Difference between revisions of "SGD Newsletter, April 2018"
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==1011 Genomes at SGD== | ==1011 Genomes at SGD== | ||
| − | [[File:1011genomes_pie_chart.jpg|thumb|left|upright=1.3| Ecological origins of the 1,011 isolates [https://www.nature.com/articles/s41586-018-0030-5 | + | [[File:1011genomes_pie_chart.jpg|thumb|left|upright=1.3| Ecological origins of the 1,011 isolates (from [https://www.nature.com/articles/s41586-018-0030-5 Peter et al., 2018]; Creative Commons License)]] |
1,011. That’s the number of different ''Saccharomyces cerevisiae'' yeast strains that were whole-genome sequenced and phenotyped by a team of researchers jointly led by Joseph Schacherer and Gianni Liti and recently published in [https://www.yeastgenome.org/reference/S000216438 Nature]. | 1,011. That’s the number of different ''Saccharomyces cerevisiae'' yeast strains that were whole-genome sequenced and phenotyped by a team of researchers jointly led by Joseph Schacherer and Gianni Liti and recently published in [https://www.yeastgenome.org/reference/S000216438 Nature]. | ||
<br><br><br> | <br><br><br> | ||
| − | SGD is happy to announce that in conjunction with the authors and publishers, we are hosting the datasets from the paper at this [https://www.yeastgenome.org/search?q=PMID%3A29643504&category=download&status=Active SGD download site] (see image below). These datasets include: the actual genome sequences of the 1,011 isolates; the list of 4,940 common “core” ORFs plus 2,856 ORFs that are variable within the population (together these make up the “pangenome”); copy number variation (CNV) data; phenotyping data for 36 conditions; SNPs and indels relative to the S288C genome; and much more. We hope that the easy availability of these large datasets will be useful to many yeast (and non-yeast) researchers, and as the authors say, will help to “guide future population genomics and genotype–phenotype studies in this classic model system.” | + | SGD is happy to announce that in conjunction with the authors and publishers, we are hosting the datasets from the paper at this [https://www.yeastgenome.org/search?q=PMID%3A29643504&category=download&status=Active SGD download site] (see image below, [https://www.yeastgenome.org/search?q=PMID%3A29643504&category=download&status=Active www.yeastgenome.org/1011-yeast-genomes]). These datasets include: the actual genome sequences of the 1,011 isolates; the list of 4,940 common “core” ORFs plus 2,856 ORFs that are variable within the population (together these make up the “pangenome”); copy number variation (CNV) data; phenotyping data for 36 conditions; SNPs and indels relative to the S288C genome; and much more. We hope that the easy availability of these large datasets will be useful to many yeast (and non-yeast) researchers, and as the authors say, will help to “guide future population genomics and genotype–phenotype studies in this classic model system.” |
| − | + | <br><br> | |
You can also read more about this exciting new data addition on our [https://www.yeastgenome.org/blog/out-of-china-changing-our-views-on-the-origins-of-budding-yeast blog!]<br><br> | You can also read more about this exciting new data addition on our [https://www.yeastgenome.org/blog/out-of-china-changing-our-views-on-the-origins-of-budding-yeast blog!]<br><br> | ||
| − | + | [[File:1011genomes_screenshot.jpg|888px|link=https://www.yeastgenome.org/search?category=download&format=TSV&page=0&q=PMID%3A29643504&status=Active]] | |
| − | [[File: | + | <br> |
| − | |||
==Yeast Genetics Meeting 2018== | ==Yeast Genetics Meeting 2018== | ||
[[File:Yeast_Genetics_Meeting_GSA.png|thumb|left|upright=1.5]] | [[File:Yeast_Genetics_Meeting_GSA.png|thumb|left|upright=1.5]] | ||
The [http://conferences.genetics-gsa.org/yeast/2018/index Yeast Genetics Meeting] will be held August 22–26, 2018 at Stanford University in Palo Alto, California. This is the premier meeting for anyone studying eukaryotic biology using the powerful experimental model Saccharomyces cerevisiae [https://twitter.com/hashtag/APOYG?src=hash #APOYG]!. In addition to oral presentations, which are selected from the submitted abstracts, there will also be awards for the best posters. [http://conferences.genetics-gsa.org/yeast/2018/submission Abstract submission] is open now and ends '''May 17, 2018'''. This meeting provides a valuable forum for graduate students and postdocs to present their research to an international audience. | The [http://conferences.genetics-gsa.org/yeast/2018/index Yeast Genetics Meeting] will be held August 22–26, 2018 at Stanford University in Palo Alto, California. This is the premier meeting for anyone studying eukaryotic biology using the powerful experimental model Saccharomyces cerevisiae [https://twitter.com/hashtag/APOYG?src=hash #APOYG]!. In addition to oral presentations, which are selected from the submitted abstracts, there will also be awards for the best posters. [http://conferences.genetics-gsa.org/yeast/2018/submission Abstract submission] is open now and ends '''May 17, 2018'''. This meeting provides a valuable forum for graduate students and postdocs to present their research to an international audience. | ||
| − | + | [[File:Super_Buddies_2.png|thumb|right|upright=1.3| Find SGD at YGM 2018 to get your exclusive Super Buddy!]] | |
The following awards and lectures will be presented at the meeting: | The following awards and lectures will be presented at the meeting: | ||
| − | |||
::*Lee Hartwell Lecture: Fred Winston, Harvard Medical School | ::*Lee Hartwell Lecture: Fred Winston, Harvard Medical School | ||
::*Ira Herskowitz Award: Mike Cherry, Stanford University | ::*Ira Herskowitz Award: Mike Cherry, Stanford University | ||
| Line 26: | Line 24: | ||
::*Winge-Lindegren Address: Virginia Zakian, Princeton University | ::*Winge-Lindegren Address: Virginia Zakian, Princeton University | ||
::*Special Presentation: David Botstein, Calico | ::*Special Presentation: David Botstein, Calico | ||
| + | ::*GSA George W. Beadle Award: Phil Hieter, University of British Columbia | ||
<br> | <br> | ||
| − | [http://conferences.genetics-gsa.org/yeast/2018/register-now Register now] to join us and hundreds of yeast researchers at Stanford University for this exciting four-day meeting. We hope to see you there! [https://twitter.com/hashtag/YEAST18?src=hash #YEAST18] | + | [http://conferences.genetics-gsa.org/yeast/2018/register-now Register now] to join us and hundreds of yeast researchers at Stanford University for this exciting four-day meeting. Make sure to come to the SGD table to help us celebrate the '''25th anniversary of SGD''' and pick up your "Super Buddy." We hope to see you there! [https://twitter.com/hashtag/YEAST18?src=hash #YEAST18] |
| − | <br> | + | <br><br> |
==In Memoriam: André Goffeau== | ==In Memoriam: André Goffeau== | ||
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The collaborative nature of the yeast community’s effort was nicely summed up in the 1996 Goffeau et al. paper: “Whether they worked in large centers or small laboratories, most of the 600 or so scientists involved in sequencing the yeast genome share the feeling that the worldwide ties created by this venture are of inestimable value to the future of yeast research” and indeed this has proved true. Prof. Goffeau was recognized with many awards and honors over his career, including the 2002 [http://www.genetics-gsa.org/awards/beadleaward.shtml Beadle Medal] of the Genetics Society of America for his work in having “initiated and successfully led the yeast genome sequencing project”. After the completion of the ''S. cerevisiae'' genome he continued to sequence whole genomes of other microbes and also worked on novel anti-cancer agents. Prof. Goffeau was a highly praised mentor and published hundreds of scientific papers of which many resulted from large collaborations; he also served on journal editorial boards, organized meetings, and performed many other valuable services to the scientific community over his career. He was an active and treasured part of the yeast community and we will miss him greatly. | The collaborative nature of the yeast community’s effort was nicely summed up in the 1996 Goffeau et al. paper: “Whether they worked in large centers or small laboratories, most of the 600 or so scientists involved in sequencing the yeast genome share the feeling that the worldwide ties created by this venture are of inestimable value to the future of yeast research” and indeed this has proved true. Prof. Goffeau was recognized with many awards and honors over his career, including the 2002 [http://www.genetics-gsa.org/awards/beadleaward.shtml Beadle Medal] of the Genetics Society of America for his work in having “initiated and successfully led the yeast genome sequencing project”. After the completion of the ''S. cerevisiae'' genome he continued to sequence whole genomes of other microbes and also worked on novel anti-cancer agents. Prof. Goffeau was a highly praised mentor and published hundreds of scientific papers of which many resulted from large collaborations; he also served on journal editorial boards, organized meetings, and performed many other valuable services to the scientific community over his career. He was an active and treasured part of the yeast community and we will miss him greatly. | ||
| + | |||
| + | <br> | ||
| + | |||
| + | ==The ALLIANCE of Genome Resources== | ||
| + | [[File:alliance_logo.png|link=www.alliancegenome.org |thumb|left|upright=1.1]] | ||
| + | In October 2017 the Alliance of Genome Resources (the Alliance) released the Alliance of Genome Resources website 1.0 ([http://www.alliancegenome.org www.alliancegenome.org]). The Alliance provides unified access to comparative genetics and genomics data from the Alliance data resources. The focus of the Alliance is to facilitate the use of these data towards better understanding of human biology and disease as well as providing cross-species comparative information. | ||
| + | |||
| + | As the integration of the MOD and GO teams progress with inclusion of additional data, the vision going forward includes the incorporation of other model organism information resources and other bioinformatic nodes within a common data platform, facilitating data recovery, analysis, and integration.<br> | ||
| + | <br> | ||
| + | As one of the founding members of the Alliance, SGD biocurators and programmers are actively working to incorporate new data to the Alliance, including expression and interaction data. <br> | ||
| + | <br><br> | ||
| + | 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]. | ||
<br> | <br> | ||
| Line 48: | Line 59: | ||
*[https://www.yeastgenome.org/blog/strung-out-chromosomes-and-coyotes Strung Out Chromosomes and Coyotes] [https://www.yeastgenome.org/reference/S000207414 Buehl and colleagues] provide evidence that if H3 is not acetylated by Gcn5p, the H3 tail can act as a secondary anchor if the tension sensing motif is mutated. | *[https://www.yeastgenome.org/blog/strung-out-chromosomes-and-coyotes Strung Out Chromosomes and Coyotes] [https://www.yeastgenome.org/reference/S000207414 Buehl and colleagues] provide evidence that if H3 is not acetylated by Gcn5p, the H3 tail can act as a secondary anchor if the tension sensing motif is mutated. | ||
*[https://www.yeastgenome.org/blog/dont-ignore-the-scullery-maid-hobbits-or-pol-iii Don't Ignore the Scullery Maid or Pol III] [https://www.yeastgenome.org/reference/S000207289 Filer and coworkers] show that Pol III plays a critical role in longevity, and like Cinderella, should not be ignored! | *[https://www.yeastgenome.org/blog/dont-ignore-the-scullery-maid-hobbits-or-pol-iii Don't Ignore the Scullery Maid or Pol III] [https://www.yeastgenome.org/reference/S000207289 Filer and coworkers] show that Pol III plays a critical role in longevity, and like Cinderella, should not be ignored! | ||
| − | *[https://www.yeastgenome.org/blog/trouble-with-triplets Trouble with Triplets] [https://www.yeastgenome.org/reference/S000207497 Koch and coworkers] found that ISW1 is important for making sure that nucleosomes get placed back | + | *[https://www.yeastgenome.org/blog/trouble-with-triplets Trouble with Triplets] [https://www.yeastgenome.org/reference/S000207497 Koch and coworkers] found that ISW1 is important for making sure that nucleosomes get placed back onto DNA after they've been removed to make room for Pol II. |
<br> | <br> | ||
| Line 66: | Line 77: | ||
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 [https://www.yeastgenome.org/suggestion contact us!] | 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 [https://www.yeastgenome.org/suggestion contact us!] | ||
| − | <br> | + | <br><br> |
| + | |||
| + | ==SGD Biocurators Out and About== | ||
| + | You might see some of our SGD members at these upcoming events: | ||
| + | [[File:KMac.jpg|thumb|left|upright=.60]] <br><br><br> | ||
| + | *Associate Biocuration Scientist Kevin MacPherson will be a collaborating instructor at the [https://coursesandconferences.wellcomegenomecampus.org/events/item.aspx?e=690 Fungal Pathogen Genomics] course at the Wellcome Genome Campus, Hinxton, Cambridge (UK) May 13-18, 2018. | ||
| + | <br><br><br> | ||
| + | [[File:RN.jpg|thumb|left|upright=.60]] <br><br><br> | ||
| + | *Senior Biocuration Scientist Rob Nash will be conducting a workshop at the annual [https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=18 Yeast Genetics & Genomics] course at Cold Spring Harbor Laboratory July 24 - August 13, 2018. | ||
| + | <br><br><br><br><br> | ||
==Recent Publications from SGD Staff== | ==Recent Publications from SGD Staff== | ||
| − | *Engel SR, Skrzypek M, Hellerstedt ST, Wong ED, Nash RS, Weng S, Binkley G, Sheppard TK, Karra K, Cherry JM (2018). Updated regulation curation model at the ''Saccharomyces'' Genome Database. Database (Oxford). | + | *Engel SR, Skrzypek M, Hellerstedt ST, Wong ED, Nash RS, Weng S, Binkley G, Sheppard TK, Karra K, Cherry JM (2018). Updated regulation curation model at the ''Saccharomyces'' Genome Database. Database (Oxford). 2018 Jan 1; 2018. doi: 10.1093/database/bay007. [https://www.ncbi.nlm.nih.gov/pubmed/?term=29688362 PMID: 29688362]. |
<br> | <br> | ||
| Line 79: | Line 99: | ||
You may have seen SGD representatives at the following meetings: | You may have seen SGD representatives at the following meetings: | ||
<br><br> | <br><br> | ||
| − | *PI Mike Cherry, | + | *PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientist Edith Wong, and Associate Biocuration Scientist Patrick Ng attended and presented talks and posters at [http://biocuration2018.cn/biocuration2018/ The 11th International Biocuration Conference] in Shanghai, China in April 2018. |
| − | <br><br> | + | <br><br><br> |
==Upcoming Meetings== | ==Upcoming Meetings== | ||
Latest revision as of 14:25, 9 May 2018
About this newsletter:
This is the April 2018 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.
Contents
- 1 1011 Genomes at SGD
- 2 Yeast Genetics Meeting 2018
- 3 In Memoriam: André Goffeau
- 4 The ALLIANCE of Genome Resources
- 5 Research Spotlight (Blog posts)
- 6 Research Spotlights now on SGD YouTube Channel
- 7 SGD Biocurators Out and About
- 8 Recent Publications from SGD Staff
- 9 What else have we been up to lately?
- 10 Upcoming Meetings
1011 Genomes at SGD
1,011. That’s the number of different Saccharomyces cerevisiae yeast strains that were whole-genome sequenced and phenotyped by a team of researchers jointly led by Joseph Schacherer and Gianni Liti and recently published in Nature.
SGD is happy to announce that in conjunction with the authors and publishers, we are hosting the datasets from the paper at this SGD download site (see image below, www.yeastgenome.org/1011-yeast-genomes). These datasets include: the actual genome sequences of the 1,011 isolates; the list of 4,940 common “core” ORFs plus 2,856 ORFs that are variable within the population (together these make up the “pangenome”); copy number variation (CNV) data; phenotyping data for 36 conditions; SNPs and indels relative to the S288C genome; and much more. We hope that the easy availability of these large datasets will be useful to many yeast (and non-yeast) researchers, and as the authors say, will help to “guide future population genomics and genotype–phenotype studies in this classic model system.”
You can also read more about this exciting new data addition on our blog!
Yeast Genetics Meeting 2018
The Yeast Genetics Meeting will be held August 22–26, 2018 at Stanford University in Palo Alto, California. This is the premier meeting for anyone studying eukaryotic biology using the powerful experimental model Saccharomyces cerevisiae #APOYG!. In addition to oral presentations, which are selected from the submitted abstracts, there will also be awards for the best posters. Abstract submission is open now and ends May 17, 2018. This meeting provides a valuable forum for graduate students and postdocs to present their research to an international audience.
The following awards and lectures will be presented at the meeting:
- Lee Hartwell Lecture: Fred Winston, Harvard Medical School
- Ira Herskowitz Award: Mike Cherry, Stanford University
- Lifetime Achievement Award: Steve Oliver, University of Cambridge
- Winge-Lindegren Address: Virginia Zakian, Princeton University
- Special Presentation: David Botstein, Calico
- GSA George W. Beadle Award: Phil Hieter, University of British Columbia
Register now to join us and hundreds of yeast researchers at Stanford University for this exciting four-day meeting. Make sure to come to the SGD table to help us celebrate the 25th anniversary of SGD and pick up your "Super Buddy." We hope to see you there! #YEAST18
In Memoriam: André Goffeau
It was with great sadness that we learned that André Goffeau, renowned yeast researcher and Professor at the Université Catholique de Louvain in Belgium, passed away on April 2, 2018.
Prof. Goffeau worked on yeast transporter genes and multidrug resistance for much of his scientific career, and made many contributions to this field. But he will forever be remembered for his visionary idea to sequence the entire genome of Saccharomyces cerevisiae, ultimately leading to the coordination of a world-wide collaborative effort during the late 1980s and early 1990s by researchers from 19 countries working in 94 laboratories. The sequencing project, which represented the first completely sequenced eukaryotic genome, culminated in the landmark publication “Life with 6000 Genes” (Goffeau et al. 1996). But of course this was only the beginning of a cascading myriad of discoveries, methods, resources and careers built upon the existence of the yeast genome sequence.
The collaborative nature of the yeast community’s effort was nicely summed up in the 1996 Goffeau et al. paper: “Whether they worked in large centers or small laboratories, most of the 600 or so scientists involved in sequencing the yeast genome share the feeling that the worldwide ties created by this venture are of inestimable value to the future of yeast research” and indeed this has proved true. Prof. Goffeau was recognized with many awards and honors over his career, including the 2002 Beadle Medal of the Genetics Society of America for his work in having “initiated and successfully led the yeast genome sequencing project”. After the completion of the S. cerevisiae genome he continued to sequence whole genomes of other microbes and also worked on novel anti-cancer agents. Prof. Goffeau was a highly praised mentor and published hundreds of scientific papers of which many resulted from large collaborations; he also served on journal editorial boards, organized meetings, and performed many other valuable services to the scientific community over his career. He was an active and treasured part of the yeast community and we will miss him greatly.
The ALLIANCE of Genome Resources
In October 2017 the Alliance of Genome Resources (the Alliance) released the Alliance of Genome Resources website 1.0 (www.alliancegenome.org). The Alliance provides unified access to comparative genetics and genomics data from the Alliance data resources. The focus of the Alliance is to facilitate the use of these data towards better understanding of human biology and disease as well as providing cross-species comparative information.
As the integration of the MOD and GO teams progress with inclusion of additional data, the vision going forward includes the incorporation of other model organism information resources and other bioinformatic nodes within a common data platform, facilitating data recovery, analysis, and integration.
As one of the founding members of the Alliance, SGD biocurators and programmers are actively working to incorporate new data to the Alliance, including expression and interaction data.
For more updates and announcements on the Alliance, check out the Alliance Facebook page, or check out our twitter page @alliancegenome.
Research Spotlight (Blog posts)
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:
- Moonlighting Proteins Do Double Duty Espinosa-Cantú and coworkers investigated which proteins have a catalytic activity and another unrelated job.
- Exploding Yeast to Protect the Wild Maselko and colleagues engineered a yeast strain so that if it doesn't form diploids within the same strain the diploids will explode!
- Strung Out Chromosomes and Coyotes Buehl and colleagues provide evidence that if H3 is not acetylated by Gcn5p, the H3 tail can act as a secondary anchor if the tension sensing motif is mutated.
- Don't Ignore the Scullery Maid or Pol III Filer and coworkers show that Pol III plays a critical role in longevity, and like Cinderella, should not be ignored!
- Trouble with Triplets Koch and coworkers found that ISW1 is important for making sure that nucleosomes get placed back onto DNA after they've been removed to make room for Pol II.
Research Spotlights now on SGD YouTube Channel
In addition to blog posts, SGD also highlights exciting yeast research on our YouTube channel. Check out our latest Research Spotlight videos below:
- Trouble with Triplets
- Now Yeast Even Finds Fungal Pathogens!
- Exploding Yeast to Protect the Wild
- A SRTain Surprise in a Lipid Droplet
Videos are accessible via SGD's YouTube channel. If you have a great idea for a video, or would like to see a particular topic covered, feel free to contact us!
SGD Biocurators Out and About
You might see some of our SGD members at these upcoming events:
- Associate Biocuration Scientist Kevin MacPherson will be a collaborating instructor at the Fungal Pathogen Genomics course at the Wellcome Genome Campus, Hinxton, Cambridge (UK) May 13-18, 2018.
- Senior Biocuration Scientist Rob Nash will be conducting a workshop at the annual Yeast Genetics & Genomics course at Cold Spring Harbor Laboratory July 24 - August 13, 2018.
Recent Publications from SGD Staff
- Engel SR, Skrzypek M, Hellerstedt ST, Wong ED, Nash RS, Weng S, Binkley G, Sheppard TK, Karra K, Cherry JM (2018). Updated regulation curation model at the Saccharomyces Genome Database. Database (Oxford). 2018 Jan 1; 2018. doi: 10.1093/database/bay007. PMID: 29688362.
What else have we been up to lately?
You may have seen SGD representatives at the following meetings:
- PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientist Edith Wong, and Associate Biocuration Scientist Patrick Ng attended and presented talks and posters at The 11th International Biocuration Conference in Shanghai, China in April 2018.
Upcoming Meetings
EMBO Workshop Gene transcription in yeast: From global analyses to single cells
Sant Feliu de Guixols, Spain
June 9 - 14, 2018
Registration deadline: March 12, 2018
RCN-UBE: Yeast ORFan Gene Project: Finding a Place for ORFans to GO (Summer Workshop)
Rhodes College, Memphis TN
June 11 - 15, 2018
Application submission deadline: February 26, 2018
Yeast Chromosome Biology and Cell Cycle
Steamboat Grand, Steamboat Springs, CO
July 15 - 20, 2018
Application submission deadline: June 13, 2018
Yeast Genetics & Genomics Course
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
July 24 - August 13, 2018
Application Deadline: April 15, 2018
5th International Synthetic & Systems Biology Summer School - SSBSS 2018
Certosa di Pontignano (Siena) Tuscany, Italy
July 25 - 29, 2018
Application and abstract submission deadline: March 31, 2018
Yeast Genetics Meeting
Stanford University, Palo Alto, California
August 22 – 26, 2018
13th International Meeting on Yeast Ageing and Apoptosis
The Irish College, Leuven, Belgium
August 26 – 30, 2018
13th Edition of the International Levures, Modèles et Outils (Yeasts, Models and Tools)
Musikinsel, Rheinau, Switzerland
September 11-14, 2018
International Specialized Symposium on Yeasts, "Yeast Odyssey: from nature to industry"
Bariloche, Patagonia, Argentina
October 1 - 4, 2018
International Workshop on Brewing Yeasts
Bariloche, Patagonia, Argentina
October 5 - 6, 2018
EMBO Workshop on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems
Heidelberg, Germany
October 17 - 20, 2018
