SGD Quarterly Newsletter, Winter 2009

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About this newsletter:

This is the February 2009 issue of the quarterly 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. You can also subscribe to SGD's RSS feed to receive updates on SGD news -

SGD links to new external resources

  • Links to the UniPROBE database, which displays DNA binding specificities of known and predicted transcription factors, have been added to the "Interactions" and "Functional Analysis" pull-down menus on the Locus Summary pages of 89 known and predicted S. cerevisiae transcription factors described in Zhu et al. Genome Res. 2009 (PMID: 19158363). Also see Newburger and Bulyk, Nucleic Acids Res. 2009 (PMID: 18842628) for more information about the UniPROBE database. Thanks to Kimberly Robasky and Martha Bulyk for helping set up these links.
  • Links to the CYC2008 (Curated Yeast Complexes 2008) resource, a manually curated catalog of S. cerevisiae protein complexes, have been added to the "Interactions" pull-down menu on the Locus Summary page and to the Protein Info pages. See Pu et al. Nucleic Acids Res. 2008 (PMID: 19095691) for more information. Thanks to Shuye Pu and Shoshana Wodak for helping set up these links.
  • Links to the PhosphoPep database, which contains MS-derived phosphorylation data for the proteins of four model organisms including S. cerevisiae, have been added to the "Protein Info & Structure" pull-down menu on the Locus Summary page and to the Protein Info pages. See Bodenmiller et al. Nat Biotechnol. 2008 (PMID: 19060867) for more information. Thanks to Bernd Bodenmiller and Dave Campbell for help in setting up the links.
  • Links to the PlasmID repository, which distributes over 5,200 fully sequence-verified S. cerevisiae genes in Gateway entry and expression vectors, have been added to the External Links section of Phenotype Details pages for individual genes in SGD. The PlasmID repository is part of the DF/HCC DNA Resource Core at the Harvard Institute of Proteomics at Harvard Medical School. Thanks to Catherine Cormier for informing SGD about this resource.

Curation Focus: Ribosomal Small Subunit RPS Genes

Ribosomes are highly conserved ribonucleoprotein (RNP) particles, consisting of a large 60S subunit and a small 40S subunit, that perform protein synthesis. As part of the GO Consortium's Reference Genome Project, GO annotations in SGD for 56 genes encoding the 32 proteins that are part of the ribosomal small 40S subunit have been recently reviewed and updated. Thanks to Jonathan Warner of Albert Einstein College of Medicine for his input.

Update your bookmarks: new URLs at SGD

We have migrated the SGD web site to new computers. This upgrade greatly improved the speed of displaying our Locus Summary pages but required many of the SGD URLs to be changed. Please update your bookmarks to SGD. If you are experiencing any problems accessing SGD, please contact us.

New Gene Summary Paragraphs

Summary Paragraphs summarize published biological information for a gene/feature, and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the last quarter new summary paragraphs have been added to their respective Locus Summary pages for 5 features. Genes with new summary paragraphs are reported weekly on SGD's 'What's New in 2008' page:

Upcoming Conferences and Meetings

Information on registration and abstract deadlines for the following conferences is available at:

  • Boston Area Yeast Meeting
Cambridge, MA
Every third Thursday of the month
  • British Yeast Group Meeting 2009
Cardiff University, Cardiff, UK
March 17 - 19, 2009
  • XXIV International Conference on Yeast Genetics and Molecular Biology
University of Manchester
Manchester, United Kingdom
July 19 - 24, 2009
  • Yeast Cell Biology
Cold Spring Harbor Laboratory
August 11 - 15, 2009
Abstract Deadline: May 22, 2009
  • 27th International Specialized Symposium on Yeasts (ISSY)
Pasteur's legacy: Yeasts for health and biotechnologies
Institut Pasteur, Paris, France
August 26 - 29, 2009
  • EMBO Conference on Comparative Genomics of Eukaryotic Microorganisms
San Feliu de Guixols, Spain
October 17-22, 2009

asterisks indicate attendance by SGD.*

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