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Where to Order Yeast Strains: A Guide to Strain Resources

June 03, 2026

One of the most frequent questions we receive at the SGD Helpdesk is: “Where can I order yeast strains for my research?”

We’ve compiled a comprehensive guide to help you locate the strains you need, whether you’re looking for deletion mutants, specific genetic backgrounds, or specialized collections.

Finding Strains Through SGD

SGD makes it easy to locate available strains directly from gene pages. Here’s how:

  1. Start at the Locus Summary page for your gene of interest (example: https://www.yeastgenome.org/locus/S000005000)
  2. Click on the “Phenotype” tab to navigate to the Phenotype Details page (example: https://www.yeastgenome.org/locus/S000005000/phenotype)
  3. Scroll to the “Resources” section at the bottom of the page

The Resources section includes direct links to several strain resources, including:

Additional Major Yeast Strain Repositories

Beyond the resources linked on SGD Phenotype pages, here are other valuable repositories:

European Collections

Euroscarf (European Saccharomyces cerevisiae Archive for Functional Analysis) https://www.euroscarf.de/ One of the largest yeast strain collections, Euroscarf provides deletion mutants, overexpression strains, and other specialized collections for the research community.

National Collection of Yeast Cultures (NCYC) https://www.ncyc.co.uk/ Maintains over 4,000 yeast strains, including wild-type isolates and reference strains.

Industrial Yeasts Collection DBVPG https://dsa3.unipg.it/DBVPG/en/ Houses over 6,000 yeast strains with a focus on industrial and wild yeasts.

Common Access to Biological Resources and Information (CABRI) http://www.cabri.org/ Provides access to catalogs from multiple European culture collections.

North American Collections

ATCC (American Type Culture Collection) https://www.atcc.org/ A premier biological resource center offering authenticated yeast strains, including reference strains and mutant collections.

Specialized Collections and Commercial Sources

Schuldiner Lab Collections and Libraries https://mayaschuldiner.wixsite.com/schuldinerlab/lab-data Includes specialized strain collections and genomic libraries.

Creative Biogene Knockout Strains https://microbiosci.creative-biogene.com/saccharomyces-cerevisiae-s288c-knockout-strains-2644.html Offers S. cerevisiae S288C knockout strains.

Horizon Discovery Yeast Tools https://horizondiscovery.com/en/non-mammalian-research-tools/products/yeast-parental-strains Provides parental strains and yeast research tools.

Need Help?

If you’re having trouble locating a specific strain or accessing any of these resources, don’t hesitate to contact the SGD Helpdesk. We’re here to help connect you with the strains you need for your research.

Categories: Tutorial

SGD Newsletter, May 2026

May 27, 2026

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

Contents

Join Us at Yeast Genetics Meeting 2026

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

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

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

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

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

Introducing BLAST Search for SGD at the Alliance of Genome Resources

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
  • Familiar BLAST functionality: All standard BLAST algorithms (BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX) are supported
  • Enhanced performance: Leveraging the Alliance’s updated infrastructure for faster search results
  • Cross-species exploration: Seamlessly explore homologs across other Alliance member databases

Part of a Broader Migration

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

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

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

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

Textpresso Literature Search: New Login System

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

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

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

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

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

Understanding Yeast Gene Nomenclature

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

The Naming Rules

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

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

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

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:

AI-generated cartoon yeast cell and bud holding a pencil

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?

You can review the nomenclature conventions for yeast on our Help pages. 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.

Alliance of Genome Resources News

Alliance of Genome Resources – Latest Releases 9.0.0 & 8.3.0

9.0.0 Release – May 13, 2026

alliance logo.png

The 9.0.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.

Updates and improvements have been made to the following pages:

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

8.3.0 Release – December 17, 2025

The 8.3.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.

Updates and improvements have been made to the following pages:

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

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:

  • Wang TK, et al. (2026) A cross-species rescue by mating method to interrogate gene essentiality across the Saccharomyces genus. MicroPubl Biol. 2026 Mar 27;2026:10.17912/micropub.biology.002022. doi: 10.17912/micropub.biology.002022. eCollection 2026.
  • Brown K, Singuluri H, Perkins F, Kuchin S (2026) The N-terminal α helix domain of the mitochondrial VDAC protein Por2 is dispensable for promoting the nuclear localization of yeast AMPK. MicroPubl Biol. 2026 Feb 23:2026:10.17912/micropub.biology.001040. doi: 10.17912/micropub.biology.001040. eCollection 2026.
  • Ackermann LM, Ro A, Dunn B, Moore R, Doss G, Armstrong JO, Dunham MJ (2026) Using Experimental Evolution to Correct Mother-Daughter Separation Defects in Brewing Yeast. MicroPubl Biol. 2026 Feb 13:2026:10.17912/micropub.biology.001962. doi: 10.17912/micropub.biology.001962. eCollection 2026.
  • Klepin S, Michalik B, Pillus L, Chik JK (2025) Mutation of a conserved anthranilate phosphoribosyltransferase active site residue supports tryptophan biosynthesis in vivo. MicroPubl Biol. 2025 Dec 15:2025:10.17912/micropub.biology.001925. doi: 10.17912/micropub.biology.001925. eCollection 2025.
  • Beckwith SL (2025) Co-expression of a retrotransposon and re-targeted restriction factor impairs yeast growth. MicroPubl Biol. 2025 Nov 3:2025:10.17912/micropub.biology.001905. doi: 10.17912/micropub.biology.001905. eCollection 2025.

Upcoming Conferences & Courses

The End of PomBase?

Recently, PomBase learned that their grant application to the UK’s Biotechnology and Biological Sciences Research Council (BBSRC) for three years of funding was unsuccessful.

This decision places PomBase on a path to closure. Without alternative support, which at present seems unlikely, Pombase will lose not only the database but also the specialist expertise required to curate, maintain, and develop it. All three staff are funded entirely through grants; when funding stops, the resource and the knowledge behind it disappear together.

PomBase, like SGD, is a core piece of scientific infrastructure. It underpins research far beyond the yeast community, enabling discovery, reproducibility, and data integration across the life sciences. Losing it would not be a local setback; it would be a permanent loss to the global research ecosystem.

This is not just about PomBase. Essential bioinformatics resources are at risk. Other model organism databases, like SGD and Flybase, are under the same funding squeeze. FlyBase now requires support by direct fees from the community to sustain its curation. The wider scientific community must choose to sustain the shared infrastructure that drives modern biology and innovation. The contraction of funding has exposed a systemic vulnerability in how we fund biological data resources. We urge funders, institutions, and the community to recognize what is at stake. Once lost, resources like PomBase, Flybase, and SGD cannot simply be rebuilt.

In Memoriam: 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 have been 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.

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.

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

Categories: Newsletter

Tags: Newsletter

How to Find UTR Lengths for Yeast Genes

May 21, 2026

Have you ever wondered where you can find information about the 5′ and 3′ UTRs (untranslated regions) for a list of yeast genes?

If you’re working with Saccharomyces cerevisiae and need UTR information, we have several solutions depending on your needs.

Option 1: Bulk Download Files for Large Datasets

If you’re analyzing multiple genes or need comprehensive UTR data, downloading our complete datasets is the most efficient approach.

Access the SGD Downloads site: http://sgd-archive.yeastgenome.org/sequence/S288C_reference/

Download these two files:

These files contain FASTA-formatted sequences for all annotated ORF UTRs in the yeast genome. Once you download and extract the files, you can easily parse the sequences to determine lengths for your genes of interest. README files with additional details are located in the same folder.

Option 2: Query Individual Genes or Gene Lists with AllianceMine

For looking up UTR data on individual genes or specific gene lists, use the Gene -> UTRs template in AllianceMine:

https://www.alliancegenome.org/bluegenes/alliancemine/templates/Gene_UTRs

This tool allows you to input your genes of interest and retrieve UTR information in a structured, easy-to-use format.

Option 3: Browse UTRs Visually with JBrowse

If you prefer to explore UTR features in their genomic context, check out the UTR tracks in SGD’s JBrowse genome browser:

https://jbrowse.yeastgenome.org

The visual browser lets you see UTRs alongside other genomic features, making it ideal for examining individual loci or exploring chromosomal regions.

Have questions about yeast genomics data? Contact the SGD Helpdesk! We’re here to help you find the information you need for your research.

Categories: Tutorial

Adding a New Gene to the Reference Genome Annotation

April 23, 2026

SGD maintains the most up-to-date version of the complete genomic sequence of S. cerevisiae strain S288C. If your lab has characterized a gene or genomic feature that isn’t yet annotated, getting it added is a meaningful contribution. Here’s what SGD needs from you to do that:

Publicly Available Data

SGD only adds features based on published data. All coordinates, strand information, and sequence data must already be explicitly reported in a peer-reviewed publication. Depositing the sequence, including the genome sequence version used, in a public repository such as GenBank is also required.

What Should be Included in the Publication:

  • Explicit chromosomal coordinates, including genome sequence version used— stated in the text or a supplemental table, not only inferred from a figure or visualization
  • Strand orientation — sense (+) or antisense (–)
  • Strain background — SGD is built on S288C; note if your data maps to a different strain such as SK1 or W303
  • Feature type — protein-coding gene, ncRNA, pseudogene, regulatory region, etc.
  • GenBank Accession — Accession number from GenBank to identify the feature

When to Reach Out

Genome annotation updates at SGD are released periodically rather than continuously. When a new feature is identified, it is added to the list of new features that will be reviewed for incorporation into the next update. There are three good moments to contact us at sgd-helpdesk@lists.stanford.edu:

Before publication — if your paper is in preparation or under review, reaching out early lets curators know to watch for it. They can review the manuscript details and be ready to act as soon as it is accepted and assigned a PMID.

At or after publication — once your paper is published and indexed in PubMed, contact us with the PMID and point curators to where the relevant data appear in the paper.

If your paper is already in SGD but the feature is missing — SGD has curated thousands of papers and may have captured some findings from a publication while missing others. If you notice that a gene from your own work hasn’t been annotated, let us know and we will revisit the paper.

Questions?

The SGD team is here to help! If you have questions about genome sequence annotations, please don’t hesitate to contact us at sgd-helpdesk@lists.stanford.edu.

Categories: Tutorial

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

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

mike gavin.jpeg

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

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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

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​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

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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

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

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​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

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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

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