Difference between revisions of "SGD Newsletter, December 2015"
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<br><br>We recently added a new tool to SGD called the [http://www.yeastgenome.org/variant-viewer Variant Viewer]. You can use the Variant Viewer to compare the nucleotide and protein sequences of your favorite genes in twelve widely-used Saccharomyces cerevisiae genomes. This tool uses sequence data derived from SGD publication [http://www.yeastgenome.org/reference/S000179596/overview Song et al., 2015] to show alignments, similarity scores, and sequence variants for open reading frames (ORFs) from the different strains relative to the S288C reference genome. | <br><br>We recently added a new tool to SGD called the [http://www.yeastgenome.org/variant-viewer Variant Viewer]. You can use the Variant Viewer to compare the nucleotide and protein sequences of your favorite genes in twelve widely-used Saccharomyces cerevisiae genomes. This tool uses sequence data derived from SGD publication [http://www.yeastgenome.org/reference/S000179596/overview Song et al., 2015] to show alignments, similarity scores, and sequence variants for open reading frames (ORFs) from the different strains relative to the S288C reference genome. | ||
| − | To get started with the Variant Viewer check out our [https://www.youtube.com/watch?v=Q_DooZIUzxk tutorial video]. You can also read more about it in recent SGD paper [http://www.yeastgenome.org/reference/S000182068/overview Sheppard et al., 2015]. | + | To get started with the Variant Viewer check out our [https://www.youtube.com/watch?v=Q_DooZIUzxk tutorial video]. You can also read more about it in this recent SGD paper [http://www.yeastgenome.org/reference/S000182068/overview Sheppard et al., 2015]. |
==SGD’s 60-second Help Videos== | ==SGD’s 60-second Help Videos== | ||
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*[http://www.yeastgenome.org/yeast-on-their-best-behavior Yeast on Their Best Behavior] Just like you might change your behavior around friends and family this holiday season, [http://www.yeastgenome.org/reference/26510787/overview Piccirillo and coworkers] show that yeast also behaves differently because of the cells around them. | *[http://www.yeastgenome.org/yeast-on-their-best-behavior Yeast on Their Best Behavior] Just like you might change your behavior around friends and family this holiday season, [http://www.yeastgenome.org/reference/26510787/overview Piccirillo and coworkers] show that yeast also behaves differently because of the cells around them. | ||
| − | *[http://www.yeastgenome.org/yeast-the-spam-filter Yeast, the | + | *[http://www.yeastgenome.org/yeast-the-spam-filter Yeast, the Spam Filter] Turns out yeast can act as a pretty good spam filter. [http://www.yeastgenome.org/reference/S000181430/overview Hamza and colleagues] put it to the test when they systematically screened for human genes that can replace their yeast equivalents, and went on to test the function of tumor-specific variants in several selected genes that maintain chromosome stability in ''S. cerevisiae''. |
*[http://www.yeastgenome.org/life-needs-to-be-more-like-a-1950s-chevy Life Needs to be More Like a 1950’s Chevy] Modern cars have a lot more bells and whistles than their older counterparts, but they just don’t seem to last as long! [http://www.yeastgenome.org/reference/S000181747/overview McCormick and coworkers] showed a similar concept in their painstaking search through deletion strains were they found that many nonessential genes seem to shorten a yeast’s life. | *[http://www.yeastgenome.org/life-needs-to-be-more-like-a-1950s-chevy Life Needs to be More Like a 1950’s Chevy] Modern cars have a lot more bells and whistles than their older counterparts, but they just don’t seem to last as long! [http://www.yeastgenome.org/reference/S000181747/overview McCormick and coworkers] showed a similar concept in their painstaking search through deletion strains were they found that many nonessential genes seem to shorten a yeast’s life. | ||
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In addition to at the International Conference on Yeast Genetics and Molecular Biology, you may have seen SGD representatives at the following meetings: | In addition to at the International Conference on Yeast Genetics and Molecular Biology, you may have seen SGD representatives at the following meetings: | ||
[[File:SuperYeast.jpg|thumb|left|upright=.75]] | [[File:SuperYeast.jpg|thumb|left|upright=.75]] | ||
| − | + | <br> | |
| − | *Senior | + | *Senior biocuration scientist Edith Wong attended the annual [http://www.ascb.org/future-ascb-annual-meetings/ ASCB] meeting in December 2015. |
| − | *Senior | + | *Senior biocuration scientists Marek Skrzypek and Maria Costanzo showcased SGD at the [https://meetings.cshl.edu/meetings.aspx?meet=yeast&year=15 Cell Biology of Yeasts] meeting in November at Cold Spring Harbor. |
*Project Manager Gail Binkley attended the [https://meetings.cshl.edu/meetings.aspx?meet=info&year=15 Genome Informatics] meeting in October at Cold Spring Harbor. | *Project Manager Gail Binkley attended the [https://meetings.cshl.edu/meetings.aspx?meet=info&year=15 Genome Informatics] meeting in October at Cold Spring Harbor. | ||
| − | *Senior | + | *Senior biocuration scientist Rama Balakrishnan and PI Mike Cherry attended the [http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Meeting_Agenda GO Consortium] meeting in Washington DC at the end of August. |
| + | <br> | ||
==Happy Holidays from SGD!== | ==Happy Holidays from SGD!== | ||
[[File:Snowflake_01.png|thumb|left|upright=.4]]<br> | [[File:Snowflake_01.png|thumb|left|upright=.4]]<br> | ||
| − | We want to take this opportunity to wish you and your family, friends and lab mates the best during the upcoming holidays. | + | We want to take this opportunity to wish you and your family, friends and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting on December 21st, reopening on January 4th, 2016. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will attempt to keep connected via email should you have any questions. |
| + | <br><br> | ||
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==Upcoming Meetings== | ==Upcoming Meetings== | ||
Latest revision as of 13:16, 18 December 2015
About this newsletter:
This is the December 2015 issue of the 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
Contents
- 1 Variant Viewer Now Available at SGD
- 2 SGD’s 60-second Help Videos
- 3 Research Spotlight (Blog Posts)
- 4 SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)
- 5 Recent Publications from SGD Staff
- 6 What else have we been up to lately?
- 7 Happy Holidays from SGD!
- 8 Upcoming Meetings
Variant Viewer Now Available at SGD
We recently added a new tool to SGD called the Variant Viewer. You can use the Variant Viewer to compare the nucleotide and protein sequences of your favorite genes in twelve widely-used Saccharomyces cerevisiae genomes. This tool uses sequence data derived from SGD publication Song et al., 2015 to show alignments, similarity scores, and sequence variants for open reading frames (ORFs) from the different strains relative to the S288C reference genome.
To get started with the Variant Viewer check out our tutorial video. You can also read more about it in this recent SGD paper Sheppard et al., 2015.
SGD’s 60-second Help Videos
SGD is actively expanding its library of short video tutorials to help you use various SGD tools and pages. Check out the latest new videos available for the following topics:
Videos are accessible via the SGD Video Tutorials page and through SGD's YouTube channel. If you have a great idea for a 60-second SGD help video, or would like to see a particular topic covered, feel free to contact us!
Research Spotlight (Blog Posts)
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:
- Yeast on Their Best Behavior Just like you might change your behavior around friends and family this holiday season, Piccirillo and coworkers show that yeast also behaves differently because of the cells around them.
- Yeast, the Spam Filter Turns out yeast can act as a pretty good spam filter. Hamza and colleagues put it to the test when they systematically screened for human genes that can replace their yeast equivalents, and went on to test the function of tumor-specific variants in several selected genes that maintain chromosome stability in S. cerevisiae.
- Life Needs to be More Like a 1950’s Chevy Modern cars have a lot more bells and whistles than their older counterparts, but they just don’t seem to last as long! McCormick and coworkers showed a similar concept in their painstaking search through deletion strains were they found that many nonessential genes seem to shorten a yeast’s life.
- You Can Take Yeast Off of the Grapevine, But… Rossouw and colleagues show the importance of looking beyond lab isolation to get clues into the evolution of gene families.
- Unleashing the Awesome Power of Yeast Transcription In today’s age of social media, communicating across large distances is much easier than it used to be. Reavey and coworkers showed in a study that they can help yeast keep up with the times and mutate away it’s inability to activate transcription at a distance.
SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)
In September 2015 members of the SGD staff attended the 27th International Conference on Yeast Genetics and Molecular Biology in Levico Terme, Trento, Italy. Several of our members presented posters on various current SGD projects:
In addition to hosting an exhibit table where we got to interact with many of you, we were thrilled to have been given the opportunity to give an SGD workshop, Getting More Out of SGD, on the first day of the conference. The workshop featured exciting new data developments at SGD including new yeast-human functional complementation data, the new variant viewer, and new data in YeastMine. Your feedback is important to us, so we loved answering questions and hearing your comments at this well-attended workshop!
If you would like to see tweets from the conference, search #yeast2015 on Twitter.
Recent Publications from SGD Staff
- Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015). The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Research. 2015 Nov 17; pii: gkv1250. doi: 10.1093/nar/gkv1250. PMID: 26578556
- Reid BJ, Culotti JG, Nash RS, Pringle JR (2015). Forty-five years of cell-cycle genetics. Mol Biol Cell. 2015 Dec 1;26(24):4307-12. doi: 10.1091/mbc.E14-10-1484. PMID: 26628751
What else have we been up to lately?
In addition to at the International Conference on Yeast Genetics and Molecular Biology, you may have seen SGD representatives at the following meetings:
- Senior biocuration scientist Edith Wong attended the annual ASCB meeting in December 2015.
- Senior biocuration scientists Marek Skrzypek and Maria Costanzo showcased SGD at the Cell Biology of Yeasts meeting in November at Cold Spring Harbor.
- Project Manager Gail Binkley attended the Genome Informatics meeting in October at Cold Spring Harbor.
- Senior biocuration scientist Rama Balakrishnan and PI Mike Cherry attended the GO Consortium meeting in Washington DC at the end of August.
Happy Holidays from SGD!
We want to take this opportunity to wish you and your family, friends and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting on December 21st, reopening on January 4th, 2016. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will attempt to keep connected via email should you have any questions.
Upcoming Meetings
- Colorado State University, Fort Collins CO, USA
- January 8, 2016
- Registration deadline extended: December 28, 2015
- Sant Feliu de Guixols, Spain
- June 11-16, 2016
- Lisbon, Portugal
- July 11-14, 2016
- Orlando, FL, USA
- July 13-17, 2016
- Abstract deadline: March 23, 2016
- Early registration deadline: March 23, 2016
- Awaji Yumebutai International Conference Center, Hyogo, Japan
- September 11-15, 2016
