August 09, 2011
Wish you were in Cold Spring Harbor for the Yeast Cell Biology meeting, Aug 16-20? 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 searching #YCB2011 for all tweets!
Categories: Conferences
August 05, 2011
We have added new data tracks to our GBrowse genome viewer from six publications covering various histone acetylation and methlyation modifications (Guillemette et al. 2011; Kirmizis et al. 2007; Liu et al. 2005 and Pokholok et al. 2005) and the mapping of histone variant H2A.Z (Albert et al. 2007 and Guillemette et al. 2005). We welcome new data submissions pre- or post-publication and invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers. Please contact us if you are interested in participating or have questions and comments.
Categories: New Data
July 12, 2011
Wish you were in Poland for the 25th International Conference on Yeast Genetics and Molecular Biology? SGD is live tweeting from the Poland meeting, highlighting topics from talks and workshops. Keep up with events at the meeting by following @yeastgenome on Twitter or searching #ICYGMB for all tweets!
Categories: Conferences
June 21, 2011
The SGD full-text literature search (powered by Textpresso) has been upgraded and updated to include 58,000 papers. Textpresso now includes the ability to restrict your searches to 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. Thanks to Arun Rangarajan and Hans-Michael Muller from Wormbase for their help upgrading the software.
Categories: Data updates
June 09, 2011
We’ve added new data tracks to our GBrowse genome viewer from eight publications, including recent surveys of nucleosome occupancy and positioning (Kaplan et al., 2009; Field et al., 2008; Mavrich et al., 2008; Lee et al., 2007); ncRNAs and RNA secondary structures (Lardenois et al., 2011 and Kertesz et al., 2010); and transcription factor and RNA Pol II occupancy (Venters et al., 2011 and Mayer et al., 2010). 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. Both GBrowse and PBrowse have been upgraded to the most recent software with several new features.
We invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers pre- and/or post-publication as we move forward. 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 participating or have questions and comments.
Categories: Data updates, New Data
May 05, 2011
SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. This Spring 2011 newsletter is also available online. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter
May 03, 2011
Registration is open for the 25th International Conference on Yeast Genetics and Molecular Biology. The meeting will take place on July 11-16 in Olsztyn-Kortowo, Poland. Visit the conference website to get more information and to register. SGD is having a workshop on July 12 at 7:30 PM; come learn about new tools and data at SGD.
Categories: Conferences
February 25, 2011
In an effort to provide a comprehensive view of all of the sequence-based functional elements in the Saccharomyces cerevisiae genome, SGD will collect sequence-based functional feature annotations from published datasets, aimed at charting the yeast transcriptome (e.g. protein-coding genes, non-coding RNAs), chromatin landscapes (e.g. nucleosome phasing, histone modifications and variations), as well as cataloging regulatory sequence elements (e.g. transcription factor binding sites, splicing signals) and more.
We have upgraded our GBrowse genome viewer to allow users to quickly and easily browse this information-rich view of the yeast genome. In addition, 17 new data tracks have been added, including recent surveys of the budding yeast transcriptome (Nagalakshmi et al. 2008; Xu et al. 2009; Yassour et al. 2009) and catalogs of regions favored for recombination and replication events (Mancera et al. 2008; Buhler et al. 2007; Xu et al. 2006; Eaton et al. 2010). We invite authors to work with us to integrate their data into our GBrowse viewer pre- and/or post-publication as we move forward. Watch for the regular addition of new tracks to SGD’s GBrowse in the future! Please contact us if you are interested in participating or have questions and comments.
Categories: New Data
February 23, 2011
Expression analysis at SGD has a new powerful interface and many new datasets. The new interface uses a tool called SPELL (Serial Pattern of Expression Levels Locator). This analysis tool facilitates the rapid identification of the most informative datasets and co-expressed genes based on patterns of expression shared with the query gene(s). By transitioning to this tool, expression data from a comprehensive collection of almost 400 datasets are now available at SGD. The expression analysis tool can be accessed via the expression tab, the expression summary histogram, and in the functional analysis pulldown located on Locus Summary pages. These new data and the SPELL interface have been provided through a collaboration with the SGD Colony at Princeton University. Thanks to Peter Koppstein, Lance Parsons, and Kara Dolinski for help with data preparation and implementation of SPELL at SGD. SPELL was developed by the Troyanskaya lab at Princeton University (Hibbs et al. (2007) Bioinformatics 23:2692).
Categories: Data updates, Website changes
February 18, 2011
SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. This Winter 2010 newsletter is also available online. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter