SGD Quarterly Newsletter, Summer 2011

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About this newsletter:

This is the Summer 2011 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 stay up-to-date on SGD news by following us on Twitter (@yeastgenome), liking us on Facebook (, or subscribing to our RSS feed:

Follow the CSHL Yeast Cell Biology Meeting on Twitter

Wish you were in Cold Spring Harbor Aug 16-20 for the Yeast Cell Biology meeting? SGD will be live tweeting from CSHL, highlighting topics from talks and posters. Keep up with events at the meeting by following @yeastgenome on Twitter or search for the #YCB2011 tag for all tweets!

New genome-wide high-throughput data tracks added to GBrowse and PBrowse

  • New data tracks in GBrowse genome viewer:
  1. Nucleosome occupancy and positioning (Kaplan et al., 2009, Field et al., 2008, Mavrich et al., 2008, Lee et al., 2007).
  2. ncRNAs and RNA secondary structures (Lardenois et al., 2011 and Kirmizis et al., 2010).
  3. Transcription factor and RNA Pol II occupancy (Venters et al., 2011 and Mayer et al., 2010).
  4. Histone acetylation and methlyation modifications (Guillemette et al., 2011, Kirmizis et al., 2007, Liu et al., 2005 and Pokholok et al., 2005).
  5. The mapping of histone variant H2A.Z (Albert et al., 2007 and Guillemette et al., 2005).
  • We have also added a data track to our PBrowse proteome browser, displaying mature N-termini of mitochondrial proteins as determined by Vögtle et al., 2009.
  • We can help promote your work by releasing new datasets on the day of publication. New datasets can be integrated on our genome browser or other appropriate pages. Watch for the regular addition of new tracks to SGD's GBrowse and PBrowse in the future! Please contact us if you are interested in working with us, or have questions and comments.

New resource link

Links to InterologFinder have been added to the "Interactions" pull-down menu on SGD Locus Summary pages. InterologFinder can be used to retrieve both known protein-protein interactions and those predicted based on the interactions of orthologous proteins in other organisms. For more information, see Wiles et al., 2010. Thanks to Mark Doderer and Alex Bishop for help in setting up these links.

Textpresso now includes papers published in 2011

The SGD full-text literature search (powered by Textpresso) has been upgraded and updated to include a total of 58,000 papers. Textpresso now provides the ability to focus your search on a subset of PMIDs as well as limit the results to a specific section of a paper. The full-text literature search can be accessed via the Full-text Search link on the home page.

Upcoming Conferences and Meetings

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

  • Yeast Cell Biology*
Cold Spring Harbor Labs, CSH, NY
August 16-20, 2011
  • Mechanisms of Eukaryotic Transcription*
Cold Spring Harbor Labs, CSH, NY
August 30-September 3, 2011
  • Genomics of Common Diseases
EBI, Hinxton, UK
August 30-September 3, 2011
  • HUPO 2011: 10th World Congress
Human Proteome Organization, Geneva
September 4-7, 2011
  • Beyond the Genome 2011
BioMed Central, Washington, DC
September 19-22, 2011
  • Structure and Function of Protein Networks
EMBO-EMBL, Heidelberg, Germany
October 13-16, 2011
  • Comparative genomics of eukaryotic microorganisms: understanding the complexity of diversity
Sant Feliux, Spain
October 15-20, 2011
  • 1st IEEE Symposium on Biological Data Visualization
IEEE, Providence, RI
October 23-26, 2011
  • Genome Informatics*
Cold Spring Harbor Labs, CSH, NY
November 2-5, 2011
  • Next Generation Sequencing Congress
Oxford Global Conferences, London
November 14-15, 2011
  • Functional Genomics and System Biology*
EBI, Hinxton, UK
November 29-December 1, 2011
  • Fifth International Biocuration Conference]
Georgetown University Conference Center, Washington D.C.
April 2-4, 2012

asterisks indicate attendance by SGD.*

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