New & Noteworthy

New Pathway Pages: Comprehensive Views of Yeast Biochemical Pathways

August 11, 2026

We’re excited to announce the release of Pathway Pages at SGD! These new pages provide comprehensive information about the 220 manually curated biochemical pathways in yeast, bringing together pathway diagrams, gene lists, functional networks, and curated experimental data all in one place.

• One-stop resource: All pathway information in a single place
• Rich context: See genes in the context of the pathway they participate in
• Evidence-based: All data tied to primary literature
• Interactive exploration: Multiple ways to explore pathway relationships

Pathway pages offer a complete view of specific biochemical pathways in Saccharomyces cerevisiae. Each page integrates information from multiple sources to help you understand what the pathway does, which genes are involved, how gene products interact, and which chemicals are involved.

What’s Included?

Interactive Pathway Diagrams

Each pathway page features a pathway diagram showing the chemical reactions and metabolic flow. The diagram displays:

• Chemical compounds involved (substrates and products)
• Enzymes catalyzing each reaction
• Reaction directionality and relationships

A “View interactive diagram at YeastPathways” button takes you to the full interactive version where you can explore the pathway in greater detail.

Pathway Summary

Expert-curated descriptive text explains:

• What the pathway does and why it’s important
• Biological context and cellular roles
• Connections to other metabolic processes
• Key regulatory mechanisms

For example, the glyoxylate cycle page explains how this essential pathway allows yeast to grow on two-carbon compounds and its role in providing precursors for biosynthesis.

Genes Involved

A comprehensive table of genes participating in the pathway includes:

• Gene names (standard and systematic)
• EC numbers for enzymatic activities
• Functional descriptions
• Direct links to gene pages for detailed information

This makes it easy to see all the players in a pathway at a glance and dive deeper into any gene of interest.

Functional Networks

Pathway pages now include the same Functional Networks features available on gene pages:

Shared Annotations Network: Visualizes how genes in the pathway share phenotype and GO annotations, helping you identify:

• Functional relationships between pathway genes
• Connections to genes in related pathways
• Potential regulatory relationships

You can filter the network by the number of shared pathway genes to focus on the most relevant connections.

GO-CAMs: When available, Gene Ontology Causal Activity Model pathway models are displayed, showing:

• Causal relationships between molecular activities
• How gene products work together mechanistically
• Regulatory interactions and dependencies

If multiple GO-CAM models involve genes from the pathway, you can switch between them using a dropdown menu.

GO Enrichment Analysis

The GO Enrichment section shows which biological processes are statistically overrepresented among pathway genes. This helps you:

• Understand the broader biological context
• See connections to related processes
• Identify key functional themes

Each enriched term links to the genes involved and shows the statistical significance (p-value).

Browse All Pathways

Explore all 220 curated pathways:

• Browse pathways: Search for pathways
• Example: Glyoxylate cycle
• YeastPathways: All metabolic pathways

We Want Your Feedback!

Pathway pages are a new addition to SGD, and we want to make them as useful as possible. Have suggestions? Questions about specific pathways? Let us know at sgd-helpdesk@lists.stanford.edu.

Categories: Announcements, Website changes

Tags: biochemical pathways, GO enrichment, GO-CAM, metabolic pathways, pathway diagrams, YeastPathways

Redesigned Chemical Pages: Comprehensive Small Molecule Information in One Place

August 07, 2026

We’re pleased to announce the redesign of SGD’s chemical pages! These updated pages provide comprehensive information about small molecules relevant to yeast biology such as metabolites, drugs, and experimental compounds, all in a more accessible, more user-friendly format.

Why Chemical Information Matters

Small molecules play crucial roles in yeast biology, from essential metabolites that keep cells functioning to experimental compounds that reveal how cellular processes work. SGD chemical pages bring together curated information about how these chemicals affect yeast, connecting chemical entities to genes, phenotypes, and biological pathways.

What’s New?

Chemical Structures Front and Center

The redesigned pages now display interactive 2D chemical structures prominently at the top of each page. These structures clearly show molecular connectivity and functional groups, providing immediate visual recognition of the compound. No more hunting for the structure because it’s the first thing you see!

All Information on One Page

No need to navigate between multiple tabs! Everything you need to know about a chemical is now presented on a single, unified page:

Comprehensive Identifiers and Database Links:

• ChEBI ID (we use the Chemical Entities of Biological Interest ontology maintained by EMBL-EBI)
• IUPAC name
• PubChem CID
• Common names and synonyms
• Molecular formula and weight

This integration makes it easy to explore the chemical across multiple resources and access broader chemical and metabolic information.

Curated Experimental Data

Each chemical page now includes rich experimental data curated from the yeast literature:

Phenotype Annotations
See the effects of the chemical on yeast:

• Growth effects
• Metabolic changes
• Other cellular processes

This section includes annotation statistics, top genes and phenotypes involving each chemical. Every phenotype annotation is linked to supporting experimental evidence and literature references, so you can trace findings back to the original research.

Gene Ontology Annotations and Enrichment

The GO Annotations section shows how the chemical is annotated within the Gene Ontology framework, connecting it to specific biological processes, molecular functions, and cellular components.

For metabolites, you’ll also find links to relevant metabolic pathways in YeastPathways throughout the GO annotation tables, connecting chemical entities to their biological context in small molecule metabolism.

The GO Enrichment section takes this further with statistical analysis showing which biological processes and molecular functions are significantly associated with genes affected by the chemical. This enrichment analysis helps you:

• Understand the broader biological context of chemical-gene interactions
• Identify patterns in how chemicals influence cellular systems
• Generate hypotheses about mechanism of action

Shared Chemicals Network

Discover related compounds! The Shared Chemicals section displays other chemical entities that share similar properties, annotations, or biological roles. This network view makes it easy to:

• Explore chemical families
• Find compounds with similar effects
• Identify potential alternative compounds for experiments

Complete Literature Coverage

The References section compiles all publications from which data about the chemical has been curated. This provides direct access to the primary literature and shows you the full scope of research on each compound.

Try It Out!

Explore the new chemical pages:

• Example: Cisplatin
• Example: Caffeine
• Browse all chemicals: Search for chemicals

We Want Your Feedback!

These improvements are part of our ongoing commitment to making SGD more comprehensive and user-friendly. Have thoughts on the new chemical pages? Contact us at sgd-helpdesk@lists.stanford.edu.

Categories: Website changes

Tags: ChEBI, chemicals, GO enrichment, metabolites, phenotypes, redesign, user experience

Redesigned Protein Complex Pages: Enhanced Data Access and Improved User Experience

August 04, 2026

We’re excited to announce a comprehensive redesign of SGD’s macromolecular complex pages! We’ve overhauled these pages to make complex information more accessible, comprehensive, and easier to navigate.

Why Protein Complexes Matter

Protein complexes are fundamental functional units in cells that operate as groups of proteins that work together to carry out specific biological processes. Since 2019, SGD has provided detailed information about yeast protein complexes, including subunit composition, functions, interactions, and references. With this major redesign, we’ve made this critical information even more accessible and useful for researchers.

What’s New?

All Gene Ontology Information on One Page

One of the most significant improvements is the reorganization of Gene Ontology (GO) annotations. Previously, GO information was tucked away on a separate tab, requiring you to navigate away from the main view. Now, all GO annotations are prominently displayed right on the Summary page.

What you can see at a glance:

• Molecular Function: What the complex does
• Biological Process: What pathways or processes it participates in
• Cellular Component: Where in the cell it’s located

No more tab-switching—everything you need is in one place!

GO-CAM Pathway Models for Complexes

We’ve also integrated GO-CAM (Gene Ontology Causal Activity Models) pathway models directly into complex pages. When available, these models appear below the GO annotations, showing how entire protein complexes fit into larger biological pathways and regulatory networks. This provides a systems-level view that complements the detailed subunit information available on individual gene pages.

Enhanced Composition Section

The new Composition section is packed with detailed subunit information:

Stoichiometry Data: For complexes where the subunit ratios have been experimentally determined, you’ll now see the exact stoichiometry. This quantitative information is crucial for understanding complex architecture.

Structural Information:

• Expert-curated notes about complex assembly and structural features
• Direct links to Protein Data Bank (PDB) entries for complexes with experimentally determined 3D structures
• Protein-protein binding regions and interaction interfaces (when characterized)

Organized Display: Subunits are now grouped by their roles or relationships within the complex, making it easier to understand how the complex is organized.

Easy Navigation: Each subunit links directly to its SGD gene page, so you can quickly dive deeper into individual components.

Shared Biology Networks

Complex pages now include a Shared Biology section that shows:

• GO annotations shared with other complexes
• Subunits shared between complexes
• Ranked lists that prioritize the most functionally related complexes

The ranking system helps you quickly identify the most relevant relationships and potential functional connections, making it easier to understand how different complexes relate to each other.

Improved User Experience Throughout

Beyond these major features, we’ve focused on overall usability:

• Clearer section headers make information easy to find
• Better spacing and organization improve readability
• Consistent styling with other SGD page types provides a unified experience
• Logical information hierarchy puts the most commonly accessed data front and center

Try It Out!

Explore the new complex pages:

• Example: Sulfite reductase complex (NADPH)
• Browse all complexes: Search for complexes

We Want Your Feedback!

These improvements are based on feedback from the yeast research community, and we want to keep making SGD better. Have suggestions? Questions? Let us know at sgd-helpdesk@lists.stanford.edu.

Categories: Announcements, Website changes

Tags: Gene Ontology, GO annotations, GO-CAM, protein complexes, redesign, stoichiometry, UI, user experience, UX

Functional Networks: A New Way to Explore Gene Relationships at SGD

August 03, 2026

We’re excited to announce new Functional Networks sections on gene and complex pages! This powerful addition helps researchers understand how genes and proteins work together in biological systems.

What Are Functional Networks?

The new Functional Networks section appears on most gene page, positioned just below the Gene Ontology section. It provides two complementary views of how gene products interact and function together:

1. Shared Annotations Networks

Ever wondered which other genes might have similar functions to your gene of interest? The Shared Annotations network visualizes genes that share similar Gene Ontology (GO) annotations with your query gene. These networks are generated based on overlapping GO terms across Molecular Function, Biological Process, and Cellular Component.

Why is this useful?

• Identify potential interaction partners
• Find paralogs with related functions
• Discover genes that may participate in similar biological processes
• Generate hypotheses for experimental design

Most genes in the S. cerevisiae genome have sufficient GO annotations to generate these networks, providing broad coverage across the yeast proteome.

2. GO-CAM Pathway Models

GO-CAMs (Gene Ontology Causal Activity Models) represent an exciting advancement in pathway representation. Unlike traditional GO annotations that link individual genes to single terms, GO-CAMs show how multiple gene products work together in integrated pathway models.

What makes GO-CAMs special?

• Causal relationships: See how one molecular activity leads to another, including activation, inhibition, and regulatory interactions
• Integrated view: Combines Molecular Function, Biological Process, and Cellular Component information in one unified model
• Evidence-based: All models are manually curated by expert biologists and supported by published experimental data

Currently, 470 yeast genes are associated with GO-CAM models, and this number continues to grow as additional pathways are curated.

When multiple GO-CAM models are available for a gene, you can easily switch between them using a pull-down menu. Each model includes a “View GO-CAM at Gene Ontology” link that opens the interactive pathway in AmiGO, where you can explore detailed evidence codes, supporting references, and connections to other pathways.

Functional Networks on Complex Pages

We’ve also added a Shared Biology section to macromolecular complex pages. This section shows:

• GO annotations shared with other complexes
• Subunits shared between complexes
• A ranked list summarizing these relationships

This helps researchers understand how protein complexes relate to each other and identify functionally similar complexes.

How to Access

Simply navigate to any gene page at SGD and scroll to the Functional Networks section (located beneath Gene Ontology). For complex pages, look for the Shared Biology section.

Try it out:

• Example gene page: https://www.yeastgenome.org/locus/MET2
• Example complex page: https://www.yeastgenome.org/complex/CPX-3163

Part of a Bigger Picture

The GO-CAM display on SGD gene pages replicates the implementation from the Alliance of Genome Resources, providing a consistent user experience across model organism databases. This integration reflects our commitment to making yeast data accessible and interoperable with other genomic resources.

We Want Your Feedback!

This new feature is designed to help you explore gene relationships and generate hypotheses more effectively. We’d love to hear what you think! Contact us at sgd-helpdesk@lists.stanford.edu with your feedback or questions.

Categories: Announcements, Website changes

Tags: functional networks, gene annotation, GO-CAM, protein complexes, shared annotations

Explore the Redesigned SGD Search Landing Page

July 31, 2026

We’re excited to announce the redesign of SGD’s search landing page, making it easier than ever to find the yeast biological information you need!

What’s New?

Enhanced Search Experience The new landing page features an improved search box with smart autocomplete functionality that suggests genes, chemicals, pathways, and other entities as you type. This makes searching faster and helps you discover relevant results even if you’re not sure of the exact name.

Quick Category Browsing Need to browse rather than search? The new page includes quick access buttons for popular categories including genes, complexes, pathways, and chemicals. Click any category to start exploring without typing a single character.

Advanced Filtering Refine your search results by category or other criteria to quickly zero in on exactly what you’re looking for. The redesigned interface provides clearer visual organization with distinct sections for different data types.

Stay Current with SGD The right side of the page now highlights SGD’s latest activity:

• New Literature Added shows the most recently curated publications
• Recent Annotations displays the latest curated data, including new phenotypes, alleles, and GO annotations

This makes it easy to stay up-to-date with the newest information added to SGD.

How to Access

There are two easy ways to reach the new search landing page:

1. Click the red “Explore SGD” button on the SGD homepage
2. Press return/enter in the search box without typing anything (empty search)

Or go directly to: https://www.yeastgenome.org/search

We Want Your Feedback

These improvements are part of our ongoing commitment to making SGD more user-friendly and accessible. We’d love to hear what you think! Contact us at sgd-helpdesk@lists.stanford.edu with your feedback or suggestions.

Happy exploring!

Categories: Website changes

Tags: search, user interface, website redesign

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:

• Addgene Plasmids – Plasmid repository
• DNASU Plasmids – Plasmid resource collection
• LibrarYeast – Yeast strain and plasmid libraries

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.

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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
• Introducing BLAST Search for SGD at the Alliance of Genome Resources
• Textpresso Literature Search: New Login System
• Naming Your Newly Characterized Yeast Gene: A Guide to SGD Gene Nomenclature
• Alliance of Genome Resources News
• microPublications – Latest Yeast Papers
• Upcoming Conferences & Courses
• The End of PomBase?
• In Memoriam: David Botstein

Join Us at Yeast Genetics Meeting 2026

Introducing BLAST Search for SGD at the Alliance of Genome Resources

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

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

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

Alliance of Genome Resources News

Alliance of Genome Resources – Latest Releases 9.0.0 & 8.3.0

9.0.0 Release – May 13, 2026

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.
  • All “Cache Search” endpoints have been removed. See release notes for examples.
  • All “Homology” endpoints have been removed (homology data can be extracted from the Orthology file on the Downloads page and endpoints for gene/orthologs and gene/paralogs). See release notes for examples.
  • Other select endpoints have been removed, replaced by the updated endpoints. See release notes for examples.
  • Modified endpoints are now compliant with our LinkML data model and deliver a different JSON format from previous releases. 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 News page https://www.alliancegenome.org/news now includes a feed for the Alliance Mastodon account.

• The Alliance BLAST Service page https://www.alliancegenome.org/blastservice has been updated to include fly, worm, yeast, fungal, and rat BLAST services. This BLAST service allows researchers to search genomic sequences using the Basic Local Alignment Search Tool (BLAST). By entering a sequence or query, users can find regions of similarity to various genomes within the Alliance. This service supports separate environments for each of the Model Organism Databases (MODs) as well as a unified environment for the Alliance. Results provide detailed alignments and annotations to aid in your research.
• Gene page 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

​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

• Yeast Genetics Meeting 2026
  • June 13 to June 17, 2026 –
  • Asilomar Conference Grounds, Pacific Grove, CA
• Chromosome Biology and Cell States in Yeasts
  • July 27 to July 29, 2026 –
  • Niagara Falls Convention Center, Niagara Falls, NY
• 41st SMYTE Small Meeting on Yeast Transport and Energetics
  • September 12 to September 16, 2026 –
  • Chaves, Portugal
• 39th International Specialized Symposium on Yeasts (ISSY39)
  • November 08 to November 12, 2026 –
  • Seoul, South Korea

The End of PomBase?

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

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:

• 5′ UTRs: http://sgd-archive.yeastgenome.org/sequence/S288C_reference/SGD_all_ORFs_5prime_UTRs.fsa.zip
• 3′ UTRs: http://sgd-archive.yeastgenome.org/sequence/S288C_reference/SGD_all_ORFs_3prime_UTRs.fsa.zip

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.

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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.

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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

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