SGD Quarterly Newsletter, Spring 2011

About this newsletter:

This is the Spring 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 subscribe to SGD's RSS feed to receive updates on SGD news: http://www.yeastgenome.org/feed

New Expression Analysis Tool and Datasets

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).

Expanding the View of the Functional Budding Yeast Genome

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.

25th International Conference on Yeast Genetics and Molecular Biology, Olsztyn, Poland

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. SGD is having a workshop on July 12 at 7:30 PM; come learn about new tools and data at SGD.

Visit the conference website to get more information and to register: http://www.yeast-2011.org/

SGD's Advanced Search Tool to be Retired

Searching for details of the yeast genome or annotations recently became much more powerful with the release of YeastMine, SGD's new search tool. YeastMine replaces all of the features provided by our classic tool called "Advanced Search" as well as allowing for more flexible queries of more data. As a result we will retire "Advanced Search" in the near future.

Find out more information about YeastMine or just try it out at: http://yeastmine.yeastgenome.org

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 4 features. Genes with new summary paragraphs are reported weekly on SGD's What's New page.

Upcoming Conferences and Meetings

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

SGD will be in attendance at those meetings marked with a *. Come find us with any questions you might have, learn about our new features and tools, or just say hi! Pick up an SGD coaster while you're at it.

• Bay Area Yeast and Other Fungi Symposium*

University of California San Francisco, San Francisco, CA

May 7, 2011

• Telomeres & Telomerase

Cold Spring Harbor Labs, CSH, NY

May 3-7, 2011

• Omics Meets Cell Biology

Keystone Symposia, Alpbach, Austria

May 8-13, 2011

• The Biology of Genomes

Cold Spring Harbor Labs, CSH, NY

May 10-14, 2011

• 10th Yeast Lipid Conference

University of Oulu, Oulu, Finland

May 26-28, 2011

• International C. elegans Meeting (GSA)

UCLA, Los Angeles, CA

June 22-26, 2011

• 25th International Conference on Yeast Genetics and Molecular Biology*

Olsztyn, Poland

July 11-16, 2011

• Society for Industrial Microbiology 61st Annual Meeting*

New Orleans, LA

July 24-28, 2011

• International Conference on Intelligent Systems for Molecular Biology (ISMB)*

Vienna, Austria

July 15-19, 2011

• 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

• Comparative genomics of eukaryotic microorganisms: understanding the complexity of diversity

Sant Feliux, Spain

October 15-20, 2011

• Genome Informatics*

Cold Spring Harbor Labs, CSH, NY

November 2-5, 2011

• Functional Genomics and System Biology*

EBI, Hinxton, UK

November 29-December 1, 2011

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