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SGD Newsletter, December 2025

December 11, 2025

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

Contents

Support SGD this Holiday Season

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Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. Donations are now critical for our work to continue. Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. To contribute using a credit card, please use this form: give.stanford.edu.

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

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

We thank you in advance for your support!

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

Baruch et al. have compiled and published A comprehensive overview of yeast libraries and their role in advancing cell biology, which describes a comprehensive list of genome-wide collections of Saccharomyces cerevisiae. They have grouped similar strain libraries together and have curated detailed descriptions, mating types, genotypes, references, and genome coverage. This information can help researchers identify strain libraries of interest to them. All of this information can also be found in tables on LibrarYeast. We have added links to these tables under the Resources section of individual Protein, Phenotype, and Interaction tabs.

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Retirement of Mike Cherry

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

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

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

Thank you, Mike, for everything.

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Reminder: Submit Data Form

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

Alliance of Genome Resources News

Alliance of Genome Resources – Latest Release 8.2.0

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The 8.2.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements. The sequence viewers on the gene and allele pages have been restored on gene pages, in the Alleles and Variants and Sequence Feature Viewer sections, and on allele pages, in the Genomic Variant Information section (see for example the mouse gene Pten and mouse allele for Pten). Also, on the gene page Alleles and Variants section, interactions between the variant sequence viewer and the alleles/variants table have been restored. Website infrastructure is upgraded to React 19 and migrated to Vite.

Alliance Webinars: MicroPublication Biology

On November 20, Tim Schedl, microPublication Biology Editorial Board member, presented an overview of the MicroPublication journal which publishes brief scholarly reports of research findings based on data presented in a single figure. View the recording of the latest Alliance of Genome Resources webinar: Introduction to MicroPublication Biology. Webinars are also planned for 2026, in January, February, and March. See the Event Calendar for the schedule of upcoming Alliance office hours and webinars.

FlyBase End of Funding

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

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

Final Release of WormBase

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

microPublications – Latest Yeast Papers

MicroPub.png

​microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral. Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others. Latest yeast microPublications:

Upcoming Conferences & Courses

Happy Holidays from SGD!

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We want to take this opportunity to wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting end of day Friday, December 19th, and reopening on Monday, January 5th, 2026. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year. 

Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

Categories: Newsletter

SGD Newsletter, Spring 2025

April 30, 2025

About this newsletter:
This is the Spring 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.

Contents

Give a Gift / Support SGD: Credit Cards Now Accepted

gift.png

Budget cuts from NIH continue to strain SGD’s finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. Donations are now critical for our work to continue.

Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card.

To contribute using a credit card, please use this form: 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

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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 March 2025 issue.

Check out the most recent updates at SGD, including:

  • 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

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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. 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. 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, 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

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The Yeast Phenome is a collaborative project from the Baryshnikova lab at Calico Life Sciences to create a comprehensive compendium of systematic loss-of-function phenotypes for the budding yeast Saccharomyces cerevisiae.

The Yeast Phenome systematically tracks, collects, and annotates all published phenotypic screens utilizing the yeast knock-out collection. 

Locus-specific links to the Yeast Phenome are now available in the Resources section of the Phenotype tab and will take you directly to the corresponding page of the Yeast Phenome data library. Try it now: the SGD phenotype page for ARP1, and the linked ARP1 page at Yeast Phenome.

microPublications – Latest Yeast Papers

MicroPub.png

​microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral. 

Consider microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others.

Latest yeast microPublications:


All yeast microPublications can be found in SGD.

Alliance of Genome Resources – Latest Release 8.1.0

alliance logo.png

The 8.1.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.

Recent changes in 8.0.0 and 8.1.0 include:

  • 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

Categories: Newsletter

Yeast Biochemical Pathways incorporated into Gene Ontology annotations

April 09, 2025

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.

Categories: Data updates

Apply Now for the 2025 Yeast Genetics and Genomics Course

March 11, 2025

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For over 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory, though the name didn’t include “Genomics” in the beginning. The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists.

The application deadline is April 15, so don’t miss your chance!

Find all the details and application form at the CSHL Meetings & Courses site. This year’s instructors – Grant Brown, Soni Lacefield, and Greg Lang – have designed a course (July 22 – August 12) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:

  • Transformation & Genome Engineering
  • Microscopy
  • Manipulating Yeast
  • Dissecting Tetrads
  • Isolating Mutants
  • Working with Essential Genes
  • Synthetic Genetic Arrays
  • Fluctuation Assays
  • Whole Genome Sequencing & Analysis

2025 Invited Speakers

Francisco Cubillos, Universidad de Santiago de Chile, Chile
Ivan Dedek, Meier’s Creek Brewing Company, Cazenovia, NY
Ian Ehrenreich, University of Southern California, Los Angeles, CA
Catherine Freudenreich, Tufts University, Medford, CT
Jonathan Friedman, University of Texas Southwestern, TX
David Garcia, University of Oregon, Eugene, OR
Kerry Geiler-Samerotte, Arizona State University, Tempe, AZ
Patrick Gibney, Cornell University, Ithaca, NY
Elena Kuzmin, Concordia University, Montreal, Canada
Jun-Yi Leu, Academia Sinica, Taipei, Taiwan 
Amy MacQueen, Wesleyan University, Middletown, CT
Rob Nash, Saccharomyces Genome Database, Stanford University, Palo Alto, CA
Ally O’Donnell, University of Pittsburgh, Pittsburgh, PA

Techniques have been summarized in the accompanying course manual, published by CSHL Press.

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There’s fierce competition between students at CSHL courses in the Plate Race, a relay in which teams carry stacks of 40 Petri dishes (used, of course).

Who should attend? Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics.

What else goes on there? Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also typically a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!

The Yeast Genetics & Genomics Course is loads of fun – don’t miss out!

Categories: Conferences

Give a Gift / Support SGD

January 31, 2025

Giving to SGD just got easier! We now accept donations by credit card with this form: give.stanford.edu.

Select ‘Other Stanford Designation’ under ‘Direct your gift’ & in the ‘Other’ box, add: Saccharomyces Genome Database – Account: GHJKO, Genetics: WAZC. Thanks for your support!

Image of SGD credit card donation form

Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. Donations are now critical for our work to continue.

To contribute via check, please make checks payable to Stanford University, and include a note stating that “these funds should be used to support the Saccharomyces Genome Database project 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

CONTACT US: 
sgd-helpdesk@lists.stanford.edu

Categories: Announcements

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