter.dewulf@unitn.it). The University of Trento offers at first a 1-year contract, which can be renewed for up to 3 years. The salary is according to University of Trento pay scale.

=='''Tenure-track position in Cell Biology in the Department of Biology at Trent University (posted 6 Dec 2022)'''==
https://www.universityaffairs.ca/search-job/?job_id=59331

:Trent University
:Location: Ontario
:Date posted: 2022-10-20
:Advertised until: 2022-12-19

Trent University invites applications for a tenure track position in the field of '''Cell Biology''', in the Department of Biology. The appointment will be at the rank of Assistant Professor and will commence July 1, 2023. This position will be located at the Trent Peterborough campus and is subject to budgetary approval.

A completed Ph.D. and relevant research experience are required, with teaching experience considered an asset. The successful candidate is expected to have a demonstrated research record and the potential to secure external funding. We seek an individual who investigates cellular responses to environmental stressors and/or environmental change. Research areas could include developmental processes at the cellular or molecular level, evolutionary developmental biology, cell physiology and metabolism, inter- and intra-cellular communication, and/or cellular stress responses, among others. A research program spanning multiple levels of biological organization (genes-to-whole organisms) and that complements current research in the Department of Biology (www.trentu.ca/biology) would be an asset. Applicants must be committed to undergraduate and graduate level training through teaching, mentorship of student research, and student advising as a member of the Department of Biology and the Environmental and Life Sciences Graduate Program (www.trentu.ca/els ).

Applications should include a cover letter, a curriculum vitae, a statement of teaching experience and philosophy, a brief description of proposed research, and the names, email addresses, and telephone numbers of three referees who would be willing to write on the candidate’s behalf. Please note that applications will only be accepted in PDF format via email. Please send applications and/or any questions to biologyjobs@trentu.ca , attention Professor Gary Burness, Chair, Department of Biology.

The deadline for receipt of applications is '''December 15, 2022'''.

Trent University is actively committed to creating a diverse and inclusive campus community and encourages applications from all qualified candidates. Trent University offers accommodation for applicants with disabilities in its recruitment processes. If you require accommodation during the recruitment process or require an accessible version of a document/publication, please contact garyburness@trentu.ca .

All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority.

https://www.trentu.ca/humanresources/careers/full-time-faculty/assistant-professor-cell-biology-tenure-track
:Assistant Professor (Cell Biology) - Tenure Track
:Date Posted: October 20, 2022
:Closing Date: December 15, 2022 - 4:00PM (or until filled)
:Faculty Position: Tenure Track
:Department: Department of Biology
:Location: Peterborough
:For more information, please view the [https://www.trentu.ca/humanresources/sites/trentu.ca.humanresources/files/documents/BIOL-TT-CellBiology.docx full Position Description] or visit [https://www.trentu.ca/employment trentu.ca/employment].

=='''Post-doctoral position on comparative transcriptomics in ''S. cerevisiae'' strains (posted 9th June 2022) '''==
Mar Albà, ICREA Research Professor, Evolutionary Genomics Group, Hospital del Mar Medical Research Institute (IMIM) – Barcelona Biomedical Research Park (PRBB), Barcelona.

'''Description''': Looking to recruit one highly motivated researcher at the postdoctoral level to perform research on comparative genomics, transcriptomics and translatomics with the goal to better understand the molecular basis of the evolution of new genes in yeast. The position is funded by an ERC Advanced Grant (NovoGenePop) and will have an initial duration of three years.
The researcher will study transcriptome diversity in wild and domesticated populations of yeast. She/he will develop computational approaches to analyze a large amount of RNA-seq and Ribo-seq data from different S. cerevisiae strains and Saccharomyces species, characterize the transcriptomic diversity in different populations and develop methods to identify recently evolved genes. Mutations and selective signatures associated with de novo gene birth will be identified using genomics data from a large number of strains.

'''Requirements''':
*Research experience in comparative genomics and transcriptomics
*Expertise in at least one programming language
*Expertise in a programmatic statistics language (ideally R)
*Sound knowledge of population genetics and molecular evolution
*Excellent verbal and written communication skills in English

'''Representative publications''':
*Blevins, W.R., Ruiz-Orera, J., Messeguer, X., Blasco-Moreno, B., Villanueva-Cañas, J.L., Espinar, L., Díez, J., Carey, L.B., Albà, M.M. (2021). Uncovering de novo gene birth in yeast using deep transcriptomics. Nature Communications, vol. 12: 604.
*Blevins, W.R., Tavella, T., Moro, S.G., Blasco-Moreno, B., Closa-Mosquera, A., Diez, J., Carey, L.B., Albà, M.M. (2019) Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker's yeast. Scientific Reports, vol. 9: 11005.

'''Location''':
We are located at the Barcelona Biomedical Research Park (PRBB), one of the most vibrant interdisciplinary research centers in Southern Europe with more than 1000 scientists in the building alone, including a large bioinformatics and evolutionary biology community. The researchers will have access to state-of-the-art resources and a wide range of in-house training opportunities.

'''Starting date and salary''':
Ideally between Oct 1st 2022 and February 1st 2023. Salary 34,636-40,531 Eur per year depending on experience.

'''Contact''':
Please send an email to Mar Albà (malba@imim.es) with subject “PostdocERC_yeast” including a CV and a motivation letter, together with the name of two contacts for references. The deadline for the first round of applications is the 15th of July 2022.

=='''Post-doctoral position in ''S. cerevisiae'' research (posted 23 May 2022)'''==
Truman lab, University of North Carolina at Charlotte, USA

'''Description''': The Truman laboratory in the Department of Biological Sciences at UNC Charlotte employs a range of molecular technologies including mass spectrometry, CRISPR-genome engineering and high-throughput screening to study the role of post-translational modifications on Hsp70 (see: http://www.trumanlab.org). We are seeking a highly motivated postdoctoral researcher with
experience working with budding yeast. 
NIH Funding is available for several years, with the expectation that the candidate will work with Dr. Truman to apply for fellowships during this time. Ideal candidates will have graduated less than one year from their start date in the Truman lab. To apply please email Dr. Truman at atruman1@uncc.edu. Please include a cover letter, CV and any relevant publications. 

'''About the Department of Biological Sciences''': The Department of Biological Sciences (https://biology.charlotte.edu/) has set as its mission to advance the frontiers of knowledge through innovation and research in the biological sciences; to facilitate development of scientists in the guidance of our bachelors, masters and doctoral Biology students, and in the training of post-doctoral fellows; to contribute to local, national, and international scientific communities through collaborations and service activities that promote education and dissemination of information; to contribute to the community by collaborating with public, nonprofit, private, and industry partners in the Charlotte metropolitan area and the State of North Carolina.
 The collaborative research environment at the UNC Charlotte offers an excellent opportunity for career development. The UNC Charlotte offers a complete benefits package and competitive salary. The Charlotte region provides wonderful environment to work and live.

'''Ideal Qualifications''':
*Ph. D in biochemistry, molecular biology, cancer biology or related field.
*Experience with budding yeast including gene deletion, transformation etc.
*Experience with general molecular techniques such as Western Blotting, DNA cloning, coimmunoprecipitation.

File:Kishore 2020 PMID 32559296.pdf

2022-11-16T17:31:42Z

Edith:

SGD Publications

2022-11-16T17:30:36Z

Edith:

This is a list of publications written by or in collaboration with members of the SGD staff.
#Engel SR, Wong ED, Nash RS, Aleksander S, Alexander M, Douglass E, Karra K, Miyasato SR, Simison M, Skrzypek MS, Weng S, Cherry JM (2022) New data and collaborations at the ''Saccharomyces'' Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. Genetics. 2022 Apr 4; 220(4):iyab224. doi: 10.1093/genetics/iyab224. [[media:Engel_2022_PMID_34897464.pdf| '''Full-Text PDF''']] | [https://pubmed.ncbi.nlm.nih.gov/34897464 '''PMID:34897464''']
#Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM, the SGD Project (2019) Incorporation of a unified protein abundance dataset into the ''Saccharomyces'' Genome Database. Database (Oxford). 2020 Jan 1; 2020. doi: 10.1093/database/baaa008.[[media:Nash_2020_PMID_32128557.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/32128557 '''PMID: 32128557''']
#Kishore R, Arnaboldi V, Van Slyke CE, Chan J, Nash RS, Urbano JM, Dolan ME, Engel SR, Shimoyama M, Sternberg PW, Genome Resources TAO (2020) Automated generation of gene summaries at the Alliance of Genome Resources. Database (Oxford). 2020 Jan 1;2020:baaa037. doi: 10.1093/database/baaa037. [[media:Kishore_2020_PMID_32559296.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/32559296 '''PMID: 32559296''']
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#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']

File:Meldal 2019 PMID 30357405.pdf

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Edith:

SGD Publications

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Edith:

This is a list of publications written by or in collaboration with members of the SGD staff.
#Engel SR, Wong ED, Nash RS, Aleksander S, Alexander M, Douglass E, Karra K, Miyasato SR, Simison M, Skrzypek MS, Weng S, Cherry JM (2022) New data and collaborations at the ''Saccharomyces'' Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. Genetics. 2022 Apr 4; 220(4):iyab224. doi: 10.1093/genetics/iyab224. [[media:Engel_2022_PMID_34897464.pdf| '''Full-Text PDF''']] | [https://pubmed.ncbi.nlm.nih.gov/34897464 '''PMID:34897464''']
#Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM, the SGD Project (2019) Incorporation of a unified protein abundance dataset into the ''Saccharomyces'' Genome Database. Database (Oxford). 2020 Jan 1; 2020. doi: 10.1093/database/baaa008.[[media:Nash_2020_PMID_32128557.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/32128557 '''PMID: 32128557''']
#Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM (2019) Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res. 2019 Oct 15; pii: gkz892. doi: 10.1093/nar/gkz892. [[media:Ng_2019_PMID_31612944.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/31612944 '''PMID: 31612944''']
#Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM, the SGD Project (2019) Integration of macromolecular complex data into the ''Saccharomyces'' Genome Database. Database (Oxford). 2019 Jan 1; 2019. doi: 10.1093/database/baz008.[[media:Wong_2019_PMID_30715277.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/30715277 '''PMID: 30715277''']
#Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S (2019) Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. Nucleic Acids Res. 2019 Jan 8;47(D1):D550-D558. doi: 10.1093/nar/gky1001. [[media:Meldal_2019_PMID_30357405.pdf| '''Full-Text PDF''']] | [https://pubmed.ncbi.nlm.nih.gov/30357405 '''PMID:30357405''']]
#Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C (2018) Model organism data evolving in support of translational medicine. Lab Anim (NY). Sep 17; 2018. doi: 10.1038/s41684-018-0150-4.[[media:Howe_2018_PMID_30224793.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/30224793 '''PMID: 30224793''']
#Lang OW, Nash RS, Hellerstedt ST, Engel SR, the SGD Project (2018) An Introduction to the Saccharomyces Genome Database (SGD). Methods Mol Biol. 2018 May 15; 1757:21-30.[[media:Lang_2018_PMID_29761454.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29761454 '''PMID: 29761454''']
#Engel SR, Skrzypek MS, Hellerstedt ST, Wong ED, Nash RS, Weng S, Binkley G, Sheppard TK, Karra K, Cherry JM (2018) Updated regulation curation model at the ''Saccharomyces'' Genome Database. Database (Oxford). 2018 Jan 1; 2018. doi: 10.1093/database/bay007.[[media:Engel_2018_PMID_29688362.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29688362 '''PMID: 29140510''']
#Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR, Cherry JM (2018) ''Saccharomyces'' genome database informs human biology. Nucleic Acids Res. 2018 Jan 4; 46:D736-D742. doi: 10.1093/nar/gkx1112. [[media:Skrzypek_2018_PMID_29140510.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29140510 '''PMID: 29140510''']
#Wong ED (2017) Exploring Protein Function Using the ''Saccharomyces'' Genome Database. Methods Mol Biol. 2017 Apr 28; 1611:169-182. doi: 10.1007/978-1-4939-7015-5_13.[[media:Wong_2017_PMID_28451979.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28451979 '''PMID: 28365719''']
#MacPherson KA, Starr B, Wong ED, Dalusag KS, Hellerstedt ST, Lang OW, Nash RS, Skrzypek MS, Engel SR, Cherry JM (2017) Outreach and online training services at the ''Saccharomyces'' Genome Database. 2017 Jan 1; pii: bax002. doi: 10.1093/database/bax002.[[media:MacPherson_2017_PMID_28365719.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28365719 '''PMID: 28365719''']
#Hellerstedt ST, Nash RS, Weng S, Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM (2017) Curated protein information in the ''Saccharomyces'' Genome Database. 2017 Mar 11; pii: bax011. doi: 10.1093/database/bax011. [[media:Hellerstedt_2017_PMID_28365727.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28365727 '''PMID: 28365727''']
#Engel SR, MacPherson KA (2016) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2016 Nov. doi: 10.1002/cpet.4. [[media:Engel_2016_UsingModelOrganisms.pdf| '''Full-Text PDF''']]
#Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag K, Demeter J, Engel S, Hellerstedt ST, Karra K, Hitz BC, Nash RS, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [[media:Song_2016_PMID_27252399.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/27252399 '''PMID: 27252399''']
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2016_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']

SGD Publications

2022-11-16T17:24:22Z

Edith:

This is a list of publications written by or in collaboration with members of the SGD staff.
#Engel SR, Wong ED, Nash RS, Aleksander S, Alexander M, Douglass E, Karra K, Miyasato SR, Simison M, Skrzypek MS, Weng S, Cherry JM (2022) New data and collaborations at the ''Saccharomyces'' Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. Genetics. 2022 Apr 4; 220(4):iyab224. doi: 10.1093/genetics/iyab224. [[media:Engel_2022_PMID_34897464.pdf| '''Full-Text PDF''']] | [https://pubmed.ncbi.nlm.nih.gov/34897464 '''PMID:34897464''']
#Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM, the SGD Project (2019) Incorporation of a unified protein abundance dataset into the ''Saccharomyces'' Genome Database. Database (Oxford). 2020 Jan 1; 2020. doi: 10.1093/database/baaa008.[[media:Nash_2020_PMID_32128557.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/32128557 '''PMID: 32128557''']
#Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM (2019) Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res. 2019 Oct 15; pii: gkz892. doi: 10.1093/nar/gkz892. [[media:Ng_2019_PMID_31612944.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/31612944 '''PMID: 31612944''']
#Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM, the SGD Project (2019) Integration of macromolecular complex data into the ''Saccharomyces'' Genome Database. Database (Oxford). 2019 Jan 1; 2019. doi: 10.1093/database/baz008.[[media:Wong_2019_PMID_30715277.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/30715277 '''PMID: 30715277''']
#Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S (2019) Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. Nucleic Acids Res. 2019 Jan 8;47(D1):D550-D558. doi: 10.1093/nar/gky1001. [[media:Meldal_2019)PMID_30357405.pdf| '''Full-Text PDF''']] | [https://pubmed.ncbi.nlm.nih.gov/30357405 '''PMID:30357405''']]
#Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C (2018) Model organism data evolving in support of translational medicine. Lab Anim (NY). Sep 17; 2018. doi: 10.1038/s41684-018-0150-4.[[media:Howe_2018_PMID_30224793.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/30224793 '''PMID: 30224793''']
#Lang OW, Nash RS, Hellerstedt ST, Engel SR, the SGD Project (2018) An Introduction to the Saccharomyces Genome Database (SGD). Methods Mol Biol. 2018 May 15; 1757:21-30.[[media:Lang_2018_PMID_29761454.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29761454 '''PMID: 29761454''']
#Engel SR, Skrzypek MS, Hellerstedt ST, Wong ED, Nash RS, Weng S, Binkley G, Sheppard TK, Karra K, Cherry JM (2018) Updated regulation curation model at the ''Saccharomyces'' Genome Database. Database (Oxford). 2018 Jan 1; 2018. doi: 10.1093/database/bay007.[[media:Engel_2018_PMID_29688362.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29688362 '''PMID: 29140510''']
#Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR, Cherry JM (2018) ''Saccharomyces'' genome database informs human biology. Nucleic Acids Res. 2018 Jan 4; 46:D736-D742. doi: 10.1093/nar/gkx1112. [[media:Skrzypek_2018_PMID_29140510.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29140510 '''PMID: 29140510''']
#Wong ED (2017) Exploring Protein Function Using the ''Saccharomyces'' Genome Database. Methods Mol Biol. 2017 Apr 28; 1611:169-182. doi: 10.1007/978-1-4939-7015-5_13.[[media:Wong_2017_PMID_28451979.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28451979 '''PMID: 28365719''']
#MacPherson KA, Starr B, Wong ED, Dalusag KS, Hellerstedt ST, Lang OW, Nash RS, Skrzypek MS, Engel SR, Cherry JM (2017) Outreach and online training services at the ''Saccharomyces'' Genome Database. 2017 Jan 1; pii: bax002. doi: 10.1093/database/bax002.[[media:MacPherson_2017_PMID_28365719.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28365719 '''PMID: 28365719''']
#Hellerstedt ST, Nash RS, Weng S, Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM (2017) Curated protein information in the ''Saccharomyces'' Genome Database. 2017 Mar 11; pii: bax011. doi: 10.1093/database/bax011. [[media:Hellerstedt_2017_PMID_28365727.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28365727 '''PMID: 28365727''']
#Engel SR, MacPherson KA (2016) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2016 Nov. doi: 10.1002/cpet.4. [[media:Engel_2016_UsingModelOrganisms.pdf| '''Full-Text PDF''']]
#Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag K, Demeter J, Engel S, Hellerstedt ST, Karra K, Hitz BC, Nash RS, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [[media:Song_2016_PMID_27252399.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/27252399 '''PMID: 27252399''']
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2016_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']

SGD Publications

2022-11-16T17:19:27Z

Edith:

This is a list of publications written by or in collaboration with members of the SGD staff.
#Engel SR, Wong ED, Nash RS, Aleksander S, Alexander M, Douglass E, Karra K, Miyasato SR, Simison M, Skrzypek MS, Weng S, Cherry JM (2022) New data and collaborations at the ''Saccharomyces'' Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. Genetics. 2022 Apr 4; 220(4):iyab224. doi: 10.1093/genetics/iyab224. [[media:Engel_2022_PMID_34897464.pdf| '''Full-Text PDF''']] | [https://pubmed.ncbi.nlm.nih.gov/34897464 '''PMID:34897464''']
#Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM, the SGD Project (2019) Incorporation of a unified protein abundance dataset into the ''Saccharomyces'' Genome Database. Database (Oxford). 2020 Jan 1; 2020. doi: 10.1093/database/baaa008.[[media:Nash_2020_PMID_32128557.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/32128557 '''PMID: 32128557''']
#Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM (2019) Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res. 2019 Oct 15; pii: gkz892. doi: 10.1093/nar/gkz892. [[media:Ng_2019_PMID_31612944.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/31612944 '''PMID: 31612944''']
#Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM, the SGD Project (2019) Integration of macromolecular complex data into the ''Saccharomyces'' Genome Database. Database (Oxford). 2019 Jan 1; 2019. doi: 10.1093/database/baz008.[[media:Wong_2019_PMID_30715277.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/30715277 '''PMID: 30715277''']
#Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C (2018) Model organism data evolving in support of translational medicine. Lab Anim (NY). Sep 17; 2018. doi: 10.1038/s41684-018-0150-4.[[media:Howe_2018_PMID_30224793.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/30224793 '''PMID: 30224793''']
#Lang OW, Nash RS, Hellerstedt ST, Engel SR, the SGD Project (2018) An Introduction to the Saccharomyces Genome Database (SGD). Methods Mol Biol. 2018 May 15; 1757:21-30.[[media:Lang_2018_PMID_29761454.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29761454 '''PMID: 29761454''']
#Engel SR, Skrzypek MS, Hellerstedt ST, Wong ED, Nash RS, Weng S, Binkley G, Sheppard TK, Karra K, Cherry JM (2018) Updated regulation curation model at the ''Saccharomyces'' Genome Database. Database (Oxford). 2018 Jan 1; 2018. doi: 10.1093/database/bay007.[[media:Engel_2018_PMID_29688362.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29688362 '''PMID: 29140510''']
#Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR, Cherry JM (2018) ''Saccharomyces'' genome database informs human biology. Nucleic Acids Res. 2018 Jan 4; 46:D736-D742. doi: 10.1093/nar/gkx1112. [[media:Skrzypek_2018_PMID_29140510.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29140510 '''PMID: 29140510''']
#Wong ED (2017) Exploring Protein Function Using the ''Saccharomyces'' Genome Database. Methods Mol Biol. 2017 Apr 28; 1611:169-182. doi: 10.1007/978-1-4939-7015-5_13.[[media:Wong_2017_PMID_28451979.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28451979 '''PMID: 28365719''']
#MacPherson KA, Starr B, Wong ED, Dalusag KS, Hellerstedt ST, Lang OW, Nash RS, Skrzypek MS, Engel SR, Cherry JM (2017) Outreach and online training services at the ''Saccharomyces'' Genome Database. 2017 Jan 1; pii: bax002. doi: 10.1093/database/bax002.[[media:MacPherson_2017_PMID_28365719.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28365719 '''PMID: 28365719''']
#Hellerstedt ST, Nash RS, Weng S, Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM (2017) Curated protein information in the ''Saccharomyces'' Genome Database. 2017 Mar 11; pii: bax011. doi: 10.1093/database/bax011. [[media:Hellerstedt_2017_PMID_28365727.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28365727 '''PMID: 28365727''']
#Engel SR, MacPherson KA (2016) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2016 Nov. doi: 10.1002/cpet.4. [[media:Engel_2016_UsingModelOrganisms.pdf| '''Full-Text PDF''']]
#Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag K, Demeter J, Engel S, Hellerstedt ST, Karra K, Hitz BC, Nash RS, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [[media:Song_2016_PMID_27252399.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/27252399 '''PMID: 27252399''']
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2016_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']

File:Engel 2022 PMID 34897464.pdf

2022-11-16T17:18:07Z

Edith:

SGD Publications

2022-11-16T17:16:20Z

Edith:

This is a list of publications written by or in collaboration with members of the SGD staff.
#Engel SR, Wong ED, Nash RS, Aleksander S, Alexander M, Douglass E, Karra K, Miyasato SR, Simison M, Skrzypek MS, Weng S, Cherry JM (2022) New data and collaborations at the ''Saccharomyces'' Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. Genetics. 2022 Apr 4; 220(4):iyab224. doi: 10.1093/genetics/iyab224. [https://pubmed.ncbi.nlm.nih.gov/34897464 '''PMID:34897464''']
#Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM, the SGD Project (2019) Incorporation of a unified protein abundance dataset into the ''Saccharomyces'' Genome Database. Database (Oxford). 2020 Jan 1; 2020. doi: 10.1093/database/baaa008.[[media:Nash_2020_PMID_32128557.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/32128557 '''PMID: 32128557''']
#Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM (2019) Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res. 2019 Oct 15; pii: gkz892. doi: 10.1093/nar/gkz892. [[media:Ng_2019_PMID_31612944.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/31612944 '''PMID: 31612944''']
#Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM, the SGD Project (2019) Integration of macromolecular complex data into the ''Saccharomyces'' Genome Database. Database (Oxford). 2019 Jan 1; 2019. doi: 10.1093/database/baz008.[[media:Wong_2019_PMID_30715277.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/30715277 '''PMID: 30715277''']
#Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C (2018) Model organism data evolving in support of translational medicine. Lab Anim (NY). Sep 17; 2018. doi: 10.1038/s41684-018-0150-4.[[media:Howe_2018_PMID_30224793.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/30224793 '''PMID: 30224793''']
#Lang OW, Nash RS, Hellerstedt ST, Engel SR, the SGD Project (2018) An Introduction to the Saccharomyces Genome Database (SGD). Methods Mol Biol. 2018 May 15; 1757:21-30.[[media:Lang_2018_PMID_29761454.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29761454 '''PMID: 29761454''']
#Engel SR, Skrzypek MS, Hellerstedt ST, Wong ED, Nash RS, Weng S, Binkley G, Sheppard TK, Karra K, Cherry JM (2018) Updated regulation curation model at the ''Saccharomyces'' Genome Database. Database (Oxford). 2018 Jan 1; 2018. doi: 10.1093/database/bay007.[[media:Engel_2018_PMID_29688362.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29688362 '''PMID: 29140510''']
#Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR, Cherry JM (2018) ''Saccharomyces'' genome database informs human biology. Nucleic Acids Res. 2018 Jan 4; 46:D736-D742. doi: 10.1093/nar/gkx1112. [[media:Skrzypek_2018_PMID_29140510.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29140510 '''PMID: 29140510''']
#Wong ED (2017) Exploring Protein Function Using the ''Saccharomyces'' Genome Database. Methods Mol Biol. 2017 Apr 28; 1611:169-182. doi: 10.1007/978-1-4939-7015-5_13.[[media:Wong_2017_PMID_28451979.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28451979 '''PMID: 28365719''']
#MacPherson KA, Starr B, Wong ED, Dalusag KS, Hellerstedt ST, Lang OW, Nash RS, Skrzypek MS, Engel SR, Cherry JM (2017) Outreach and online training services at the ''Saccharomyces'' Genome Database. 2017 Jan 1; pii: bax002. doi: 10.1093/database/bax002.[[media:MacPherson_2017_PMID_28365719.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28365719 '''PMID: 28365719''']
#Hellerstedt ST, Nash RS, Weng S, Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM (2017) Curated protein information in the ''Saccharomyces'' Genome Database. 2017 Mar 11; pii: bax011. doi: 10.1093/database/bax011. [[media:Hellerstedt_2017_PMID_28365727.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28365727 '''PMID: 28365727''']
#Engel SR, MacPherson KA (2016) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2016 Nov. doi: 10.1002/cpet.4. [[media:Engel_2016_UsingModelOrganisms.pdf| '''Full-Text PDF''']]
#Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag K, Demeter J, Engel S, Hellerstedt ST, Karra K, Hitz BC, Nash RS, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [[media:Song_2016_PMID_27252399.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/27252399 '''PMID: 27252399''']
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2016_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']

SGD Publications

2022-11-16T17:15:13Z

Edith:

This is a list of publications written by or in collaboration with members of the SGD staff.
#Engel SR, Wong ED, Nash RS, Aleksander S, Alexander M, Douglass E, Karra K, Miyasato SR, Simison M, Skrzypek MS, Weng S, Cherry JM (2022) New data and collaborations at the ''Saccharomyces'' Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. Genetics. 2022 Apr 4; 220(4):iyab224. doi: 10.1093/genetics/iyab224.
#Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM, the SGD Project (2019) Incorporation of a unified protein abundance dataset into the ''Saccharomyces'' Genome Database. Database (Oxford). 2020 Jan 1; 2020. doi: 10.1093/database/baaa008.[[media:Nash_2020_PMID_32128557.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/32128557 '''PMID: 32128557''']
#Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM (2019) Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res. 2019 Oct 15; pii: gkz892. doi: 10.1093/nar/gkz892. [[media:Ng_2019_PMID_31612944.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/31612944 '''PMID: 31612944''']
#Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM, the SGD Project (2019) Integration of macromolecular complex data into the ''Saccharomyces'' Genome Database. Database (Oxford). 2019 Jan 1; 2019. doi: 10.1093/database/baz008.[[media:Wong_2019_PMID_30715277.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/30715277 '''PMID: 30715277''']
#Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C (2018) Model organism data evolving in support of translational medicine. Lab Anim (NY). Sep 17; 2018. doi: 10.1038/s41684-018-0150-4.[[media:Howe_2018_PMID_30224793.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/30224793 '''PMID: 30224793''']
#Lang OW, Nash RS, Hellerstedt ST, Engel SR, the SGD Project (2018) An Introduction to the Saccharomyces Genome Database (SGD). Methods Mol Biol. 2018 May 15; 1757:21-30.[[media:Lang_2018_PMID_29761454.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29761454 '''PMID: 29761454''']
#Engel SR, Skrzypek MS, Hellerstedt ST, Wong ED, Nash RS, Weng S, Binkley G, Sheppard TK, Karra K, Cherry JM (2018) Updated regulation curation model at the ''Saccharomyces'' Genome Database. Database (Oxford). 2018 Jan 1; 2018. doi: 10.1093/database/bay007.[[media:Engel_2018_PMID_29688362.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29688362 '''PMID: 29140510''']
#Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR, Cherry JM (2018) ''Saccharomyces'' genome database informs human biology. Nucleic Acids Res. 2018 Jan 4; 46:D736-D742. doi: 10.1093/nar/gkx1112. [[media:Skrzypek_2018_PMID_29140510.pdf| '''Full-Text PDF''']] | [https://www.ncbi.nlm.nih.gov/pubmed/29140510 '''PMID: 29140510''']
#Wong ED (2017) Exploring Protein Function Using the ''Saccharomyces'' Genome Database. Methods Mol Biol. 2017 Apr 28; 1611:169-182. doi: 10.1007/978-1-4939-7015-5_13.[[media:Wong_2017_PMID_28451979.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28451979 '''PMID: 28365719''']
#MacPherson KA, Starr B, Wong ED, Dalusag KS, Hellerstedt ST, Lang OW, Nash RS, Skrzypek MS, Engel SR, Cherry JM (2017) Outreach and online training services at the ''Saccharomyces'' Genome Database. 2017 Jan 1; pii: bax002. doi: 10.1093/database/bax002.[[media:MacPherson_2017_PMID_28365719.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28365719 '''PMID: 28365719''']
#Hellerstedt ST, Nash RS, Weng S, Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM (2017) Curated protein information in the ''Saccharomyces'' Genome Database. 2017 Mar 11; pii: bax011. doi: 10.1093/database/bax011. [[media:Hellerstedt_2017_PMID_28365727.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/28365727 '''PMID: 28365727''']
#Engel SR, MacPherson KA (2016) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2016 Nov. doi: 10.1002/cpet.4. [[media:Engel_2016_UsingModelOrganisms.pdf| '''Full-Text PDF''']]
#Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag K, Demeter J, Engel S, Hellerstedt ST, Karra K, Hitz BC, Nash RS, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [[media:Song_2016_PMID_27252399.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/27252399 '''PMID: 27252399''']
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2016_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']

Strains

2022-10-10T17:00:55Z

Edith:

=Strain Backgrounds=
*View genotypes and descriptions of [[Commonly_used_strains|commonly used strains]].

*Table of [[Commonly_used_auxotrophic_markers|commonly used auxotrophic markers]], with sequence information where known.

=Stock Centers=
*[http://www.atcc.org/ American Type Culture Collection] (ATCC) maintains yeast stocks and clones.

*[http://www.euroscarf.de EUROSCARF], the EUROpean Saccharomyces Cerevisiae ARchive for Functional analysis, maintains a collection of systematic deletion strains [http://cgi.server.uni-frankfurt.de/fb15/rose/index.html searchable] by gene name.

*[http://www.ncyc.co.uk/ National Collection of Yeast Cultures (NCYC)] maintains over 3,100 non-pathogenic yeasts, including type strains, strains of general interest for education and research, strains of industrial importance, and genetically marked strains.

*[http://www.cabri.org/ Common Access to Biological Resources and Information] (CABRI) includes catalogs from European culture collections for yeast and other organisms.

*[http://www.addgene.org Addgene] is a non-profit plasmid repository that distributes many plasmids for yeast research. In particular, Addgene is distributing a collection of [http://www.addgene.org/yeast_gateway Yeast Advanced Gateway Destination Vectors] created by Dr. Susan Lindquist's laboratory.

*[http://yeast.lab.nig.ac.jp/yeast/ Yeast Genetic Resource Center (YGRC)] maintains over 4,800 S. pombe strains and over 9,000 S. cerevisiae strains.

*[http://www.dbvpg.unipg.it/ Industrial Yeasts Collection DBVPG]. The Industrial Yeasts Collection DBVPG, an academic biological resource centre (BRC) specialized in yeasts and yeast-like microorganisms, distributes strains and offers services to the international scientific community and to other private Institutions. DBVPG maintains over 6,000 yeast strains and over 300 yeast-like (Prototheca sp. ) strains.

=Strain Collections=

*[http://clones.invitrogen.com/cloneinfo.php?clone=yeastgfp Yeast-GFP Clone Collection] from Dr. Erin O'Shea and Dr. Jonathan Weissman at UCSF, consisting of C-terminal tagged open reading frames (ORFs). Hosted by [http://www.invitrogen.com/site/us/en/home/brands/Invitrogen.html Invitrogen].

*[http://www.thermoscientificbio.com/non-mammalian-cdna-and-orf/yeast-gst-tagged-orfs/ Yeast GST-Tagged Collection] for inducible overexpression of yeast ORFs, developed in the Andrews lab at the University of Toronto. Hosted by [http://www.thermoscientificbio.com/openbiosystems/?redirect=true Open Biosystems].

*[http://yeastdeletion-sgtc.yeastgenome.org/downloads.html#strainsavail Yeast Knockout (YKO) Collection] from the [http://yeastdeletion-sgtc.yeastgenome.org/consortium.html Saccharomyces Genome Deletion Consortium].

*[http://www.thermoscientificbio.com/non-mammalian-cdna-and-orf/yeast-tap-tagged-orfs/ Yeast-TAP Fusion Library] from Dr. Erin O'Shea and Dr. Jonathan Weissman at UCSF, containing open reading frames (ORFs) tagged with a high-affinity epitope and expressed from their natural chromosomal locations. Hosted by [http://www.thermoscientificbio.com/openbiosystems/?redirect=true Open Biosystems].

*[http://www.openbiosystems.com/GeneExpression/Yeast/Tet-Promoters/ Yeast Tet-promoters Hughes Collection] containing 800 essential yeast genes for which expression is regulated by doxycycline. Hosted by [http://www.openbiosystems.com Open Biosystems].

*The Yeast Transposon Insertion Library Collection, derived by using mini-transposons (mTns) to mutagenize a yeast genomic DNA library, is available from the [http://snyderlab.stanford.edu/ Mike Snyder lab] at Stanford University. Please contact Minyi Shi (minyishi at stanford dot edu) with requests.

Primer Set Sequences

2022-10-10T16:58:28Z

Edith: /* Primer sets used by the Yeast Knockout (YKO) Consortium */

This page contains links to download the sequences of several primer sets that were constructed to amplify various regions of the yeast genome.

==Primer sets from ResGen/Invitrogen==
These primers are no longer being made or distributed by ResGen, but their sequences are available for download from SGD:

* GenePairs, a set of primers for each ORF in the genome used for amplifying entire ORFs ([http://downloads.yeastgenome.org/sequence/S288C_reference/primer_sequences/ Download])

* pORF Yeast GenePairs, a set of primers for each gene in the genome used for amplifying partial ORFs ([http://downloads.yeastgenome.org/sequence/S288C_reference/primer_sequences/ Download])

* Yeast Intergenic Region Primers ([http://downloads.yeastgenome.org/sequence/S288C_reference/primer_sequences/ Download])

==Primer sets used by the Yeast Knockout (YKO) Consortium==

* [http://yeastdeletion-sgtc.yeastgenome.org/downloads.html Primers] for making knockouts ([http://www-sequence.stanford.edu/group/yeast_deletion_project/downloads.html#orfprime Download] sequence from the consortium's website.)

* [http://yeastdeletion-sgtc.yeastgenome.org/downloads.html#strainsavail Information] on the strains made by the deletion consortium

SGD Newsletter, Summer 2022

2022-07-28T18:14:21Z

Edith: /* SGD collaborates to add new data links */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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_2022 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)
 

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.
 

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the [https://genetics-gsa.org/yeast-2022/ Yeast Genetics Meeting] is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the [https://genetics-gsa.org/yeast-2022/invited-speakers/ invited speakers] for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the YGM website.
 

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work, [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.
 

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is [https://www.weizmann.ac.il/molgen/AnalogYeast AnalogYeast], a dataset of analogs to yeast proteins in non-fungal organisms predicted by sequence similarity, which was created by the [https://mayaschuldiner.wixsite.com/schuldinerlab Schuldiner lab]. Links have been added to the Resources sections of SGD [https://yeastgenome.org/locus/S000005737/protein#resources Protein] and [https://yeastgenome.org/locus/S000005737/homology#resources Homology] pages.

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==microPublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

microPublication is part of the emerging genre of rapidly-published research communications. We are seeing a strong set of microPublications come through the database and are glad for this venue to publish brief, novel findings, negative and/or reproduced results, and results which may lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and 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.

To see recent micropublications in yeast, visit the [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Gene Ontology Consortium Fall Meeting
**Virtual plus in person
**California Institute of Technology, Pasadena
**October 11 – 13, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

SGD Newsletter, Summer 2022

2022-07-28T17:28:56Z

Edith: /* Congratulations to Jeremy Thorner */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)
 

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.
 

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].
 

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.
 

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is [https://www.weizmann.ac.il/molgen/AnalogYeast AnalogYeast], a dataset of analogs to yeast proteins in non-fungal organisms predicted by sequence similarity, that was created by the Schuldiner lab. Links have been added to the Resources sections of SGD Protein and Homology pages.

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:28:33Z

Edith: /* SGD collaborates to add new data links */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)
 

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.
 

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].
 

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is [https://www.weizmann.ac.il/molgen/AnalogYeast AnalogYeast], a dataset of analogs to yeast proteins in non-fungal organisms predicted by sequence similarity, that was created by the Schuldiner lab. Links have been added to the Resources sections of SGD Protein and Homology pages.

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:12:40Z

Edith: /* Upcoming Yeast Genetics Meeting */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)
 

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.
 

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].
 

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is the [Shuldiner analog yeast] - can anyone flesh this out?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:12:11Z

Edith: /* Performance updates at SGD */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)
 

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.
 

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is the [Shuldiner analog yeast] - can anyone flesh this out?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:12:00Z

Edith: /* Performance updates at SGD */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)
 

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.
 

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is the [Shuldiner analog yeast] - can anyone flesh this out?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:10:27Z

Edith: /* Performance updates at SGD */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)
 

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.
 

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is the [Shuldiner analog yeast] - can anyone flesh this out?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:10:16Z

Edith: /* Performance updates at SGD */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)
 

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.
 

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is the [Shuldiner analog yeast] - can anyone flesh this out?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:09:56Z

Edith: /* Research Spotlights are back */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.
 

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is the [Shuldiner analog yeast] - can anyone flesh this out?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:09:40Z

Edith: /* Research Spotlights are back */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.
 

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is the [Shuldiner analog yeast] - can anyone flesh this out?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:06:53Z

Edith: /* Performance updates at SGD */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is the [Shuldiner analog yeast] - can anyone flesh this out?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:06:24Z

Edith: /* Performance updates at SGD */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)
 
 

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is the [Shuldiner analog yeast] - can anyone flesh this out?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

SGD Newsletter, Summer 2022

2022-07-28T17:06:07Z

Edith: /* Performance updates at SGD */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Summer 2022 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Performance updates at SGD==
[[Image:sgd_maintenanceguy.jpeg |thumb|left|upright=.5]]

Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)
 

==Research Spotlights are back==
[[Image:ResearchSpotlight_2022-07-26_at_9.32.28_AM.png|link=https://www.yeastgenome.org/ |thumb|left|upright=.5]]

SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.

==Upcoming Yeast Genetics Meeting==
[[image:YGM2022.png | link=https://genetics-gsa.org/yeast-2022/|thumb|left|upright=.9]]

We may have forgotten how to talk to other people ''in person'', but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the [https://genetics-gsa.org/yeast-2022 YGM website].

==Congratulations to Jeremy Thorner==
[[image:JeremyThorner.png |thumb|left|upright=.3]]

While on the subject of congratulations, a past recipient of the YGM Lifetime Achievement Award and a longtime friend and advisor of SGD has been further honored with a full issue of the journal ''Biomolecules'' dedicated to his work. Special Issue: [https://www.mdpi.com/journal/biomolecules/special_issues/Jeremy_Thorner Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner]

We are grateful to have Dr. Thorner’s work integrated into the SGD database and into our wider community’s ongoing mission to understand yeast.

==SGD collaborates to add new data links==
[[Image:AlphaFoldPrediction.png|thumb|right|upright=.4]]

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the [http://www.science.org/doi/10.1126/science.abm4805 AlphaFold] predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is the [Shuldiner analog yeast] - can anyone flesh this out?

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

==Micropublications enter log phase==
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

We are seeing a strong set of micropublications come through the database and are glad for this venue to publish small but useful findings. Consider [https://www.micropublication.org MicroPubublications] when you have a result that will be of value to others but doesn't belong with a larger story.

For a [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= list of micropubs in SGD].

==Alliance of Genome Resources - Release 5.2==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 5.2] this past May.

*The Alliance is now using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources.

*Much of this release focused on backend enhancements, particularly the continued efforts to develop software to provide a single interface for Alliance curators from all the Model Organism Databases (MODs). This single interface will reduce software development redundancies and free up resources for new features. Future releases will continue to add more modules for entering different data types.

==Upcoming Conferences and Courses==
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 Yeast Genetics & Genomics] - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast ''Saccharomyces cerevisiae''
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022
*Fungal Pathogen Genomics - Hands-on training in web-based data-mining resources for fungal genomes
**Wellcome Genome Campus, Hinxton, Cambridge, UK
**May 07 to May 12, 2023

==Gene Ontology Consortium Fall 2022==

[Suzi says it won't be a user meeting so we could probably wait until the Fall newsletter to report out on what happened]

[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14??, SGD biocurators will attend the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but are not limited to:
*[https

Positions in yeast labs

2022-05-23T20:13:04Z

Edith: /* Post-doctoral position in S. cerevisiae research (posted 13 December 2021) */

=='''Post-doctoral position in ''S. cerevisiae'' research (posted 23 May 2022)'''==
Truman lab, University of North Carolina at Charlotte, USA

'''Description''': The Truman laboratory in the Department of Biological Sciences at UNC Charlotte employs a range of molecular technologies including mass spectrometry, CRISPR-genome engineering and high-throughput screening to study the role of post-translational modifications on Hsp70 (see: http://www.trumanlab.org). We are seeking a highly motivated postdoctoral researcher with
experience working with budding yeast. 
NIH Funding is available for several years, with the expectation that the candidate will work with Dr. Truman to apply for fellowships during this time. Ideal candidates will have graduated less than one year from their start date in the Truman lab. To apply please email Dr. Truman at atruman1@uncc.edu. Please include a cover letter, CV and any relevant publications. 

'''About the Department of Biological Sciences''': The Department of Biological Sciences (https://biology.charlotte.edu/) has set as its mission to advance the frontiers of knowledge through innovation and research in the biological sciences; to facilitate development of scientists in the guidance of our bachelors, masters and doctoral Biology students, and in the training of post-doctoral fellows; to contribute to local, national, and international scientific communities through collaborations and service activities that promote education and dissemination of information; to contribute to the community by collaborating with public, nonprofit, private, and industry partners in the Charlotte metropolitan area and the State of North Carolina.
 The collaborative research environment at the UNC Charlotte offers an excellent opportunity for career development. The UNC Charlotte offers a complete benefits package and competitive salary. The Charlotte region provides wonderful environment to work and live.

'''Ideal Qualifications''':
*Ph. D in biochemistry, molecular biology, cancer biology or related field.
*Experience with budding yeast including gene deletion, transformation etc.
*Experience with general molecular techniques such as Western Blotting, DNA cloning, coimmunoprecipitation.

=='''Post-doctoral position in ''S. cerevisiae'' research (posted 13 December 2021)'''==
De Wulf lab, University of Trento, Italy

'''Description''': The De Wulf lab at the Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy, is looking for an outstanding, highly motivated post-doctoral scientist to study the biological activity of oncogenic kinetochore kinase Rio1. The research will aim to understand how this kinase regulates the chromatin at centromeres and pericentromeres to ensure correct levels of centromeric RNAs, required for faithful kinetochore recruitment. Candidates with expertise in yeast genetics, cell and molecular biology are encouraged to apply. Experience with live-cell fluorescence imaging is greatly appreciated. For publications related to the topic: Bock LJ et al (2012) Nature Cell Biology, Iacovella MG et al (2015) Nature Communications, Iacovella MG et al (2018) Nucleic Acids Research, Berto G et al (2019) Current Genetics. More details of currently submitted work and of the project itself will be provided upon request.

'''Position overview''': The candidate should hold a recent PhD degree and a good publication record (at least one first-author publication in a reputable peer-reviewed journal). S/he must be motivated to excel in science, be curious, open-minded, and pro-active.

The lab is located in the city of Trento (150K inhabitants), near lakes and mountains, and lies close to Bolzano, Verona, and Venice.

Trento University is top 3-ranked in Italy, and CIBIO is the nr. 1 department of biology in Italy. State-of-the art equipment and facilities are available in our lab and in the department. Please visit our website for more information on our group, research interests and publications: http://www.cibio.unitn.it/510/chromosome-segregation-biology

'''How to apply''': Please send a motivation letter, CV with publications, and the names and emails of 2-3 referees to Peter De Wulf (peter.dewulf@unitn.it). The University of Trento offers at first a 1-year contract, which can be renewed for up to 5 years. The salary is according to University of Trento pay scale.

Positions in yeast labs

2022-05-23T20:12:53Z

Edith: /* Post-doctoral position in S. cerevisiae research (posted 23 May 2022) */

=='''Post-doctoral position in ''S. cerevisiae'' research (posted 23 May 2022)'''==
Truman lab, University of North Carolina at Charlotte, USA

'''Description''': The Truman laboratory in the Department of Biological Sciences at UNC Charlotte employs a range of molecular technologies including mass spectrometry, CRISPR-genome engineering and high-throughput screening to study the role of post-translational modifications on Hsp70 (see: http://www.trumanlab.org). We are seeking a highly motivated postdoctoral researcher with
experience working with budding yeast. 
NIH Funding is available for several years, with the expectation that the candidate will work with Dr. Truman to apply for fellowships during this time. Ideal candidates will have graduated less than one year from their start date in the Truman lab. To apply please email Dr. Truman at atruman1@uncc.edu. Please include a cover letter, CV and any relevant publications. 

'''About the Department of Biological Sciences''': The Department of Biological Sciences (https://biology.charlotte.edu/) has set as its mission to advance the frontiers of knowledge through innovation and research in the biological sciences; to facilitate development of scientists in the guidance of our bachelors, masters and doctoral Biology students, and in the training of post-doctoral fellows; to contribute to local, national, and international scientific communities through collaborations and service activities that promote education and dissemination of information; to contribute to the community by collaborating with public, nonprofit, private, and industry partners in the Charlotte metropolitan area and the State of North Carolina.
 The collaborative research environment at the UNC Charlotte offers an excellent opportunity for career development. The UNC Charlotte offers a complete benefits package and competitive salary. The Charlotte region provides wonderful environment to work and live.

'''Ideal Qualifications''':
*Ph. D in biochemistry, molecular biology, cancer biology or related field.
*Experience with budding yeast including gene deletion, transformation etc.
*Experience with general molecular techniques such as Western Blotting, DNA cloning, coimmunoprecipitation.

=='''Post-doctoral position in S. cerevisiae research (posted 13 December 2021)'''==
De Wulf lab, University of Trento, Italy

'''Description''': The De Wulf lab at the Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy, is looking for an outstanding, highly motivated post-doctoral scientist to study the biological activity of oncogenic kinetochore kinase Rio1. The research will aim to understand how this kinase regulates the chromatin at centromeres and pericentromeres to ensure correct levels of centromeric RNAs, required for faithful kinetochore recruitment. Candidates with expertise in yeast genetics, cell and molecular biology are encouraged to apply. Experience with live-cell fluorescence imaging is greatly appreciated. For publications related to the topic: Bock LJ et al (2012) Nature Cell Biology, Iacovella MG et al (2015) Nature Communications, Iacovella MG et al (2018) Nucleic Acids Research, Berto G et al (2019) Current Genetics. More details of currently submitted work and of the project itself will be provided upon request.

'''Position overview''': The candidate should hold a recent PhD degree and a good publication record (at least one first-author publication in a reputable peer-reviewed journal). S/he must be motivated to excel in science, be curious, open-minded, and pro-active.

The lab is located in the city of Trento (150K inhabitants), near lakes and mountains, and lies close to Bolzano, Verona, and Venice.

Trento University is top 3-ranked in Italy, and CIBIO is the nr. 1 department of biology in Italy. State-of-the art equipment and facilities are available in our lab and in the department. Please visit our website for more information on our group, research interests and publications: http://www.cibio.unitn.it/510/chromosome-segregation-biology

'''How to apply''': Please send a motivation letter, CV with publications, and the names and emails of 2-3 referees to Peter De Wulf (peter.dewulf@unitn.it). The University of Trento offers at first a 1-year contract, which can be renewed for up to 5 years. The salary is according to University of Trento pay scale.

Positions in yeast labs

2022-05-23T19:50:24Z

Edith: /* Post-doctoral position in S. cerevisiae research (posted 23 March 2022) */

=='''Post-doctoral position in S. cerevisiae research (posted 23 May 2022)'''==
Truman lab, University of North Carolina at Charlotte, USA

'''Description''': The Truman laboratory in the Department of Biological Sciences at UNC Charlotte employs a range of molecular technologies including mass spectrometry, CRISPR-genome engineering and high-throughput screening to study the role of post-translational modifications on Hsp70 (see: http://www.trumanlab.org). We are seeking a highly motivated postdoctoral researcher with
experience working with budding yeast. 
NIH Funding is available for several years, with the expectation that the candidate will work with Dr. Truman to apply for fellowships during this time. Ideal candidates will have graduated less than one year from their start date in the Truman lab. To apply please email Dr. Truman at atruman1@uncc.edu. Please include a cover letter, CV and any relevant publications. 

'''About the Department of Biological Sciences''': The Department of Biological Sciences (https://biology.charlotte.edu/) has set as its mission to advance the frontiers of knowledge through innovation and research in the biological sciences; to facilitate development of scientists in the guidance of our bachelors, masters and doctoral Biology students, and in the training of post-doctoral fellows; to contribute to local, national, and international scientific communities through collaborations and service activities that promote education and dissemination of information; to contribute to the community by collaborating with public, nonprofit, private, and industry partners in the Charlotte metropolitan area and the State of North Carolina.
 The collaborative research environment at the UNC Charlotte offers an excellent opportunity for career development. The UNC Charlotte offers a complete benefits package and competitive salary. The Charlotte region provides wonderful environment to work and live.

'''Ideal Qualifications''':
*Ph. D in biochemistry, molecular biology, cancer biology or related field.
*Experience with budding yeast including gene deletion, transformation etc.
*Experience with general molecular techniques such as Western Blotting, DNA cloning, coimmunoprecipitation.

=='''Post-doctoral position in S. cerevisiae research (posted 13 December 2021)'''==
De Wulf lab, University of Trento, Italy

'''Description''': The De Wulf lab at the Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy, is looking for an outstanding, highly motivated post-doctoral scientist to study the biological activity of oncogenic kinetochore kinase Rio1. The research will aim to understand how this kinase regulates the chromatin at centromeres and pericentromeres to ensure correct levels of centromeric RNAs, required for faithful kinetochore recruitment. Candidates with expertise in yeast genetics, cell and molecular biology are encouraged to apply. Experience with live-cell fluorescence imaging is greatly appreciated. For publications related to the topic: Bock LJ et al (2012) Nature Cell Biology, Iacovella MG et al (2015) Nature Communications, Iacovella MG et al (2018) Nucleic Acids Research, Berto G et al (2019) Current Genetics. More details of currently submitted work and of the project itself will be provided upon request.

'''Position overview''': The candidate should hold a recent PhD degree and a good publication record (at least one first-author publication in a reputable peer-reviewed journal). S/he must be motivated to excel in science, be curious, open-minded, and pro-active.

The lab is located in the city of Trento (150K inhabitants), near lakes and mountains, and lies close to Bolzano, Verona, and Venice.

Trento University is top 3-ranked in Italy, and CIBIO is the nr. 1 department of biology in Italy. State-of-the art equipment and facilities are available in our lab and in the department. Please visit our website for more information on our group, research interests and publications: http://www.cibio.unitn.it/510/chromosome-segregation-biology

'''How to apply''': Please send a motivation letter, CV with publications, and the names and emails of 2-3 referees to Peter De Wulf (peter.dewulf@unitn.it). The University of Trento offers at first a 1-year contract, which can be renewed for up to 5 years. The salary is according to University of Trento pay scale.

Positions in yeast labs

2022-05-23T19:39:15Z

Edith: /* Post-doctoral position in S. cerevisiae research (posted 13 December 2021) */

=='''Post-doctoral position in S. cerevisiae research (posted 23 March 2022)'''==
Truman lab, University of North Carolina at Charlotte, USA

'''Description''': The Truman laboratory in the Department of Biological Sciences at UNC Charlotte employs a range of molecular technologies including mass spectrometry, CRISPR-genome engineering and high-throughput screening to study the role of post-translational modifications on Hsp70 (see: http://www.trumanlab.org). We are seeking a highly motivated postdoctoral researcher with
experience working with budding yeast. 
NIH Funding is available for several years, with the expectation that the candidate will work with Dr. Truman to apply for fellowships during this time. Ideal candidates will have graduated less than one year from their start date in the Truman lab. To apply please email Dr. Truman at atruman1@uncc.edu. Please include a cover letter, CV and any relevant publications. 

'''About the Department of Biological Sciences''': The Department of Biological Sciences (https://biology.charlotte.edu/) has set as its mission to advance the frontiers of knowledge through innovation and research in the biological sciences; to facilitate development of scientists in the guidance of our bachelors, masters and doctoral Biology students, and in the training of post-doctoral fellows; to contribute to local, national, and international scientific communities through collaborations and service activities that promote education and dissemination of information; to contribute to the community by collaborating with public, nonprofit, private, and industry partners in the Charlotte metropolitan area and the State of North Carolina.
 The collaborative research environment at the UNC Charlotte offers an excellent opportunity for career development. The UNC Charlotte offers a complete benefits package and competitive salary. The Charlotte region provides wonderful environment to work and live.

'''Ideal Qualifications''':
*Ph. D in biochemistry, molecular biology, cancer biology or related field.
*Experience with budding yeast including gene deletion, transformation etc.
*Experience with general molecular techniques such as Western Blotting, DNA cloning, coimmunoprecipitation.

=='''Post-doctoral position in S. cerevisiae research (posted 13 December 2021)'''==
De Wulf lab, University of Trento, Italy

'''Description''': The De Wulf lab at the Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy, is looking for an outstanding, highly motivated post-doctoral scientist to study the biological activity of oncogenic kinetochore kinase Rio1. The research will aim to understand how this kinase regulates the chromatin at centromeres and pericentromeres to ensure correct levels of centromeric RNAs, required for faithful kinetochore recruitment. Candidates with expertise in yeast genetics, cell and molecular biology are encouraged to apply. Experience with live-cell fluorescence imaging is greatly appreciated. For publications related to the topic: Bock LJ et al (2012) Nature Cell Biology, Iacovella MG et al (2015) Nature Communications, Iacovella MG et al (2018) Nucleic Acids Research, Berto G et al (2019) Current Genetics. More details of currently submitted work and of the project itself will be provided upon request.

'''Position overview''': The candidate should hold a recent PhD degree and a good publication record (at least one first-author publication in a reputable peer-reviewed journal). S/he must be motivated to excel in science, be curious, open-minded, and pro-active.

The lab is located in the city of Trento (150K inhabitants), near lakes and mountains, and lies close to Bolzano, Verona, and Venice.

Trento University is top 3-ranked in Italy, and CIBIO is the nr. 1 department of biology in Italy. State-of-the art equipment and facilities are available in our lab and in the department. Please visit our website for more information on our group, research interests and publications: http://www.cibio.unitn.it/510/chromosome-segregation-biology

'''How to apply''': Please send a motivation letter, CV with publications, and the names and emails of 2-3 referees to Peter De Wulf (peter.dewulf@unitn.it). The University of Trento offers at first a 1-year contract, which can be renewed for up to 5 years. The salary is according to University of Trento pay scale.

SGD Newsletter, Fall 2021

2021-12-13T21:28:55Z

Edith: /* DIOPT Orthologs and new queries in YeastMine */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Fall 2021 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,_Fall_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Protein Complex Page Updates==
[[File:Complex3.png|thumb|left|upright=1.3|link=https://www.yeastgenome.org/complex/CPX-1275]]

SGD has made recent updates to our protein complex pages to improve clarity and ease of use. The new pages for each complex will have the same format as gene pages, with tabs across the top for each category of information, including a [https://www.yeastgenome.org/complex/S000218162/ Summary] page, a [https://www.yeastgenome.org/complex/S000218162/go Gene Ontology] page, and a [https://www.qa.yeastgenome.org/complex/S000218162/literature Literature] page. Just as we do for all of your favorite genes, Gene Ontology and Literature curation for complexes will be ongoing.

If you have any questions or feedback about the updates to our complex pages, please do not hesitate to [mailto:sgd-helpdesk@lists.stanford.edu contact us] at any time.

==Nomenclature Updates==

===Legacy gene names===
SGD has long been the keeper of the official ''Saccharomyces cerevisiae'' gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years.

The accepted format for gene names in ''S. cerevisiae'' comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the "Name Description" in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example "ADE" for "ADEnine biosynthesis" or "CDC" for "Cell Division Cycle". Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an [https://www.yeastgenome.org/search?category=locus&feature_type=ORF&page=0&q= ORF], a [https://www.yeastgenome.org/search?category=locus&feature_type=tRNA%20gene&page=0&q= tRNA], another type of [https://www.yeastgenome.org/search?q=YNC*&category=locus non-coding RNA], an [https://www.yeastgenome.org/search?category=locus&feature_type=ARS&page=0&q=ars ARS], or a [https://www.yeastgenome.org/search?category=locus&feature_type=Unmapped%20Genetic%20Loci&page=0&q= genetic locus]. Some ''S. cerevisiae'' gene names that pre-date the current nomenclature standards do not conform to this format, such as [https://www.yeastgenome.org/locus/S000001653 MRLP38], [https://www.yeastgenome.org/locus/S000006141 RPL1A], and [https://www.yeastgenome.org/locus/S000001398 OM45].

A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.

{| border="1" class="wikitable"
|-
!|ORF!!Old gene name!!New gene name
|-
|[http://www.yeastgenome.org/locus/YGL234W YGL234W]
|ADE5,7
|ADE57
|-
|[http://www.yeastgenome.org/locus/YER069W YER069W]
|ARG5,6
|ARG56
|-
|[http://www.yeastgenome.org/locus/YBR298C YBR298C]
|DUR1,2
|DUR12
|-
|[http://www.yeastgenome.org/locus/YIL154C YIL154C]
|IMP2'
|IMP21
|-
|}

===New Systematic Nomenclature for yeast genes not in the reference genome===
For many years, a widely adopted systematic nomenclature has existed for yeast protein-coding genes, or ORFs, as many yeast researchers call them. Readers of the [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Spring_2021 last SGD newsletter] will recall that, earlier this year, SGD adopted a new systematic nomenclature for the [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs].

We have just put into place a new systematic nomenclature for ''S. cerevisiae'' genes that are not found in the reference genome of strain S288C ([https://www.yeastgenome.org/search?q=YSC0&category=locus "non-reference" genes]). This new systematic nomenclature is similar to, but distinct from, that used for ORFs and that used for ncRNAs. Non-reference genes are designated by a symbol consisting of three uppercase letters and a four-digit number, as follows: Y for "Yeast", SC for "Saccharomyces cerevisiae", and a four-digit number corresponding to the sequential order in which the gene was added to SGD. We currently have 55 of these genes in SGD, some of which are old favorites like [https://www.yeastgenome.org/locus/S000029681 MAL21/YSC0004] and [https://www.yeastgenome.org/locus/S000124955 MATA/YSC0046], while others are more recent additions like [https://www.yeastgenome.org/locus/S000133140 XDH1/YSC0051]. Going forward, as evidence is published pointing to other ''S. cerevisiae'' genes not present in the S288C reference genome, they will be added to the annotation using the next sequential number available. We already have 15 more of these YSC0000 names reserved by researchers and awaiting publication.

If you have some non-reference genes for which these names would be appropriate, please [mailto:sgd-helpdesk@lists.stanford.edu let us know]!

==New links to AlphaFold 3D Predicted Protein Structure Database==

Would you like to see the shape of your protein?
[[File:Hog1_structure.png|thumb|left|upright=.5|link=https://alphafold.ebi.ac.uk/entry/P32485]]

SGD now contains links to [https://www.alphafold.ebi.ac.uk/ AlphaFold] in the Resources sections of the [https://www.yeastgenome.org/locus/S000004103#resources/ Summary], [https://www.yeastgenome.org/locus/hog1/protein#resources/ Protein], and [https://www.yeastgenome.org/locus/S000004103/homology#resources/ Homology] pages for every gene.

*The links through SGD give quick access to [https://www.embl.org EMBL]’s [https://www.ebi.ac.uk/ European Bioinformatics Institute] (EMBL-EBI), which offers a new, highly accurate tool for predicting protein structure with speed and clarity.

*Given a peptide sequence for an uncharacterized protein, AlphaFold will model predicted domains and provide relative confidence levels for each portion of the prediction.

*The predicted domains can then be compared to known protein structures (using a tool such as [https://www.ebi.ac.uk/msd-srv/ssm/ PDBeFold]) to seek matches to characterized protein families.

*Whether or not a family is identified, the comparison will yield clues to protein function to help design the next experiments.

==DIOPT Orthologs and new queries in YeastMine ==

We recently replaced HomoloGene, Ensembl, TreeFam and Panther homology datasets in YeastMine with homology data from [https://www.flyrnai.org/diopt DIOPT (DRSC integrative ortholog prediction tool)]. DIOPT integrates orthology predictions from multiple sources, including HomoloGene, Ensembl, TreeFam, and Panther. Using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Homologs&scope=all Gene->Non-fungal and S. cerevisiae Homologs] pre-generated query, you can look for DIOPT homologs for a single or multiple yeast genes. The results table provides identifiers and standard names for the yeast and homologous genes, as well as organism and predictive score information. As with other YeastMine templates, results can be saved as lists and analyzed further. 

Pre-generated [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_OMIM_Disease&scope=all queries] for human homolog(s) of your favorite yeast gene and their corresponding disease associations remain largely unchanged. You can begin with your favorite human gene or disease keyword and retrieve the yeast counterparts of the relevant gene(s). As an example, you can search for the ''S. cerevisiae'' homologs of all human genes associated with disorders that contain the keyword “diabetes” ([https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Disease_Human_Yeast&scope=all view search]). The results table provides identifiers and standard names for the yeast and human genes, OMIM gene and disease identifiers and name, as well as predictive algorithm sources and scores.

==Alliance of Genome Resources - latest release==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 4.1] this past August. Notable improvements and new features include:
*Human and model organism high throughput (HTP) variant data
**Human variants are imported from Ensembl
**Model organism HTP variants are submitted by Alliance members (FlyBase, RGD, SGD, Wormbase) or imported from EVA (MGI and ZFIN).
**Added HTP variants to the Alleles and Variants table on gene pages (e.g. rat Lepr Gene page) and to the table on the Alleles and Variants Details page (e.g. rat Lepr Alleles and Variants Details.
**Created a report page for Human and model organism HTP variants (e.g. human variant rs1041354454).
**Expanded Allele Category in search to “Allele/Variant” and added a search for HTP variants.
*On Gene Pages, a new Pathways widget displays via tabs:
**Reactome models of pathways for human gene products as well as inferred pathways for model organism genes based on orthology to human genes.
**Reactome reactions for gene products (e.g. human TP53 Gene page)
**Gene Ontology Causal Activity Models (GO-CAMs). These provide a framework to represent a biological system by linking together multiple GO annotations. PMID:31548717 (e.g. worm nsy-1 Gene page).
*Experimental conditions are include for Disease and Phenotype data in tables on Gene, Allele, and Disease pages (e.g. zebrafish scn1lab Gene page).
*AllianceMine added Orthologs, and Allele and Variants (low throughput) data types to this release. You can now query for these data types via pre-made template queries.
*The Alliance Community Forum is released. The Forum permits discussions across six model organism communities—flies, mice, yeast, rats, worms, and zebrafish. More details will follow.

==Upcoming Conferences and Courses==
*[https://genetics-gsa.org/fungal/ Fungal Genetics] - the premier meeting for the international community of fungal geneticists
**Asilomar Conference Grounds, Pacific Grove, California (and Online)
**March 15 - 20, 2022
*[https://issy36.com 36th International Specialised Symposium on Yeasts (ISSY36)] - Yeast Sea to Sky - Yeast in the Genomics Era
**University of British Columbia, Vancouver
**July 12 - 16, 2022
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 CSHL Yeast Genetics & Genomics] - modern, intensive laboratory course that teaches students full repertoire of genetic and genomic approaches
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022

==Gene Ontology Consortium Fall 2021 Meeting==
[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14, SGD biocurators attended the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but were not limited to:
*[https://www.ncbi.nlm.nih.gov/research/litsuggest/ LitSuggest] - web-based system for biomedical literature recommendation and curation
*[https://evidenceontology.org ECO], Evidence and Conclusions Ontology - terms used to describe types of evidence and assertion methods
*PAINT, Phylogenetic Annotation and INference Tool from [http://www.pantherdb.org/about.jsp PANTHER] - orthology between reference genome genes and human disease genes

==Happy Holidays from SGD!==

[[File:SnowShmoo.png|thumb|left|upright=.25]]

We know that 2021 has been another challenging year for everyone. Our thoughts go out to all those who have been impacted by recent events. We wish you and your family, friends, and lab mates the best during the upcoming holidays.

'''Stanford University will be closed for two weeks starting December 20, and will reopen on January 3rd, 2022'''. 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.

Positions in yeast labs

2021-12-13T16:56:33Z

Edith:

=='''Post-doctoral position in S. cerevisiae research (posted 13 December 2021)'''==
De Wulf lab, University of Trento, Italy

'''Description''': The De Wulf lab at the Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy, is looking for an outstanding, highly motivated post-doctoral scientist to study the biological activity of oncogenic kinetochore kinase Rio1. The research will aim to understand how this kinase regulates the chromatin at centromeres and pericentromeres to ensure correct levels of centromeric RNAs, required for faithful kinetochore recruitment. Candidates with expertise in yeast genetics, cell and molecular biology are encouraged to apply. Experience with live-cell fluorescence imaging is greatly appreciated. For publications related to the topic: Bock LJ et al (2012) Nature Cell Biology, Iacovella MG et al (2015) Nature Communications, Iacovella MG et al (2018) Nucleic Acids Research, Berto G et al (2019) Current Genetics. More details of currently submitted work and of the project itself will be provided upon request.

'''Position overview''': The candidate should hold a recent PhD degree and a good publication record (at least one first-author publication in a reputable peer-reviewed journal). S/he must be motivated to excel in science, be curious, open-minded, and pro-active.

The lab is located in the city of Trento (150K inhabitants), near lakes and mountains, and lies close to Bolzano, Verona, and Venice.

Trento University is top 3-ranked in Italy, and CIBIO is the nr. 1 department of biology in Italy. State-of-the art equipment and facilities are available in our lab and in the department. Please visit our website for more information on our group, research interests and publications: http://www.cibio.unitn.it/510/chromosome-segregation-biology

'''How to apply''': Please send a motivation letter, CV with publications, and the names and emails of 2-3 referees to Peter De Wulf (peter.dewulf@unitn.it). The University of Trento offers at first a 1-year contract, which can be renewed for up to 5 years. The salary is according to University of Trento pay scale.

SGD Newsletter, Fall 2021

2021-11-12T22:51:41Z

Edith: /* DIPOT Orthologs and new queries in YeastMine */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Fall 2021 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,_Spring_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Updated Protein Complex pages==
==Nomenclature Updates==

===Legacy gene names===
SGD has long been the keeper of the official ''Saccharomyces cerevisiae'' gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years.

The accepted format for gene names in ''S. cerevisiae'' comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the "Name Description" in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example "ADE" for "ADEnine biosynthesis" or "CDC" for "Cell Division Cycle". Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an [https://www.yeastgenome.org/search?category=locus&feature_type=ORF&page=0&q= ORF], a [https://www.yeastgenome.org/search?category=locus&feature_type=tRNA%20gene&page=0&q= tRNA], another type of [https://www.yeastgenome.org/search?q=YNC*&category=locus non-coding RNA], an [https://www.yeastgenome.org/search?category=locus&feature_type=ARS&page=0&q=ars ARS], or a [https://www.yeastgenome.org/search?category=locus&feature_type=Unmapped%20Genetic%20Loci&page=0&q= genetic locus]. Some ''S. cerevisiae'' gene names that pre-date the current nomenclature standards do not conform to this format, such as [https://www.yeastgenome.org/locus/S000001653 MRLP38], [https://www.yeastgenome.org/locus/S000006141 RPL1A], and [https://www.yeastgenome.org/locus/S000001398 OM45].

A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.

{| border="1" class="wikitable"
|-
!|ORF!!Old gene name!!New gene name
|-
|[http://www.yeastgenome.org/locus/YGL234W YGL234W]
|ADE5,7
|ADE57
|-
|[http://www.yeastgenome.org/locus/YER069W YER069W]
|ARG5,6
|ARG56
|-
|[http://www.yeastgenome.org/locus/YBR298C YBR298C]
|DUR1,2
|DUR12
|-
|[http://www.yeastgenome.org/locus/YIL154C YIL154C]
|IMP2'
|IMP21
|-
|}

===New Systematic Nomenclature for yeast genes not in the reference genome===
For many years, a widely adopted systematic nomenclature has existed for yeast protein-coding genes, or ORFs, as many yeast researchers call them. Readers of the [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Spring_2021 last SGD newsletter] will recall that, earlier this year, SGD adopted a new systematic nomenclature for the [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs].

We have just put into place a new systematic nomenclature for ''S. cerevisiae'' genes that are not found in the reference genome of strain S288C ([https://www.yeastgenome.org/search?q=YSC0&category=locus "non-reference" genes]). This new systematic nomenclature is similar to, but distinct from, that used for ORFs and that used for ncRNAs. Non-reference genes are designated by a symbol consisting of three uppercase letters and a four-digit number, as follows: Y for "Yeast", SC for "Saccharomyces cerevisiae", and a four-digit number corresponding to the sequential order in which the gene was added to SGD. We currently have 55 of these genes in SGD, some of which are old favorites like [https://www.yeastgenome.org/locus/S000029681 MAL21/YSC0004] and [https://www.yeastgenome.org/locus/S000124955 MATA/YSC0046], while others are more recent additions like [https://www.yeastgenome.org/locus/S000133140 XDH1/YSC0051]. Going forward, as evidence is published pointing to other ''S. cerevisiae'' genes not present in the S288C reference genome, they will be added to the annotation using the next sequential number available. We already have 15 more of these YSC0000 names reserved by researchers and awaiting publication.

If you have some non-reference genes for which these names would be appropriate, please [mailto:sgd-helpdesk@lists.stanford.edu let us know]!

==New links to AlphaFold 3D Predicted Protein Structure Database==

Would you like to see the shape of your protein?
[[File:Hog1_structure.png|thumb|left|upright=.5|link=https://alphafold.ebi.ac.uk/entry/P32485]]

SGD now contains links to [https://www.alphafold.ebi.ac.uk/ AlphaFold] in the Resources sections of the [https://www.yeastgenome.org/locus/S000004103#resources/ Summary], [https://www.yeastgenome.org/locus/hog1/protein#resources/ Protein], and [https://www.yeastgenome.org/locus/S000004103/homology#resources/ Homology] pages for every gene.

*The links through SGD give quick access to [https://www.embl.org EMBL]’s [https://www.ebi.ac.uk/ European Bioinformatics Institute] (EMBL-EBI) offers a new, highly accurate tool for predicting protein structure with speed and clarity.

*Given a peptide sequence for an uncharacterized protein, AlphaFold will model predicted domains and provide relative confidence levels for each portion of the prediction.

*The predicted domains can then be compared to known protein structures (using a tool such as [https://www.ebi.ac.uk/msd-srv/ssm/ PDBeFold]) to seek matches to characterized protein families.

*Whether or not a family is identified, the comparison will yield clues to protein function to help design the next experiments.

==DIPOT Orthologs and new queries in YeastMine ==

We recently replaced HomoloGene, Ensembl, TreeFam and Panther homology datasets in YeastMine with homology data from [https://www.flyrnai.org/diopt DIOPT (DRSC integrative ortholog prediction tool)]. DIOPT integrates orthology predictions from multiple sources, including HomoloGene, Ensembl, TreeFam, and Panther. Using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Homologs&scope=all Gene->Non-fungal and S. cerevisiae Homologs] pre-generated query, you can look for DIOPT homologs for a single or multiple yeast genes. The results table provides identifiers and standard names for the yeast and homologous genes, as well as organism and predictive score information. As with other YeastMine templates, results can be saved as lists and analyzed further. 

Pre-generated [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_OMIM_Disease&scope=all queries] for human homolog(s) of your favorite yeast gene and their corresponding disease associations remain largely unchanged. You can begin with your favorite human gene or disease keyword and retrieve the yeast counterparts of the relevant gene(s). As an example, you can search for the ''S. cerevisiae'' homologs of all human genes associated with disorders that contain the keyword “diabetes” ([http://yeastmine.yeastgenome.org/yeastmine/template.doname=Disease_Human_Yeast&scope=global view search]). The results table provides identifiers and standard names for the yeast and human genes, OMIM gene and disease identifiers and name, as well as predictive algorithm sources and scores.

==Alliance of Genome Resources - latest release==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 4.1] this past August. Notable improvements and new features include:
*Human and model organism high throughput (HTP) variant data
**Human variants are imported from Ensembl
**Model organism HTP variants are submitted by Alliance members (FlyBase, RGD, SGD, Wormbase) or imported from EVA (MGI and ZFIN).
**Added HTP variants to the Alleles and Variants table on gene pages (e.g. rat Lepr Gene page) and to the table on the Alleles and Variants Details page (e.g. rat Lepr Alleles and Variants Details.
**Created a report page for Human and model organism HTP variants (e.g. human variant rs1041354454).
**Expanded Allele Category in search to “Allele/Variant” and added a search for HTP variants.
*On Gene Pages, a new Pathways widget displays via tabs:
**Reactome models of pathways for human gene products as well as inferred pathways for model organism genes based on orthology to human genes.
**Reactome reactions for gene products (e.g. human TP53 Gene page)
**Gene Ontology Causal Activity Models (GO-CAMs). These provide a framework to represent a biological system by linking together multiple GO annotations. PMID:31548717 (e.g. worm nsy-1 Gene page).
*Experimental conditions are include for Disease and Phenotype data in tables on Gene, Allele, and Disease pages (e.g. zebrafish scn1lab Gene page).
*AllianceMine added Orthologs, and Allele and Variants (low throughput) data types to this release. You can now query for these data types via pre-made template queries.
*The Alliance Community Forum is released. The Forum permits discussions across six model organism communities—flies, mice, yeast, rats, worms, and zebrafish. More details will follow.

==Upcoming Conferences and Courses==
*[https://genetics-gsa.org/fungal/ Fungal Genetics] - the premier meeting for the international community of fungal geneticists
**Asilomar Conference Grounds, Pacific Grove, California (and Online)
**March 15 - 20, 2022
*[https://issy36.com 36th International Specialised Symposium on Yeasts (ISSY36)] - Yeast Sea to Sky - Yeast in the Genomics Era
**University of British Columbia, Vancouver
**July 12 - 16, 2022
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 CSHL Yeast Genetics & Genomics] - modern, intensive laboratory course that teaches students full repertoire of genetic and genomic approaches
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022

==Gene Ontology Consortium Fall 2021 Meeting==
[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14, SGD biocurators attended the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but were not limited to:
*[https://www.ncbi.nlm.nih.gov/research/litsuggest/ LitSuggest] - web-based system for biomedical literature recommendation and curation
*[https://evidenceontology.org ECO], Evidence and Conclusions Ontology - terms used to describe types of evidence and assertion methods
*PAINT, Phylogenetic Annotation and INference Tool from [http://www.pantherdb.org/about.jsp PANTHER] - orthology between reference genome genes and human disease genes

==Happy Holidays from SGD!==

[[File:SnowShmoo.png|thumb|left|upright=.25]]

We know that 2021 has been another challenging year for everyone. Our thoughts go out to all those who have been impacted by recent events. We wish you and your family, friends, and lab mates the best during the upcoming holidays.

'''Stanford University will be closed for two weeks starting December 20, and will reopen on January 3rd, 2022'''. 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.

SGD Newsletter, Fall 2021

2021-11-12T22:50:32Z

Edith: /* DIPOT Orthologs and new queries in YeastMine */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Fall 2021 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,_Spring_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Updated Protein Complex pages==
==Nomenclature Updates==

===Legacy gene names===
SGD has long been the keeper of the official ''Saccharomyces cerevisiae'' gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years.

The accepted format for gene names in ''S. cerevisiae'' comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the "Name Description" in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example "ADE" for "ADEnine biosynthesis" or "CDC" for "Cell Division Cycle". Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an [https://www.yeastgenome.org/search?category=locus&feature_type=ORF&page=0&q= ORF], a [https://www.yeastgenome.org/search?category=locus&feature_type=tRNA%20gene&page=0&q= tRNA], another type of [https://www.yeastgenome.org/search?q=YNC*&category=locus non-coding RNA], an [https://www.yeastgenome.org/search?category=locus&feature_type=ARS&page=0&q=ars ARS], or a [https://www.yeastgenome.org/search?category=locus&feature_type=Unmapped%20Genetic%20Loci&page=0&q= genetic locus]. Some ''S. cerevisiae'' gene names that pre-date the current nomenclature standards do not conform to this format, such as [https://www.yeastgenome.org/locus/S000001653 MRLP38], [https://www.yeastgenome.org/locus/S000006141 RPL1A], and [https://www.yeastgenome.org/locus/S000001398 OM45].

A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.

{| border="1" class="wikitable"
|-
!|ORF!!Old gene name!!New gene name
|-
|[http://www.yeastgenome.org/locus/YGL234W YGL234W]
|ADE5,7
|ADE57
|-
|[http://www.yeastgenome.org/locus/YER069W YER069W]
|ARG5,6
|ARG56
|-
|[http://www.yeastgenome.org/locus/YBR298C YBR298C]
|DUR1,2
|DUR12
|-
|[http://www.yeastgenome.org/locus/YIL154C YIL154C]
|IMP2'
|IMP21
|-
|}

===New Systematic Nomenclature for yeast genes not in the reference genome===
For many years, a widely adopted systematic nomenclature has existed for yeast protein-coding genes, or ORFs, as many yeast researchers call them. Readers of the [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Spring_2021 last SGD newsletter] will recall that, earlier this year, SGD adopted a new systematic nomenclature for the [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs].

We have just put into place a new systematic nomenclature for ''S. cerevisiae'' genes that are not found in the reference genome of strain S288C ([https://www.yeastgenome.org/search?q=YSC0&category=locus "non-reference" genes]). This new systematic nomenclature is similar to, but distinct from, that used for ORFs and that used for ncRNAs. Non-reference genes are designated by a symbol consisting of three uppercase letters and a four-digit number, as follows: Y for "Yeast", SC for "Saccharomyces cerevisiae", and a four-digit number corresponding to the sequential order in which the gene was added to SGD. We currently have 55 of these genes in SGD, some of which are old favorites like [https://www.yeastgenome.org/locus/S000029681 MAL21/YSC0004] and [https://www.yeastgenome.org/locus/S000124955 MATA/YSC0046], while others are more recent additions like [https://www.yeastgenome.org/locus/S000133140 XDH1/YSC0051]. Going forward, as evidence is published pointing to other ''S. cerevisiae'' genes not present in the S288C reference genome, they will be added to the annotation using the next sequential number available. We already have 15 more of these YSC0000 names reserved by researchers and awaiting publication.

If you have some non-reference genes for which these names would be appropriate, please [mailto:sgd-helpdesk@lists.stanford.edu let us know]!

==New links to AlphaFold 3D Predicted Protein Structure Database==

Would you like to see the shape of your protein?
[[File:Hog1_structure.png|thumb|left|upright=.5|link=https://alphafold.ebi.ac.uk/entry/P32485]]

SGD now contains links to [https://www.alphafold.ebi.ac.uk/ AlphaFold] in the Resources sections of the [https://www.yeastgenome.org/locus/S000004103#resources/ Summary], [https://www.yeastgenome.org/locus/hog1/protein#resources/ Protein], and [https://www.yeastgenome.org/locus/S000004103/homology#resources/ Homology] pages for every gene.

*The links through SGD give quick access to [https://www.embl.org EMBL]’s [https://www.ebi.ac.uk/ European Bioinformatics Institute] (EMBL-EBI) offers a new, highly accurate tool for predicting protein structure with speed and clarity.

*Given a peptide sequence for an uncharacterized protein, AlphaFold will model predicted domains and provide relative confidence levels for each portion of the prediction.

*The predicted domains can then be compared to known protein structures (using a tool such as [https://www.ebi.ac.uk/msd-srv/ssm/ PDBeFold]) to seek matches to characterized protein families.

*Whether or not a family is identified, the comparison will yield clues to protein function to help design the next experiments.

==DIPOT Orthologs and new queries in YeastMine ==

We recently replaced HomoloGene, Ensembl, TreeFam and Panther homology datasets in YeastMine with homology data from [https://www.flyrnai.org/diopt DIOPT (DRSC integrative ortholog prediction tool)]. DIOPT integrates orthology predictions from multiple sources, including HomoloGene, Ensembl, TreeFam, and Panther. Using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Homologs&scope=all Gene->Non-fungal and S. cerevisiae Homologs] pregenerated query, you can look for DIOPT homologs for a single or multiple yeast genes. The results table provides identifiers and standard names for the yeast and homologous genes, as well as organism and predictive score information. As with other YeastMine templates, results can be saved as lists and analyzed further. 

Pre-generated queries for human homolog(s) of your favorite yeast gene and their corresponding disease associations
(https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_OMIM_Disease&scope=all) remain largely unchanged. You can begin with your favorite human gene or disease keyword and retrieve the yeast counterparts of the relevant gene(s). As an example, you can search for the ''S. cerevisiae'' homologs of all human genes associated with disorders that contain the keyword “diabetes” ([http://yeastmine.yeastgenome.org/yeastmine/template.doname=Disease_Human_Yeast&scope=global view search]). The results table provides identifiers and standard names for the yeast and human genes, OMIM gene and disease identifiers and name, as well as predictive algorithm sources and scores.

==Alliance of Genome Resources - latest release==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 4.1] this past August. Notable improvements and new features include:
*Human and model organism high throughput (HTP) variant data
**Human variants are imported from Ensembl
**Model organism HTP variants are submitted by Alliance members (FlyBase, RGD, SGD, Wormbase) or imported from EVA (MGI and ZFIN).
**Added HTP variants to the Alleles and Variants table on gene pages (e.g. rat Lepr Gene page) and to the table on the Alleles and Variants Details page (e.g. rat Lepr Alleles and Variants Details.
**Created a report page for Human and model organism HTP variants (e.g. human variant rs1041354454).
**Expanded Allele Category in search to “Allele/Variant” and added a search for HTP variants.
*On Gene Pages, a new Pathways widget displays via tabs:
**Reactome models of pathways for human gene products as well as inferred pathways for model organism genes based on orthology to human genes.
**Reactome reactions for gene products (e.g. human TP53 Gene page)
**Gene Ontology Causal Activity Models (GO-CAMs). These provide a framework to represent a biological system by linking together multiple GO annotations. PMID:31548717 (e.g. worm nsy-1 Gene page).
*Experimental conditions are include for Disease and Phenotype data in tables on Gene, Allele, and Disease pages (e.g. zebrafish scn1lab Gene page).
*AllianceMine added Orthologs, and Allele and Variants (low throughput) data types to this release. You can now query for these data types via pre-made template queries.
*The Alliance Community Forum is released. The Forum permits discussions across six model organism communities—flies, mice, yeast, rats, worms, and zebrafish. More details will follow.

==Upcoming Conferences and Courses==
*[https://genetics-gsa.org/fungal/ Fungal Genetics] - the premier meeting for the international community of fungal geneticists
**Asilomar Conference Grounds, Pacific Grove, California (and Online)
**March 15 - 20, 2022
*[https://issy36.com 36th International Specialised Symposium on Yeasts (ISSY36)] - Yeast Sea to Sky - Yeast in the Genomics Era
**University of British Columbia, Vancouver
**July 12 - 16, 2022
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 CSHL Yeast Genetics & Genomics] - modern, intensive laboratory course that teaches students full repertoire of genetic and genomic approaches
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022

==Gene Ontology Consortium Fall 2021 Meeting==
[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14, SGD biocurators attended the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but were not limited to:
*[https://www.ncbi.nlm.nih.gov/research/litsuggest/ LitSuggest] - web-based system for biomedical literature recommendation and curation
*[https://evidenceontology.org ECO], Evidence and Conclusions Ontology - terms used to describe types of evidence and assertion methods
*PAINT, Phylogenetic Annotation and INference Tool from [http://www.pantherdb.org/about.jsp PANTHER] - orthology between reference genome genes and human disease genes

==Happy Holidays from SGD!==

[[File:SnowShmoo.png|thumb|left|upright=.25]]

We know that 2021 has been another challenging year for everyone. Our thoughts go out to all those who have been impacted by recent events. We wish you and your family, friends, and lab mates the best during the upcoming holidays.

'''Stanford University will be closed for two weeks starting December 20, and will reopen on January 3rd, 2022'''. 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.

SGD Newsletter, Fall 2021

2021-11-12T19:37:41Z

Edith: /* DIPOT Orthologs and new queries in YeastMine */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Fall 2021 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,_Spring_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Updated Protein Complex pages==
==Nomenclature Updates==

===Legacy gene names===
SGD has long been the keeper of the official ''Saccharomyces cerevisiae'' gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years.

The accepted format for gene names in ''S. cerevisiae'' comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the "Name Description" in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example "ADE" for "ADEnine biosynthesis" or "CDC" for "Cell Division Cycle". Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an [https://www.yeastgenome.org/search?category=locus&feature_type=ORF&page=0&q= ORF], a [https://www.yeastgenome.org/search?category=locus&feature_type=tRNA%20gene&page=0&q= tRNA], another type of [https://www.yeastgenome.org/search?q=YNC*&category=locus non-coding RNA], an [https://www.yeastgenome.org/search?category=locus&feature_type=ARS&page=0&q=ars ARS], or a [https://www.yeastgenome.org/search?category=locus&feature_type=Unmapped%20Genetic%20Loci&page=0&q= genetic locus]. Some ''S. cerevisiae'' gene names that pre-date the current nomenclature standards do not conform to this format, such as [https://www.yeastgenome.org/locus/S000001653 MRLP38], [https://www.yeastgenome.org/locus/S000006141 RPL1A], and [https://www.yeastgenome.org/locus/S000001398 OM45].

A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.

{| border="1" class="wikitable"
|-
!|ORF!!Old gene name!!New gene name
|-
|[http://www.yeastgenome.org/locus/YGL234W YGL234W]
|ADE5,7
|ADE57
|-
|[http://www.yeastgenome.org/locus/YER069W YER069W]
|ARG5,6
|ARG56
|-
|[http://www.yeastgenome.org/locus/YBR298C YBR298C]
|DUR1,2
|DUR12
|-
|[http://www.yeastgenome.org/locus/YIL154C YIL154C]
|IMP2'
|IMP21
|-
|}

===New Systematic Nomenclature for yeast genes not in the reference genome===
For many years, a widely adopted systematic nomenclature has existed for yeast protein-coding genes, or ORFs, as many yeast researchers call them. Readers of the [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Spring_2021 last SGD newsletter] will recall that, earlier this year, SGD adopted a new systematic nomenclature for the [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs].

We have just put into place a new systematic nomenclature for ''S. cerevisiae'' genes that are not found in the reference genome of strain S288C ([https://www.yeastgenome.org/search?q=YSC0&category=locus "non-reference" genes]). This new systematic nomenclature is similar to, but distinct from, that used for ORFs and that used for ncRNAs. Non-reference genes are designated by a symbol consisting of three uppercase letters and a four-digit number, as follows: Y for "Yeast", SC for "Saccharomyces cerevisiae", and a four-digit number corresponding to the sequential order in which the gene was added to SGD. We currently have 55 of these genes in SGD, some of which are old favorites like [https://www.yeastgenome.org/locus/S000029681 MAL21/YSC0004] and [https://www.yeastgenome.org/locus/S000124955 MATA/YSC0046], while others are more recent additions like [https://www.yeastgenome.org/locus/S000133140 XDH1/YSC0051]. Going forward, as evidence is published pointing to other ''S. cerevisiae'' genes not present in the S288C reference genome, they will be added to the annotation using the next sequential number available. We already have 15 more of these YSC0000 names reserved by researchers and awaiting publication.

If you have some non-reference genes for which these names would be appropriate, please [mailto:sgd-helpdesk@lists.stanford.edu let us know]!

==New links to AlphaFold 3D Predicted Protein Structure Database==

Would you like to see the shape of your protein?
[[File:Hog1_structure.png|thumb|left|upright=.5|link=https://alphafold.ebi.ac.uk/entry/P32485]]

SGD now contains links to [https://www.alphafold.ebi.ac.uk/ AlphaFold] in the Resources sections of the [https://www.yeastgenome.org/locus/S000004103#resources/ Summary], [https://www.yeastgenome.org/locus/hog1/protein#resources/ Protein], and [https://www.yeastgenome.org/locus/S000004103/homology#resources/ Homology] pages for every gene.

*The links through SGD give quick access to [https://www.embl.org EMBL]’s [https://www.ebi.ac.uk/ European Bioinformatics Institute] (EMBL-EBI) offers a new, highly accurate tool for predicting protein structure with speed and clarity.

*Given a peptide sequence for an uncharacterized protein, AlphaFold will model predicted domains and provide relative confidence levels for each portion of the prediction.

*The predicted domains can then be compared to known protein structures (using a tool such as [https://www.ebi.ac.uk/msd-srv/ssm/ PDBeFold]) to seek matches to characterized protein families.

*Whether or not a family is identified, the comparison will yield clues to protein function to help design the next experiments.

==DIPOT Orthologs and new queries in YeastMine ==

We have recently replaced HomoloGene, Ensembl, TreeFam and Panther homology datasets in YeastMine with homology data from [https://www.flyrnai.org/diopt DIOPT (DRSC integrative ortholog prediction tool)]. DIOPT integrates orthology predictions from multiple sources, including HomoloGene, Ensembl, TreeFam, and Panther. Using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Homologs&scope=all Gene->Non-fungal and S. cerevisiae Homologs] pregenerated query, you can look for DIOPT homologs for a single or multiple yeast genes. The results table provides identifiers and standard names for the yeast and homologous genes, as well as organism and predictive score information. As with other YeastMine templates, results can be saved as lists and analyzed further. 

Pre-generated queries for human homolog(s) of your favorite yeast gene and their corresponding disease associations
(https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_OMIM_Disease&scope=all) remain largely unchanged. You can also begin with your favorite human gene or disease keyword and retrieve the yeast counterparts of the relevant gene(s). As an example, you can search for the ''S. cerevisiae'' homologs of all human genes associated with disorders that contain the keyword “diabetes” ([http://yeastmine.yeastgenome.org/yeastmine/template.doname=Disease_Human_Yeast&scope=global view search]). The results table provides identifiers and standard names for the yeast and human genes, OMIM gene and disease identifiers and name, as well as predictive algorithm sources and scores.

==Alliance of Genome Resources - latest release==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 4.1] this past August. Notable improvements and new features include:
*Human and model organism high throughput (HTP) variant data
**Human variants are imported from Ensembl
**Model organism HTP variants are submitted by Alliance members (FlyBase, RGD, SGD, Wormbase) or imported from EVA (MGI and ZFIN).
**Added HTP variants to the Alleles and Variants table on gene pages (e.g. rat Lepr Gene page) and to the table on the Alleles and Variants Details page (e.g. rat Lepr Alleles and Variants Details.
**Created a report page for Human and model organism HTP variants (e.g. human variant rs1041354454).
**Expanded Allele Category in search to “Allele/Variant” and added a search for HTP variants.
*On Gene Pages, a new Pathways widget displays via tabs:
**Reactome models of pathways for human gene products as well as inferred pathways for model organism genes based on orthology to human genes.
**Reactome reactions for gene products (e.g. human TP53 Gene page)
**Gene Ontology Causal Activity Models (GO-CAMs). These provide a framework to represent a biological system by linking together multiple GO annotations. PMID:31548717 (e.g. worm nsy-1 Gene page).
*Experimental conditions are include for Disease and Phenotype data in tables on Gene, Allele, and Disease pages (e.g. zebrafish scn1lab Gene page).
*AllianceMine added Orthologs, and Allele and Variants (low throughput) data types to this release. You can now query for these data types via pre-made template queries.
*The Alliance Community Forum is released. The Forum permits discussions across six model organism communities—flies, mice, yeast, rats, worms, and zebrafish. More details will follow.

==Upcoming Conferences and Courses==
*[https://genetics-gsa.org/fungal/ Fungal Genetics] - the premier meeting for the international community of fungal geneticists
**Asilomar Conference Grounds, Pacific Grove, California (and Online)
**March 15 - 20, 2022
*[https://issy36.com 36th International Specialised Symposium on Yeasts (ISSY36)] - Yeast Sea to Sky - Yeast in the Genomics Era
**University of British Columbia, Vancouver
**July 12 - 16, 2022
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 CSHL Yeast Genetics & Genomics] - modern, intensive laboratory course that teaches students full repertoire of genetic and genomic approaches
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022

==Gene Ontology Consortium Fall 2021 Meeting==
[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14, SGD biocurators attended the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but were not limited to:
*[https://www.ncbi.nlm.nih.gov/research/litsuggest/ LitSuggest] - web-based system for biomedical literature recommendation and curation
*[https://evidenceontology.org ECO], Evidence and Conclusions Ontology - terms used to describe types of evidence and assertion methods
*PAINT, Phylogenetic Annotation and INference Tool from [http://www.pantherdb.org/about.jsp PANTHER] - orthology between reference genome genes and human disease genes

==Happy Holidays from SGD!==

[[File:SnowShmoo.png|thumb|left|upright=.25]]

We know that 2021 has been another challenging year for everyone. Our thoughts go out to all those who have been impacted by recent events. We wish you and your family, friends, and lab mates the best during the upcoming holidays.

'''Stanford University will be closed for two weeks starting December 20, and will reopen on January 3rd, 2022'''. 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.

SGD Newsletter, Fall 2021

2021-11-12T19:21:39Z

Edith: /* YeastMine Updates */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Fall 2021 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,_Spring_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Updated Protein Complex pages==
==Nomenclature Updates==

===Legacy gene names===
SGD has long been the keeper of the official ''Saccharomyces cerevisiae'' gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years.

The accepted format for gene names in ''S. cerevisiae'' comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the "Name Description" in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example "ADE" for "ADEnine biosynthesis" or "CDC" for "Cell Division Cycle". Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an [https://www.yeastgenome.org/search?category=locus&feature_type=ORF&page=0&q= ORF], a [https://www.yeastgenome.org/search?category=locus&feature_type=tRNA%20gene&page=0&q= tRNA], another type of [https://www.yeastgenome.org/search?q=YNC*&category=locus non-coding RNA], an [https://www.yeastgenome.org/search?category=locus&feature_type=ARS&page=0&q=ars ARS], or a [https://www.yeastgenome.org/search?category=locus&feature_type=Unmapped%20Genetic%20Loci&page=0&q= genetic locus]. Some ''S. cerevisiae'' gene names that pre-date the current nomenclature standards do not conform to this format, such as [https://www.yeastgenome.org/locus/S000001653 MRLP38], [https://www.yeastgenome.org/locus/S000006141 RPL1A], and [https://www.yeastgenome.org/locus/S000001398 OM45].

A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.

{| border="1" class="wikitable"
|-
!|ORF!!Old gene name!!New gene name
|-
|[http://www.yeastgenome.org/locus/YGL234W YGL234W]
|ADE5,7
|ADE57
|-
|[http://www.yeastgenome.org/locus/YER069W YER069W]
|ARG5,6
|ARG56
|-
|[http://www.yeastgenome.org/locus/YBR298C YBR298C]
|DUR1,2
|DUR12
|-
|[http://www.yeastgenome.org/locus/YIL154C YIL154C]
|IMP2'
|IMP21
|-
|}

===New Systematic Nomenclature for yeast genes not in the reference genome===
For many years, a widely adopted systematic nomenclature has existed for yeast protein-coding genes, or ORFs, as many yeast researchers call them. Readers of the [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Spring_2021 last SGD newsletter] will recall that, earlier this year, SGD adopted a new systematic nomenclature for the [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs].

We have just put into place a new systematic nomenclature for ''S. cerevisiae'' genes that are not found in the reference genome of strain S288C ([https://www.yeastgenome.org/search?q=YSC0&category=locus "non-reference" genes]). This new systematic nomenclature is similar to, but distinct from, that used for ORFs and that used for ncRNAs. Non-reference genes are designated by a symbol consisting of three uppercase letters and a four-digit number, as follows: Y for "Yeast", SC for "Saccharomyces cerevisiae", and a four-digit number corresponding to the sequential order in which the gene was added to SGD. We currently have 55 of these genes in SGD, some of which are old favorites like [https://www.yeastgenome.org/locus/S000029681 MAL21/YSC0004] and [https://www.yeastgenome.org/locus/S000124955 MATA/YSC0046], while others are more recent additions like [https://www.yeastgenome.org/locus/S000133140 XDH1/YSC0051]. Going forward, as evidence is published pointing to other ''S. cerevisiae'' genes not present in the S288C reference genome, they will be added to the annotation using the next sequential number available. We already have 15 more of these YSC0000 names reserved by researchers and awaiting publication.

If you have some non-reference genes for which these names would be appropriate, please [mailto:sgd-helpdesk@lists.stanford.edu let us know]!

==New links to AlphaFold 3D Predicted Protein Structure Database==

Would you like to see the shape of your protein?
[[File:Hog1_structure.png|thumb|left|upright=.5|link=https://alphafold.ebi.ac.uk/entry/P32485]]

SGD now contains links to [https://www.alphafold.ebi.ac.uk/ AlphaFold] in the Resources sections of the [https://www.yeastgenome.org/locus/S000004103#resources/ Summary], [https://www.yeastgenome.org/locus/hog1/protein#resources/ Protein], and [https://www.yeastgenome.org/locus/S000004103/homology#resources/ Homology] pages for every gene.

*The links through SGD give quick access to [https://www.embl.org EMBL]’s [https://www.ebi.ac.uk/ European Bioinformatics Institute] (EMBL-EBI) offers a new, highly accurate tool for predicting protein structure with speed and clarity.

*Given a peptide sequence for an uncharacterized protein, AlphaFold will model predicted domains and provide relative confidence levels for each portion of the prediction.

*The predicted domains can then be compared to known protein structures (using a tool such as [https://www.ebi.ac.uk/msd-srv/ssm/ PDBeFold]) to seek matches to characterized protein families.

*Whether or not a family is identified, the comparison will yield clues to protein function to help design the next experiments.

==DIPOT Orthologs and new queries in YeastMine ==

We have recently replaced HomoloGene, Ensembl, TreeFam and Panther homology datasets in YeastMine with homology data from [https://www.flyrnai.org/diopt DIOPT (DRSC integrative ortholog prediction tool)]. DIOPT integrates orthology predictions from other sources, including HomoloGene, Ensembl, and TreeFam. Using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Homologs&scope=all Gene->Non-fungal and S. cerevisiae Homologs] pregenerated query, users can look for DIOPT homologs for a single or multiple yeast genes. The results table provides identifiers and standard names for the yeast and homologous genes, as well as organism and predictive score information. As with other YeastMine templates, results can be saved as lists and analyzed further. 

Pregenerated queries for human homolog(s) of your favorite yeast gene and their corresponding disease associations
https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_OMIM_Disease&scope=all

==Alliance of Genome Resources - latest release==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 4.1] this past August. Notable improvements and new features include:
*Human and model organism high throughput (HTP) variant data
**Human variants are imported from Ensembl
**Model organism HTP variants are submitted by Alliance members (FlyBase, RGD, SGD, Wormbase) or imported from EVA (MGI and ZFIN).
**Added HTP variants to the Alleles and Variants table on gene pages (e.g. rat Lepr Gene page) and to the table on the Alleles and Variants Details page (e.g. rat Lepr Alleles and Variants Details.
**Created a report page for Human and model organism HTP variants (e.g. human variant rs1041354454).
**Expanded Allele Category in search to “Allele/Variant” and added a search for HTP variants.
*On Gene Pages, a new Pathways widget displays via tabs:
**Reactome models of pathways for human gene products as well as inferred pathways for model organism genes based on orthology to human genes.
**Reactome reactions for gene products (e.g. human TP53 Gene page)
**Gene Ontology Causal Activity Models (GO-CAMs). These provide a framework to represent a biological system by linking together multiple GO annotations. PMID:31548717 (e.g. worm nsy-1 Gene page).
*Experimental conditions are include for Disease and Phenotype data in tables on Gene, Allele, and Disease pages (e.g. zebrafish scn1lab Gene page).
*AllianceMine added Orthologs, and Allele and Variants (low throughput) data types to this release. You can now query for these data types via pre-made template queries.
*The Alliance Community Forum is released. The Forum permits discussions across six model organism communities—flies, mice, yeast, rats, worms, and zebrafish. More details will follow.

==Upcoming Conferences and Courses==
*[https://genetics-gsa.org/fungal/ Fungal Genetics] - the premier meeting for the international community of fungal geneticists
**Asilomar Conference Grounds, Pacific Grove, California (and Online)
**March 15 - 20, 2022
*[https://issy36.com 36th International Specialised Symposium on Yeasts (ISSY36)] - Yeast Sea to Sky - Yeast in the Genomics Era
**University of British Columbia, Vancouver
**July 12 - 16, 2022
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 CSHL Yeast Genetics & Genomics] - modern, intensive laboratory course that teaches students full repertoire of genetic and genomic approaches
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022

==Gene Ontology Consortium Fall 2021 Meeting==
[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14, SGD biocurators attended the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but were not limited to:
*[https://www.ncbi.nlm.nih.gov/research/litsuggest/ LitSuggest] - web-based system for biomedical literature recommendation and curation
*[https://evidenceontology.org ECO], Evidence and Conclusions Ontology - terms used to describe types of evidence and assertion methods
*PAINT, Phylogenetic Annotation and INference Tool from [http://www.pantherdb.org/about.jsp PANTHER] - orthology between reference genome genes and human disease genes

==Happy Holidays from SGD!==

[[File:SnowShmoo.png|thumb|left|upright=.25]]

We know that 2021 has been another challenging year for everyone. Our thoughts go out to all those who have been impacted by recent events. We wish you and your family, friends, and lab mates the best during the upcoming holidays.

'''Stanford University will be closed for two weeks starting December 20, and will reopen on January 3rd, 2022'''. 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.

SGD Newsletter, Fall 2021

2021-11-12T19:21:21Z

Edith: /* YeastMine Updates */

[[Category: Newsletter]]
'''About this newsletter:''' This is the Fall 2021 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,_Spring_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==Updated Protein Complex pages==
==Nomenclature Updates==

===Legacy gene names===
SGD has long been the keeper of the official ''Saccharomyces cerevisiae'' gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years.

The accepted format for gene names in ''S. cerevisiae'' comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the "Name Description" in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example "ADE" for "ADEnine biosynthesis" or "CDC" for "Cell Division Cycle". Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an [https://www.yeastgenome.org/search?category=locus&feature_type=ORF&page=0&q= ORF], a [https://www.yeastgenome.org/search?category=locus&feature_type=tRNA%20gene&page=0&q= tRNA], another type of [https://www.yeastgenome.org/search?q=YNC*&category=locus non-coding RNA], an [https://www.yeastgenome.org/search?category=locus&feature_type=ARS&page=0&q=ars ARS], or a [https://www.yeastgenome.org/search?category=locus&feature_type=Unmapped%20Genetic%20Loci&page=0&q= genetic locus]. Some ''S. cerevisiae'' gene names that pre-date the current nomenclature standards do not conform to this format, such as [https://www.yeastgenome.org/locus/S000001653 MRLP38], [https://www.yeastgenome.org/locus/S000006141 RPL1A], and [https://www.yeastgenome.org/locus/S000001398 OM45].

A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.

{| border="1" class="wikitable"
|-
!|ORF!!Old gene name!!New gene name
|-
|[http://www.yeastgenome.org/locus/YGL234W YGL234W]
|ADE5,7
|ADE57
|-
|[http://www.yeastgenome.org/locus/YER069W YER069W]
|ARG5,6
|ARG56
|-
|[http://www.yeastgenome.org/locus/YBR298C YBR298C]
|DUR1,2
|DUR12
|-
|[http://www.yeastgenome.org/locus/YIL154C YIL154C]
|IMP2'
|IMP21
|-
|}

===New Systematic Nomenclature for yeast genes not in the reference genome===
For many years, a widely adopted systematic nomenclature has existed for yeast protein-coding genes, or ORFs, as many yeast researchers call them. Readers of the [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Spring_2021 last SGD newsletter] will recall that, earlier this year, SGD adopted a new systematic nomenclature for the [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs].

We have just put into place a new systematic nomenclature for ''S. cerevisiae'' genes that are not found in the reference genome of strain S288C ([https://www.yeastgenome.org/search?q=YSC0&category=locus "non-reference" genes]). This new systematic nomenclature is similar to, but distinct from, that used for ORFs and that used for ncRNAs. Non-reference genes are designated by a symbol consisting of three uppercase letters and a four-digit number, as follows: Y for "Yeast", SC for "Saccharomyces cerevisiae", and a four-digit number corresponding to the sequential order in which the gene was added to SGD. We currently have 55 of these genes in SGD, some of which are old favorites like [https://www.yeastgenome.org/locus/S000029681 MAL21/YSC0004] and [https://www.yeastgenome.org/locus/S000124955 MATA/YSC0046], while others are more recent additions like [https://www.yeastgenome.org/locus/S000133140 XDH1/YSC0051]. Going forward, as evidence is published pointing to other ''S. cerevisiae'' genes not present in the S288C reference genome, they will be added to the annotation using the next sequential number available. We already have 15 more of these YSC0000 names reserved by researchers and awaiting publication.

If you have some non-reference genes for which these names would be appropriate, please [mailto:sgd-helpdesk@lists.stanford.edu let us know]!

==New links to AlphaFold 3D Predicted Protein Structure Database==

Would you like to see the shape of your protein?
[[File:Hog1_structure.png|thumb|left|upright=.5|link=https://alphafold.ebi.ac.uk/entry/P32485]]

SGD now contains links to [https://www.alphafold.ebi.ac.uk/ AlphaFold] in the Resources sections of the [https://www.yeastgenome.org/locus/S000004103#resources/ Summary], [https://www.yeastgenome.org/locus/hog1/protein#resources/ Protein], and [https://www.yeastgenome.org/locus/S000004103/homology#resources/ Homology] pages for every gene.

*The links through SGD give quick access to [https://www.embl.org EMBL]’s [https://www.ebi.ac.uk/ European Bioinformatics Institute] (EMBL-EBI) offers a new, highly accurate tool for predicting protein structure with speed and clarity.

*Given a peptide sequence for an uncharacterized protein, AlphaFold will model predicted domains and provide relative confidence levels for each portion of the prediction.

*The predicted domains can then be compared to known protein structures (using a tool such as [https://www.ebi.ac.uk/msd-srv/ssm/ PDBeFold]) to seek matches to characterized protein families.

*Whether or not a family is identified, the comparison will yield clues to protein function to help design the next experiments.

==YeastMine Updates==
==DIPOT Orthologs and new queries in YeastMine ==

We have recently replaced HomoloGene, Ensembl, TreeFam and Panther homology datasets in YeastMine with homology data from [https://www.flyrnai.org/diopt DIOPT (DRSC integrative ortholog prediction tool)]. DIOPT integrates orthology predictions from other sources, including HomoloGene, Ensembl, and TreeFam. Using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Homologs&scope=all Gene->Non-fungal and S. cerevisiae Homologs] pregenerated query, users can look for DIOPT homologs for a single or multiple yeast genes. The results table provides identifiers and standard names for the yeast and homologous genes, as well as organism and predictive score information. As with other YeastMine templates, results can be saved as lists and analyzed further. 

Pregenerated queries for human homolog(s) of your favorite yeast gene and their corresponding disease associations
https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_OMIM_Disease&scope=all

==Alliance of Genome Resources - latest release==
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.5]]
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 4.1] this past August. Notable improvements and new features include:
*Human and model organism high throughput (HTP) variant data
**Human variants are imported from Ensembl
**Model organism HTP variants are submitted by Alliance members (FlyBase, RGD, SGD, Wormbase) or imported from EVA (MGI and ZFIN).
**Added HTP variants to the Alleles and Variants table on gene pages (e.g. rat Lepr Gene page) and to the table on the Alleles and Variants Details page (e.g. rat Lepr Alleles and Variants Details.
**Created a report page for Human and model organism HTP variants (e.g. human variant rs1041354454).
**Expanded Allele Category in search to “Allele/Variant” and added a search for HTP variants.
*On Gene Pages, a new Pathways widget displays via tabs:
**Reactome models of pathways for human gene products as well as inferred pathways for model organism genes based on orthology to human genes.
**Reactome reactions for gene products (e.g. human TP53 Gene page)
**Gene Ontology Causal Activity Models (GO-CAMs). These provide a framework to represent a biological system by linking together multiple GO annotations. PMID:31548717 (e.g. worm nsy-1 Gene page).
*Experimental conditions are include for Disease and Phenotype data in tables on Gene, Allele, and Disease pages (e.g. zebrafish scn1lab Gene page).
*AllianceMine added Orthologs, and Allele and Variants (low throughput) data types to this release. You can now query for these data types via pre-made template queries.
*The Alliance Community Forum is released. The Forum permits discussions across six model organism communities—flies, mice, yeast, rats, worms, and zebrafish. More details will follow.

==Upcoming Conferences and Courses==
*[https://genetics-gsa.org/fungal/ Fungal Genetics] - the premier meeting for the international community of fungal geneticists
**Asilomar Conference Grounds, Pacific Grove, California (and Online)
**March 15 - 20, 2022
*[https://issy36.com 36th International Specialised Symposium on Yeasts (ISSY36)] - Yeast Sea to Sky - Yeast in the Genomics Era
**University of British Columbia, Vancouver
**July 12 - 16, 2022
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=22 CSHL Yeast Genetics & Genomics] - modern, intensive laboratory course that teaches students full repertoire of genetic and genomic approaches
**Cold Spring Harbor Laboratory, NY
**July 26 - August 15, 2022
*[https://genetics-gsa.org/yeast/ Yeast Genetics Meeting] - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
**University of California, Los Angeles
**August 17 – 21, 2022

==Gene Ontology Consortium Fall 2021 Meeting==
[[File:logo_GOC.png|thumb|left|upright=.25|link=http://geneontology.org]]
From October 12-14, SGD biocurators attended the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but were not limited to:
*[https://www.ncbi.nlm.nih.gov/research/litsuggest/ LitSuggest] - web-based system for biomedical literature recommendation and curation
*[https://evidenceontology.org ECO], Evidence and Conclusions Ontology - terms used to describe types of evidence and assertion methods
*PAINT, Phylogenetic Annotation and INference Tool from [http://www.pantherdb.org/about.jsp PANTHER] - orthology between reference genome genes and human disease genes

==Happy Holidays from SGD!==

[[File:SnowShmoo.png|thumb|left|upright=.25]]

We know that 2021 has been another challenging year for everyone. Our thoughts go out to all those who have been impacted by recent events. We wish you and your family, friends, and lab mates the best during the upcoming holidays.

'''Stanford University will be closed for two weeks starting December 20, and will reopen on January 3rd, 2022'''. 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.