New & Noteworthy

Protein Complex Page Updates

December 01, 2021

SGD has updated our protein complex pages to have the same format as gene pages, with tabs across the top for each category of information, including a Summary page, a new Gene Ontology page, and a new Literature page for each complex. Just as we do for all of your favorite genes, Gene Ontology and Literature curation for complexes will be ongoing.

Summary page and new Literature page

If you have any questions or feedback about the updates to our complex pages, please do not hesitate to contact us at any time.

Categories: Website changes, Announcements, Data updates

Tags: protein complex, Saccharomyces cerevisiae

Updates to legacy gene names

November 05, 2021

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

The accepted format for gene names in S. cerevisiae comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the “Name Description” in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example “ADE” for “ADEnine biosynthesis” or “CDC” for “Cell Division Cycle”. Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an ORF, a tRNA, another type of non-coding RNA, an ARS, or a genetic locus. Some S. cerevisiae gene names that pre-date the current nomenclature standards do not conform to this format, such as MRLP38RPL1A, and OM45

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

ORFOld gene nameNew gene name
YGL234WADE5,7ADE57
YER069WARG5,6ARG56
YBR208CDUR1,2DUR12
YIL154CIMP2′IMP21

Categories: Announcements, Data updates

Tags: gene nomenclature

BREWMOR Workshop: Preparing Undergraduate Students for Research Experiences

February 03, 2021

BREWMOR: Bridging Research and Education With Model ORganisms (formerly BREW) will be hosting a virtual workshop titled, “Preparing Undergraduate Students for Research Experiences,” on Friday February 19th, 2021 from 4 – 6:30 PM US Eastern time.

After a very successful virtual BREW (Bridging Research and Education Workshop) in July of 2020 as part of the TAGC meeting, a steering committee was formed to coordinate activities of the BREW community. The name of the community was changed to BREWMOR: Bridging Research and Education With Model ORganisms, to include model organisms beyond yeast. 

A micro-BREWMOR event that will be held virtually on Friday February 19th, 2021 from 4-6:30 PM US Eastern time. The main purpose of the event is to provide a forum for social interactions and building a community for support and resource sharing.  The theme of this micro-BREWMOR will be “Preparing Undergraduate Students for Research Experiences”. The workshop will include a session related to the event’s main theme and opportunities to connect and collaborate with other undergraduate research mentors and teachers in multiple small breakout rooms focused on various topics.

Please register by February 8th at https://forms.gle/fdBCFxYjWuY38tSG6 . Registration is free. 

We hope you can join us at the micro-BREWMOR!

https://brewmor.weebly.com/gatherings.html

Categories: Announcements

Apply Now for the 2021 Fungal Pathogen Genomics (Virtual) Course

January 21, 2021

Fungal Pathogen Genomics is an exciting several day long course that provides experimental biologists working on fungal organisms with hands-on experience in genomic-scale data analysis. Through a collaborative teaching effort between the web-based fungal data mining resources FungiDB, EnsemblFungi, PomBase, SGD, CGD, MycoCosm, and JGI, students will learn how to utilize the unique tools provided by each database, develop testable hypotheses, and analyze various ‘omics’ datasets across multiple databases.

Please note: Due to the ongoing Covid-19 pandemic, the 2021 Fungal Pathogen Genomics course will be delivered in a virtual format.

Daily activities will include individual and group training exercises, supplementary lectures on bioinformatics techniques and tools used by various databases, and presentations by distinguished guest speakers covering the following topics:

  • Comparative genomics, gene trees, whole-genome alignment
  • Identification of orthologs and orthology-based inference
  • Genome browsers and gene pages
  • RNA-Seq analysis and visualization in VEuPathDB Galaxy
  • Variant calling analysis and Ensembl Variant Effect Predictor (VEP) tool
  • Development of advanced biologically relevant queries using FungiDB ‘search strategies’ and mining integrated datasets (proteomics, transcriptomics, phenotypes, etc.)
  • Genetic interactions, virulence genes, secondary metabolites
  • Overview of ontology structure, evidence, available tools, slimming and enrichment
  • Introduction to annotation and curation of fungal genomes (e.g. Apollo in EnsemblFungi, FungiDB, and MycoCosm/JGI)

The application deadline for the Fungal Pathogen Genomics workshop to be held May 10-14, 2021 in virtual format is February 18, 2021.

Don’t miss out – apply now!

Categories: Announcements

Interactions Page Updates

November 06, 2020

SGD has made recent updates to our Gene Interactions Page for improved clarity. Previously, genetic and physical interaction annotations were combined in one table, but now these annotations are recorded in separate annotation tables. The menu in the top left corner can be used to view and navigate to each section of the Interactions page.

Additionally, alleles, SGA Scores, and P-values are now included for annotations from the global interactions paper by Costanzo M, et al. (2016).

Please be sure to watch our Interactions Page Updates tutorial video for a quick walk-through of the changes:

If you have any questions or feedback about the updates to our Interactions Pages, please do not hesitate to contact us at any time.

Categories: Announcements, Data updates

Announcement from Jeremy Thorner

October 27, 2020

NOTICE:  After 47 years at the University of California, Berkeley, the laboratory of Professor Jeremy Thorner will be closing permanently, as of 30 June 2021.  After that date, there will be no way to distribute any strains, plasmids, enzymes, or antibodies generated during the course of the studies on Saccharomyces cerevisiae conducted by the Thorner laboratory over those many years.

Categories: Announcements

26th Anniversary of SGD Website

May 13, 2020


Happy Birthday to Us!  May 8, 2020 marked the 26th anniversary of the day the SGD website first went live, bringing yeast genome information to all!  In May 1994, the “World Wide Web” had only been in existence for about 22 months, but starting way back then, anyone (especially yeast researchers!) could easily access the “SacchDB” database from our old server “genome-www.stanford.edu” to find information on our favorite model organism, the budding yeast.  We’ve grown a lot since then, and have even migrated to the cloud!  But as always, we’d like to express our gratitude to all of our users, collaborators, advisors, staff, and anyone else who has supported SGD over the last 26 years.  Without such a great community behind us, SGD would not be the fantastic resource it is today.

The SGD Team zoomed in to celebrate the anniversary with cupcakes and fuzzy budders:

Screen Shot 2020-05-13 at 5.01.28 PM

“26 years and still your best bud!” #APOYG!

Categories: Announcements

Submit Data to SGD

April 15, 2020

Help SGD annotate your paper by pointing us to your novel results, datasets, or other important information! Authors can submit their own data for their publications using SGD’s simple submit data form.

Be sure to contact us if you have any questions or feedback!

Categories: Announcements

Apply Now for the 2019 Yeast Genetics and Genomics Course

March 05, 2019

yeast_course_panorama

For almost 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory. (OK, 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 1st, so don’t miss your chance! Find all the details and application form here. This year’s instructors – Grant Brown, Greg Lang, and Elçin Ünal – have designed a course (July 23 – 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:

  • Finding and Analyzing Yeast Information Using SGD
  • Isolation and Characterization of Mutants
  • Yeast Transformation, Gene Replacement by PCR, and Construction and Analysis of Gene Fusions
  • Tetrad Analysis
  • Genome-scale Screens Using Synthetic Genetic Array (SGA) Methodology    
  • Deep Sequencing Applied to SNP Mapping and Deep Mutational Scanning
  • Exploring Synthetic Biology with CRISPR/Cas9-directed Engineering of Biosynthetic Pathways
  • Computational Methods for Data Analysis
  • Modern Cytological Approaches Including Epitope Tagging and Imaging Yeast Cells Using Fluorescence Microscopy

Techniques have been summarized in a completely updated course manual, which was recently 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).

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. Significant stipends (in the 30-50% range of total fees) are available to individuals expressing a need for financial support and who are selected into the course.

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 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: Announcements

New Protein Localization Resource: YeastRGB

November 14, 2018


yeastRGB

Multiple display units in YeastRGB

YeastRGB is a new resource for exploring protein abundance and localization. Utilizing data from the classical C-terminally tagged GFP yeast library along with new-generation collections derived from SWAp Tag (SWAT) technology, YeastRGB enables simultaneous visualization of dozens of yeast strains imaged with multiple fluorescent tags.

From SGD, you can access YeastRGB through any Protein page (example: Atp12p). The YeastRGB link is located in the Resources section, under Localization. Alternatively, you can visit the YeastRGB website and search for your favorite genes or keywords.

For more information on YeastRGB, see the publication by Dubreuil et al. at Nucleic Acids Research: https://doi.org/10.1093/nar/gky941

Categories: Announcements

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