SGD Newsletter, December 2016 - Revision history

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2016-12-20T16:32:45Z

‎New JBrowse Tracks

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2016-12-20T16:32:20Z

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2016-12-20T16:31:55Z

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2016-12-20T16:31:41Z

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Stacia: /* New Protein Half-life Data */

2016-12-19T18:13:37Z

‎New Protein Half-life Data

Stacia: /* New JBrowse Tracks */

2016-12-19T18:13:09Z

‎New JBrowse Tracks

Sage: Created page with "Category:Newsletter '''About this newsletter:'''
This is the December 2016 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new ..."

2016-12-19T17:51:47Z

Created page with "Category:Newsletter '''About this newsletter:''' This is the December 2016 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new ..."

New page

[[Category:Newsletter]]
'''About this newsletter:''' 

This is the December 2016 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.

==New Phenotype Data==
[[File:Mulleder_phenotype.png|700px|link=http://www.yeastgenome.org/locus/S000003736/phenotype#annotations]]
 
4217 new phenotypes for 1520 genes have been added to SGD from [http://yeastgenome.org/reference/S000185113/overview Mülleder et al]. They determined the free amino acid concentration profiles of null mutants from the systematic knockout set in S288C to see which genes have similar profiles. In addition to adding these phenotypes, we've also added links on the Phenotype pages to the Metabolic Gene Card for each ORF that has a profile. For example, [http://yeastgenome.org/locus/S000003736/phenotype#overview ACO2/YJL200C] has increased arginine, tyrosine and alanine accumulation and decreased proline and lysine accumulation (see above image). These are all found within the table on the Phenotype page. The [http://ralser.sysbiol.cam.ac.uk/metabogenecards/Chr_10/YJL200C.html MetaboGeneCard] link in the "Resources" section will show other genes with similar profiles.

Thank you to Michael Mülleder for his help in preparing this large dataset.
 

==New JBrowse Tracks==
[[File:JBrowse.png|link=http://www.yeastgenome.org/browse/?loc=chrI%3A1..230218&tracks=DNA%2CAll%20Annotated%20Sequence%20Features%2CHop1-ChIP-seq%2CRec8-ChIP-seq%2CRed1-ChIP-seq%2CSmc3-ChIP-seq%2COstrow_2014_FKH1_FKH2_binding_sites&highlight=| thumb|left|upright=1]]
 
New tracks have been added to SGD's instance of [http://www.yeastgenome.org/browse/ JBrowse]. [http://yeastgenome.org/reference/S000156933/overview Ostrow et al's] genome-wide study of Fkh1p and Fkh2p chromatin binding sites is now available in JBrowse. [http://yeastgenome.org/reference/S000181164/overview Sun et al's] genome-wide study of axis protein binding to chromosomes is now also available for visualization on JBrowse. All track files are available for download in the [http://www.yeastgenome.org/download-data/published-datasets Published Datasets] directory of our downloads site.

We keep adding new tracks to JBrowse for visualization. Please let us know of any publicly available datasets that you think should be added!
 

==New Protein Half-life Data==
[[File:Protein_Half_Life.png|700px|link=http://www.yeastgenome.org/locus/S000001388/protein]]
 
Protein half-life data is now available in the "Experimental Data" section of our protein tab pages (see example above from STH1 protein tab). The protein half-life data is based on data from a study by [http://www.yeastgenome.org/reference/S000178561/overview Christiano et al. (2014)]. Additionally, this half-life data can also be retrieved using YeastMine templates '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Protein_Half_Life&scope=all Gene-->Protein Half-life]''' and '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinHalfLife_Range&scope=all Retrieve-->Proteins with half-life in a given range]''' . Both of the [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] half-life templates are accessible from the “templates” section under the “protein” category.

==SGD Webinar Series==
[[File:SGDwebinars-redbud.png|175px|link=http://wiki.yeastgenome.org/index.php/SGD_Webinar_Series]]

SGD is hosting webinars to help you, our users, learn more about useful SGD tools, see expanded research examples, and ask SGD biocuration scientists questions live. The latest webinar in our webinar series was on December 14, 2016 and discussed how to use SGD to find human/yeast homologs and their disease implications. If you are interested in this topic, but were unable to attend the webinar, watch the recorded version [https://www.youtube.com/watch?v=PI-nuN8uLdI here]!

To read about and register for SGD's latest webinars, or to browse the videos and materials of past webinars, visit our [http://wiki.yeastgenome.org/index.php/SGD_Webinar_Series SGD Webinars] page.

Check out our latest recorded webinars:
*[https://www.youtube.com/watch?v=PI-nuN8uLdI SGD Webinars: Homology and Disease Data at SGD]
*[https://www.youtube.com/watch?v=NAUOx1BxmJ8 SGD Webinars: Exploring Expression Datasets & Coexpressed Genes with SPELL]

==SGD Help Videos==
[[File:SGD-on-youtube-words.png|link=https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg |thumb|left|upright=.9|Subscribe to the SGD YouTube channel!]]
 
SGD is actively expanding our library of short video tutorials to help you use various SGD tools and pages. Check out our latest help videos:
 
*[https://www.youtube.com/watch?v=hzBHJZILkIE SGD Help: Finding Human Homology & Disease Information]
*[https://www.youtube.com/watch?v=PnYD1D2ZjWU SGD Help: Exploring Expression Datasets with SPELL]
 
Videos are accessible via SGD's [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel. If you have a great idea for a video, or would like to see a particular topic covered, feel free to [http://www.yeastgenome.org/cgi-bin/suggestion contact us!]
 

==The ALLIANCE of Genome Resources==
[[File:alliance_logo.png|300px]]

Work on the collaboration with [http://www.wormbase.org/#012-34-5 WormBase], [http://flybase.org/ FlyBase], [https://zfin.org/ ZFIN], [http://www.informatics.jax.org/ MGI], [http://rgd.mcw.edu/ RGD], and the [http://geneontology.org/ Gene Ontology Consortium] to establish the '''Alliance of Genome Resources''' is well under way! Scientists from all groups are coming together to develop the best integrated tools for our users and to provide users with easy access to all the data from the Model Organism Databases.

For more updates and announcements on the Alliance, check out the Alliance [https://www.facebook.com/alliancegenome/ Facebook page], or check out our twitter page [https://twitter.com/alliancegenome @alliancegenome].
 

==Another Nobel Prize for Yeast!==
[[File:SuperYeast.jpg|thumb|left|upright=.5]]
 
In October Dr. Yoshinori Ohsumi won the 2016 [http://www.nobelprize.org/nobel_prizes/medicine/laureates/2016/press.html Nobel Prize] in Physiology or Medicine for his work on autophagy in yeast. Dr. Ohsumi used ''Sacchamomyces cerevisiae'' as a model organism to make discoveries about the autophagy mechanism which has important human disease applications. Read more about it [http://www.yeastgenome.org/a-nobel-prize-for-work-in-yeast-again here!] Behold the [https://twitter.com/hashtag/APOYG?src=hash #APOYG]!
 

==Research Spotlight (Blog posts)==
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:
*'''[http://www.yeastgenome.org/a-biological-tour-de-force A Biological Tour de Force Reveals the Complexity of a Yeast Cell]''' [http://www.yeastgenome.org/reference/S000185095/overview Costanzo and colleagues] constructed more than 23 million double mutants in order to generate a global genetic interaction network which will provide information to researchers for years to come. Explore these interactions at [http://thecellmap.org http://thecellmap.org]
*'''[http://www.yeastgenome.org/winter-is-coming-for-cancer Winter is Coming (for Cancer)]''' [http://www.yeastgenome.org/reference/S000184758/overview Reid and coworkers] used a yeast synthetic dosage lethality assay to find new potential cancer targets.
*'''[http://www.yeastgenome.org/personalized-essential-genes Personalized Essential Genes]''' [http://www.yeastgenome.org/reference/S000185120/overview Rowley and coworkers] demonstrated that while XRN1 could be swapped across four different ''Saccharomyces'' species and maintain basic function, personalized XRN1 genes were much better at protecting their own species against species-specific viruses than the XRN1 genes from other species.
*'''[http://www.yeastgenome.org/too-much-of-a-good-thing Too Much of a Good Thing]''' [http://www.yeastgenome.org/reference/S000184846/overview Ang and coworkers] investigated which genes might have an increased mutation rate when they are overexpressed - yet another example of how yeast can be a powerful tool in human disease research!
*'''[http://www.yeastgenome.org/yeast-tackles-climate-change Yeast Tackles Climate Change]''' [http://www.yeastgenome.org/reference/S000185488/overview Sato and coworkers] conducted evolution experiments in order to investigate the genes involved in yeast that was able to grow on only xylose, which has implications in biofuel production.

==SGD swag: out and about==

''Do you have pictures to share of SGD swag out and about? Send them to SGD curators for possible inclusion in a future newsletter!''

{|
| [[File:newsletter2016_SuperBud_Mexico.png|300px|thumb|left|SGD Senior Biocuration Scientist Edith Wong shows off her nice catch and superbud hat in Mexico!]]
| [[File:newsletter2016_Grad_Shirt.png|200px|thumb|Grad student Masha Evpak sports her superbud t-shirt while walking around campus.]]
|}

==Recent Publications from SGD Staff==

1. [http://www.yeastgenome.org/reference/S000185577/overview Engel, S.R., and MacPherson, K.A.] 2016. Using model organism databases (MODs). Curr. Protoc. Essential Lab. Tech. 13:11.4.1-11.4.22. doi: 10.1002/cpet.4
 

==Happy Holidays from SGD!==
[[File:SnowShmoo.png|thumb|left|upright=.55]] 
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, 2017. 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==

[http://serym2017.ua.edu 24th Annual Southeastern Regional Yeast Meeting (SERYM 2017)] 
Hotel Capstone Conference Center, University of Alabama, Tuscalossa, AL 
March 3-5, 2017 

[http://www.genetics-gsa.org/fungal/2017/ 29th Fungal Genetics Conference] 
Asilomar Conference Center, Pacific Grove, CA 
March 14-19, 2017 
Abstract submission and registration deadline: December 8, 2016 

[http://www.pombe2017.com 9th INTERNATIONAL FISSION YEAST MEETING] 
The Banff Centre, Banff, Alberta, Canada 
May 14-19, 2017 
Abstract submission deadline: February 17, 2017 
Registration deadlines: December 1, 2016 (Early bird), February 15, 2017 (regular) and April 1, 2017 (late) 

[https://imya12.azuleon.org/welcome.php 12th International Meeting on Yeast Apoptosis] 
Camera di Commercio di Bari, Bari, Italy 
May 14-18, 2017 

[http://www.yeastlipidconference.com/next-ylc-2017.html 13th Yeast Lipid Conference] 
AgroParisTech Claude Bernard campus, Paris, France 
May 17-19, 2017 

[http://www.microbiologysociety.org/events/event-listing/index.cfm/issy33 ISSY33: Exploring and Engineering Yeasts for Industrial Application] 
University College Cork, Ireland 
June 26-29, 2017 

[http://www.yeast2017.cz 28th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)] 
Prague Congress Centre, Prague, Czech Republic 
August 27 – September 1, 2017

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 We keep adding new tracks to JBrowse for visualization. Please let us know of any publicly available datasets that you think should be added!
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 ==New Protein Half-life Data==

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 We keep adding new tracks to JBrowse for visualization. Please let us know of any publicly available datasets that you think should be added!
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 ==New Protein Half-life Data==

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 We keep adding new tracks to JBrowse for visualization. Please let us know of any publicly available datasets that you think should be added!
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 ==New Protein Half-life Data==

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 We keep adding new tracks to JBrowse for visualization. Please let us know of any publicly available datasets that you think should be added!
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 ==New Protein Half-life Data==

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 [[File:Protein_Half_Life.png|700px|link=http://www.yeastgenome.org/locus/S000001388/protein]]
 <br><br>
-Protein half-life data is now available in the "Experimental Data" section of our protein tab pages (see example above from STH1 protein tab).  The protein half-life data is based on data from a study by [http://www.yeastgenome.org/reference/S000178561/overview Christiano et al. (2014)].  Additionally, this half-life data can also be retrieved using YeastMine templates '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Protein_Half_Life&scope=all Gene-->Protein Half-life]''' and '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinHalfLife_Range&scope=all Retrieve-->Proteins with half-life in a given range]''' .  Both of the [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] half-life templates are accessible from the “templates” section under the “protein” category.
+Protein half-life measurements are now available in the "Experimental Data" section of our protein tab pages (see example above from STH1 protein tab).  The protein half-life data is based on data from a study by [http://www.yeastgenome.org/reference/S000178561/overview Christiano et al. (2014)].  Additionally, this half-life data can also be retrieved using YeastMine templates '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Protein_Half_Life&scope=all Gene-->Protein Half-life]''' and '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinHalfLife_Range&scope=all Retrieve-->Proteins with half-life in a given range]''' .  Both of the [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] half-life templates are accessible from the “templates” section under the “protein” category.
 ==SGD Webinar Series==

SGD Newsletter, December 2016 - Revision history

Sage: /* New JBrowse Tracks */

Sage: /* New JBrowse Tracks */

Sage: /* New JBrowse Tracks */

Sage: /* New JBrowse Tracks */

Stacia: /* New Protein Half-life Data */

Stacia: /* New JBrowse Tracks */

Sage: Created page with "Category:Newsletter '''About this newsletter:''' This is the December 2016 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new ..."

Sage: Created page with "Category:Newsletter '''About this newsletter:'''
This is the December 2016 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new ..."