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

April 03, 2026

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

Understanding Yeast Gene Nomenclature

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

The Naming Rules

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

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

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

How to Reserve Your Gene Name

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

The Reservation Process

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

Best Practices for Publication

When you’re ready to publish, we recommend:

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

Need More Information?

The complete gene naming process is described in detail in our Gene Naming Guidelines.

Questions?

The SGD team is here to help! If you have questions about the gene name reservation process or nomenclature guidelines, please don’t hesitate to contact us at sgd-helpdesk@lists.stanford.edu.

Contributing to yeast nomenclature is an important part of advancing our collective understanding of this remarkable model organism. Thank you for following these guidelines and helping maintain the clarity and consistency of yeast gene names!

Categories: Tutorial

In Memoriam: David Botstein

March 02, 2026

David Botstein

We are deeply saddened to share the news of the passing of David Botstein, a towering figure in modern genetics and a foundational force behind the Saccharomyces Genome Database (SGD). SGD began in the early 1990s in David’s lab at Stanford University, and his vision for a rigorously curated, community-centered resource set the course for what SGD is today. His belief that carefully organized, interoperable data would accelerate discovery has guided our work from the start and continues to shape our mission.

David’s scientific impact is vast and enduring. He co-authored the landmark 1980 paper introducing the use of restriction fragment length polymorphisms (RFLPs) for human genetic mapping, a conceptual breakthrough that opened the door to finding disease genes well before whole-genome sequencing was possible. He later helped usher in the era of genome-wide expression analysis, demonstrating how systematic measurement and clustering of gene expression could illuminate cellular pathways, regulatory programs, and physiological states. Across decades, his work, leadership, and mentorship helped define the fields of genetics and genomics.

Yeast, and the global community that studies it, benefited enormously from David’s clarity of thought and sense of purpose. He championed model organisms as engines of insight, insisting that fundamental principles uncovered in yeast could illuminate biology more broadly. From the beginning, he advocated for standards, reproducibility, and open data, principles that remain at the heart of SGD. Many of the practices we still rely on, including careful literature-based curation, genotype-to-phenotype integration, and community engagement, grew directly from his vision.

David was also a gifted mentor and collaborator. He trained and inspired generations of scientists, curators, engineers, and students, encouraging bold ideas and rigorous tests of those ideas. Those who worked with him remember his incisive questions, his generosity with time and credit, and his unwavering commitment to getting the science right. His influence extends through the many people he mentored and the communities and institutes he helped build at MIT, Stanford, Princeton, and beyond.

To the SGD team, David’s legacy is personal. We are honored to steward a resource he helped bring into being, and we remain committed to the principles he championed: accuracy, openness, and service to the community. As we continue to evolve SGD in a multi-omic, data-rich era, we do so with gratitude for the foundation he laid and the example he set.

We extend our deepest condolences to David’s family, friends, colleagues, and the many people around the world who learned from and were inspired by him.

Categories: News and Views

Introducing BLAST Search for SGD at the Alliance of Genome Resources

February 17, 2026

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

What’s New

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

Key Features

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

Part of a Broader Migration

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

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

Getting Started

Visit the Alliance of Genome Resources to access the new service for SGD BLAST, including Fungal BLAST. The datasets will be familiar to longtime SGD users.

Looking Ahead

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

Categories: Announcements

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

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

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.

LibrarYeast.jpeg

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.

mike r party.jpeg

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

alliance logo.png

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

alliance logo wormbase.png

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!

SnowShmoo.png

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

genetics 229 3cover.jpeg

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

figure1GENETICS2025.jpg

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

calico life sciences llc logo.jpg

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

yeast_course_panorama

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.

IMG_2185
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

SGD Newsletter, December 2024

December 13, 2024

About this newsletter:
This is the December 2024 issue of the SGD newsletter. The goal of this newsletter is to inform SGD users about new features from SGD and to foster communication within the yeast community.

Contents

AlphaFold protein structures now on SGD protein pages

AlphaFoldSET1.png

We are thrilled to announce that we have now integrated AlphaFold protein structures into our protein pages! This cutting-edge addition provides detailed, high-accuracy 3D models of protein structures, offering invaluable insights into protein function and interactions. Researchers can now explore these comprehensive structural predictions directly within SGD, facilitating advanced studies in molecular biology and bioinformatics. Dive into the new AlphaFold protein structures and elevate your research with this powerful tool!

AlphaFold, developed by DeepMind, is an AI program that accurately predicts protein structures from amino acid sequences, enabling visualization of protein conformations.

The predicted structures can be accessed through the Protein Data Bank (PDB) and AlphaFold Protein Structure Database. Thanks to Kim Rutherford and Val Wood of Pombase for tips about adding AlphaFold structures to SGD.

YeastMine data available in AllianceMine

yeastmineLogo.png

Here at SGD we provide high-quality curated genomic, genetic, and molecular information on the genes and gene products of the budding yeast Saccharomyces cerevisiae. In 2011, SGD implemented InterMine, an open-source data warehouse system with a sophisticated querying interface, to better meet the complex and diverse needs of researchers searching and comparing data, resulting in the creation of YeastMine.

YeastMine is a multifaceted search and retrieval environment that provides access to diverse data types. Searches can be initiated with a list of genes, a list of Gene Ontology terms, or lists of many other data types. The results from queries can be combined for further analysis and saved or downloaded in customizable file formats. Queries themselves can be customized by modifying predefined templates or by creating a new template to access a combination of specific data types.

In July 2024, YeastMine was discontinued due to ongoing cuts in funding at SGD. However, we have moved the YeastMine data into AllianceMine, hosted by the Alliance of Genome Resources, of which SGD is a founding member. You can even access lists like “ALL_Verified_Uncharacterized_Dubious_ORFs” through the AllianceMine Lists just as you could in the previous versions of YeastMine. Ensure any bookmarks to YeastMine have been updated to match the new URL: https://www.alliancegenome.org/bluegenes/alliancemine. User documentation for the new YeastMine interface is available from InterMine.

Help maintain your genomic databases! Sign open letter supporting funding for biodata resources

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The Global Biodata Coalition has an open letter campaign to show support for sustainable funding for biodata resources.

Please take a minute to read and sign- the form takes only seconds to fill out. Everyone – including students and postdocs, bioinformaticians and curators, PIs and directors – is invited to join those of us that have already added our signatures in support of the GBC. Find more information and sign at the GBC site.

Community wiki shutting down

As another casualty of decreased funding, SGD will no longer provide the Community Wiki. Some of the resources hosted on the wiki have been moved to our Help pages, the Alliance Community Forum, or remain available though the SGD downloads site. We thank all our past and current Community Wiki contributors, and invite the yeast community to join SGD on the Alliance Community forum.

SGD’s new 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 as an accepted manuscript. 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, and other enhancements to the SGD website and user interface.

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 7.4

alliance logo.png

The Alliance of Genome Resources, a collaborative effort between SGD and other model organism databases (MODs), released version 7.4 in October 2024.

The 7.4.0 release includes ~2.5 million variants of clinical significance from ClinVar. The Alliance removed 400 million human variants from the search because their inclusion was hampering site performance. The removed variants are mostly of unknown or uncertain clinical significance. The Alliance has instead included over 2.5 million human variants of known clinical significance from ClinVar. This should speed up the performance of the search function and improve site stability. The Alliance will address inclusion of the other high throughput human variants in the future. More detailed information about the 7.4 Alliance release can be found in the release notes.

Give a Gift / Support SGD

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 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

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

Upcoming conferences and courses

Happy Holidays from SGD!

SnowShmoo.png

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 20th, and reopening on Monday, January 6th, 2025. 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 by email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

Categories: Newsletter

AlphaFold protein structures now on SGD protein pages

November 18, 2024

We are thrilled to announce that we have now integrated AlphaFold protein structures into our protein pages! This cutting-edge addition provides detailed, high-accuracy 3D models of protein structures, offering invaluable insights into protein function and interactions. Researchers can now explore these comprehensive structural predictions directly within SGD, facilitating advanced studies in molecular biology and bioinformatics. Dive into the new AlphaFold protein structures and elevate your research with this powerful tool!

AlphaFold, developed by DeepMind, is an AI program that accurately predicts protein structures from amino acid sequences, enabling visualization of protein conformations. The predicted structures can be accessed through the Protein Data Bank (PDB) and AlphaFold Protein Structure Database.

Thanks to Kim Rutherford and Val Wood of Pombase for tips about adding AlphaFold structures to SGD.

Categories: Announcements

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