SGD-Wiki - User contributions [en]

Career Resources

2014-05-05T21:36:00Z

Selinad:

Following is a list of sites that post biology related job openings. Please note that this is not a comprehensive list. Some of these sites may be free (may require registration) for job seekers, job posters or both.

'''Note''': ''Please include the posting date with your entry and remember to remove your entry once the position has been filled; old entries with broken links will be periodically cleaned up.''

* [[Positions in yeast labs]] posted by members of the research community

* Postdoctoral Position Available in Systems Biology at E&J Gallo Winery, Modesto, CA [http://hrsjobs.gallo.com/psp/ert/EJGAPP/PSFT_HR/c/HRS_HRAM.HRS_CE.GBL?Page=HRS_CE_JOB_DTL&Action=A&JobOpeningId=6210&SiteId=1&PostingSeq=1]

* Computational and Systems Biology at Memorial Sloan-Kettering Cancer Center - [http://cbio.mskcc.org/jobs Faculty] and [http://cbio.mskcc.org/jobs/postdoc.html Postdoc] Recruitment.

* Technical Director, Enzymes position available through CPL Executive Search http://www.cplsearch.com/technical-director-enzymes/

== Links to other Career Resources ==

*[http://careers.genetics-gsa.org/ Open positions] offered by [http://www.genetics-gsa.org/ Genetics Society of America]

*[http://jobboard.ascb.org/ Career Services] offered by [http://www.ascb.org/ American Society for Cell Biology]

*[http://www.asmcareerconnections.org/home/index.cfm?site_id=756 ASM Career Connections] offered by [http://www.asm.org/ American Society for Microbiology]

*[http://careers.faseb.org/home/index.cfm?site_id=521 Career Resources] offered by [http://www.faseb.org/#sthash.NzYbAjmD.dpbs FASEB]

*[http://www.sdbonline.org/index.php?option=com_jobs&Itemid=36 Job Openings] offered by [http://www.sdbonline.org Society for Developmental Biology]

*[http://sciencecareers.sciencemag.org/ Science Careers] offered by [http://www.sciencemag.org/ Science Magazine Online]

*[http://www.nature.com/naturejobs/science/ Nature Jobs] offered by [http://www.nature.com Nature Online]

*[http://www.biospace.com Career Center] offered by [http://www.biospace.com Biospace.com]

2014-04-17T21:35:31Z

Selinad: /* Upcoming Meetings */

[[Category:Newsletter]]
 '''About this newsletter:''' 
 This is the Spring 2014 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 
==Human Disease & Fungal Homologs in YeastMine==
You can now use SGD's advanced search tool, [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine], to find the human homolog(s) of your favorite yeast gene and their corresponding disease associations. Or, begin with your favorite human gene or disease keyword and retrieve the yeast counterparts of the relevant gene(s). As an example, you can search for the ''S. cerevisiae'' homologs of all human genes associated with disorders that contain the keyword “diabetes” ([http://yeastmine.yeastgenome.org/yeastmine/template.doname=Disease_Human_Yeast&scope=global view search]). 

We have recently loaded data from [http://omim.org/ OMIM (Online Mendelian Inheritance in Man)] into our fast, flexible search resource, YeastMine, and provided 3 predefined queries (templates) that make it simple to perform the above searches. Newly updated HomoloGene, Ensembl, TreeFam, and Panther data sets are used to define the homology between ''S. cerevisiae'' and human genes. The results table provides identifiers and standard names for the yeast and human genes, as well as OMIM gene and disease identifiers and names. As with other YeastMine templates, results can be saved as lists and analyzed further. You can also now create a list of human names and/or identifiers using the updated [http://yeastmine.yeastgenome.org/yeastmine/bag.do Create Lists] feature that allows you to specify the organism representing the genes in your list. The query for yeast homologs can then be made against this list. 

In addition to human disease homologs, we have incorporated fungal homolog data for 24 additional species of fungi. You can now query for the fungal homologs of a given ''S. cerevisiae'' gene using the template [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_FungalHomologs&scope=global Gene--> Fungal Homologs]. This fungal homology data comes from various sources including [http://fungidb.org/fungidb/ FungiDB], the [http://cgob.ucd.ie/"> Candida Gene Order Browser (CGOB)] and [http://www.pombase.org/ PomBase], and the results link directly to the corresponding gene pages in the relevant databases, including [http://www.candidagenome.org/ Candida Genome Database (CGD)] and [http://www.aspgd.org/ Aspergillus Genome Database (AspGD)]. 
All of the new templates that query human and fungal homolog data can be found on the YeastMine Home page under the new tab "Homology." These templates complement the template [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Homologs&scope=global Gene--> Non-Fungal] and ''S. cerevisiae'' Homologs] that retrieves homologs of ''S. cerevisiae'' genes in human, rat, mouse, worm, fly, mosquito, and zebrafish.

==Transcriptome Data in YeastMine==
Towards the goal of compiling datasets to produce a complete transcriptome of yeast (the set of all RNA molecules produced in a single cell or population of cells), we have loaded a defined set of transcripts, based primarily on data from [http://www.yeastgenome.org/reference/S000153368/overview Pelechano, et al], but supported by other datasets, into SGD's flexible search tool, [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine]. The representative set includes transcripts that Pelechano et al. identified by simultaneous determination of the 5’ and 3’ ends of mRNA molecules whose end coordinates are supported by datasets from other laboratories. 

The transcript data can be accessed in YeastMine using the [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Transcript&scope=all Gene -> Transcripts] template, which allows you to specify a gene name or list of gene names and return the list of all associated transcripts based on the collection of data described above. The results include the start and end coordinates for each transcript, the number of counts observed for each transcript in glucose and galactose, notes, and references for the relevant datasets.

==Explore a Large New Chemogenomics Dataset Via SGD==
What happens when you cross two comprehensive deletion mutant collections with a library of more than 1800 structurally diverse chemicals? HIP HOP happens. Not the music, but a whole lot of very informative phenotype data - over 40 million data points! 

The response of ''S. cerevisiae'' mutant strains to a chemical can tell us a lot about which pathways or processes the chemical affects. This is not only interesting for yeast biologists, but also has important implications for human molecular biology and disease research. So a group at [href="http://www.nibr.com/ The Novartis Institutes of Biomedical Research] decided to test the sensitivity of nearly 6,000 mutant yeast strains to a panel of about 1,800 compounds. 

[http://www.yeastgenome.org/reference/S000156575/overview Hoepfner and colleagues] have published these results and have also generously offered them to SGD. They used the [http://www.yeastgenome.org/reference/20946813/overview HIP and HOP methods] (HIP, '''H'''aplo'''I'''nsufficiency '''P'''rofiling, using diploid heterozygous deletion mutant strains; HOP, '''HO'''mozygous deletion '''P'''rofiling, using diploid homozygous deletion mutant strains) that have proven very useful in yeast since the creation of the systematic deletion mutant collections. 

To do this mammoth series of experiments they obviously needed to set up an automated pipeline. These sorts of experiments have been done before, but in this study Hoepfner et al. improved on existing procedures in many ways: the physical techniques, the controls and replicates included, and the methods for data analysis. 

'''Phenotype annotations in SGD'''. We’ve incorporated a subset of these results into SGD as mutant phenotype annotations. Why a subset? Some of the chemicals that were used in these experiments are un-named proprietary compounds, so the individual phenotypes would not be very informative in the context of SGD. We've added the phenotypes that involve named chemicals to SGD - more than 5,500 annotations. These may be viewed on Phenotype Details pages for individual genes ([http://www.yeastgenome.org/locus/S000000396/phenotype see example]), retrieved as a set using [http://yeastmine.yeastgenome.org/yeastmine/loadTemplate.do?name=Literature_Phenotype&constraint1=Gene.phenotypes.publications&op1=LOOKUP&method=results&value1=24360837 YeastMine], or downloaded along with all SGD mutant phenotype annotations in our [http://www.yeastgenome.org/download-data/curation phenotype data download file]. 

'''Easy access to the full dataset and analyses'''. We've also added a new set of links to SGD that take you directly from your favorite gene to the authors' [http://www.fmi.ch/hiphop/index website], which provides full access to all of the data and interesting ways to look at it (see below). When you click on a [http://www.fmi.ch/hiphop/profile/gene?ID=YML008C "HIP HOP Profile" link] from the Locus Summary page or the Phenotype Details page of a gene in SGD, the landing page at the authors' website allows you to explore data for mutants in that gene or for chemicals affecting that mutant strain. You can see which chemicals had the greatest effects, which other mutant strains have a similar range of phenotypes, and much more. And if a chemical that has interesting effects is proprietary, don’t worry; Hoepfner and colleagues have stated that they "encourage future academic collaborations around individual compounds used in this study." 

'''Information about mutant strains'''. In the course of this study, the authors also generated some very useful data about particular mutant strains in the deletion collection. Some of them were hypersensitive to more than 100 different chemicals. Others turned out to be carrying additional background mutations that could affect the phenotypes of the mutant strain. We are planning to display this kind of information (from this and other studies) directly on SGD Phenotype Details pages in the future. 

We thank Dominic Hoepfner and colleagues for sharing these data with SGD and for helping us to incorporate the data. And we encourage you to explore this new resource and [http://www.yeastgenome.org/cgi-bin/suggestion contact us] with any questions or suggestions.

==Educational Resources on the SGD Community Wiki==
Did you know you can find and contribute teaching and other educational resources to SGD? We have updated our [http://wiki.yeastgenome.org/index.php/Educational_Resources Educational Resources] page, found on the [http://wiki.yeastgenome.org/index.php/Main_Page SGD Community Wiki]. There are links to teaching resources such as classroom materials, courses, and fun sites, as well as pointers to books, dedicated learning sites, and tutorials that can help you learn more about basic genetics. Many thanks to Dr. Erin Strome and Dr. Bethany Bowling of Northern Kentucky University for being the first to contribute to this updated site by providing a series of Bioinformatics Project Modules designed to introduce undergraduates to using SGD and other bioinformatics resources. 

We would like to encourage others to contribute additional teaching or general educational resources to this page. To do so, just request a wiki account by contacting us at the [mailto:sgd-helpdesk@lists.stanford.edu SGD Help Desk] - you will then be able to edit the SGD Community Wiki. If you prefer, we would also be happy to assist you directly with these edits. 

Note that there are many other types of information you can add to the SGD Community Wiki, including information about your favorite genes, protocols, upcoming meetings, and job postings. The Community Wiki can be accessed from most SGD pages by clicking on "Community" on the main menu bar and selecting "Wiki." The Educational Resources page is linked from the left menu bar under "Resources" from all the SGD Community Wiki pages. For more information on this newly updated page, please view the video [http://youtu.be/hvi0mb4kjEc Educational Resources on the SGD Community Wiki].

==Yeast Researchers Take the Lion's Share of GSA 2014 Awards==
Congratulations to fellow yeasties Angelika Amon, Charlie Boone, and Robin Wright for winning three of the five annual [http://www.genetics-gsa.org/awards/ Genetics Society of America] awards for 2014! Just another confirmation that the awesome power of yeast genetics attracts excellent researchers... 

Angelika Amon, of MIT and the Howard Hughes Medical Institute, has been awarded the Genetics Society of America Medal for outstanding contributions to the field of genetics during the past 15 years. Charlie Boone, of the University of Toronto and a longstanding member of SGD’s [http://www.yeastgenome.org/about/scientific-advisory-board Scientific Advisory Board], received the Edward Novitski Prize for his extraordinary level of creativity and intellectual ingenuity in solving significant problems in genetics research. Robin Wright, of the University of Minnesota, has been awarded the Elizabeth W. Jones Award for Excellence in Education, which recognizes significant and sustained impact in genetics education. Find full details about the awards and recipients at the [http://www.genetics-gsa.org/ GSA website].

==GO Annotation Extension Data, Redesigned GO and Phenotype Pages==
Annotation Extension data for select GO annotations are now available at SGD. The [http://www.geneontology.org/GO.annotation.extension.shtml] Annotation Extension field] (also referred to as column 16 after its position in the gene_association file of GO annotations) was introduced by the Gene Ontology Consortium (GOC) to capture details such as substrates of a protein kinase, targets of regulators, or spatial/temporal aspects of processes. The information in this field serves to provide more biological context to the GO annotation. At SGD, these data are accessible for select GO annotations via the small blue 'i' icon on the newly redesigned GO Details pages. See, for example, the substrate information for MEK1 kinase (image below). Currently, a limited number of GO annotations contain data in this field because we have only recently begun to capture this information; more will be added in the future. 

We have also redesigned the GO Details and Phenotype Details tab pages to make it easier to understand and make connections within the data. In addition to all of the annotations that were previously displayed, these pages now include graphical summaries, interactive network diagrams displaying relationships between genes and tables that can be sorted, filtered, or downloaded. In addition, SGD Paper pages, each focusing on a particular reference that has been curated in SGD, now show all of the various types of data that are derived from that paper in addition to the list of genes covered in the paper ([http://www.yeastgenome.org/reference/S000069091/overview example]). These pages provide seamless access to other tools at SGD such as GO Term Finder, GO Slim Mapper, and YeastMine. Please explore all of these new features from your favorite Locus Summary page and send us your feedback.

==Changes to the SGD GAF File of Gene Ontology Annotations==
The SGD Gene Associations file (GAF; gene_association.sgd) contains Gene Ontology (GO) annotations for all yeast genes, in a [http://www.geneontology.org/GO.format.gaf-2_0.shtml standard file format] specified by the [http://www.geneontology.org/ GO Consortium]. We are changing the taxon identifier in this file to be consistent with the reference genome sequence at GenBank and protein entries at UniProt. 

Until now, the taxon identifier in column 13 of SGD's GAF has been [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4932 4932], which refers to ''Saccharomyces cerevisiae'' in general rather than to a specific ''S. cerevisiae'' strain. Starting March 8th, 2014, we have changed this to taxon ID [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=559292 559292], which is specific to the S288C strain used for the ''S. cerevisiae''reference genome sequence. 

Please note that the taxon ID 559292 merely reflects the sequence (genome) to which the geneIDs in column 2 are mapped. SGD will continue to capture gene functions (GO annotations) for all strains of ''S. cerevisiae''. Please [http://www.yeastgenome.org/cgi-bin/suggestion contact us] if you have any questions. 

The S. cerevisiae GO annotations (GAF) can be downloaded from [http://www.yeastgenome.org/download-data/curation SGD's Download site].

==Upcoming Meetings==
*[http://wiki.yeastgenome.org/index.php/Bay_Area_Yeast_Meeting Bay Area Yeast Meeting] *
:Room M106, Alway Building, Stanford University, Stanford, CA
:April 19, 2014

*[http://events.embo.org/14-transcription-yeast/ EMBO Conference] *
:Gene Transcription in Yeast: from Regulatory Networks to Mechanisms
:Sant Feliu de Guixols, Spain
:June 14-19, 2014

*[http://www.faseb.org/SRC/ Yeast Chromosome Structure, Replication and Segregation]
:Steamboat Springs, Colorado
:July 13-16, 2014

*[http://meetings.cshl.edu/courses/2014/c-yeas14.shtml Yeast Genetics & Genomics Course] *
:Cold Spring Harbor Labs, Cold Spring Harbor, New York
:July 22 - August 11, 2014

*[http://www.genetics-gsa.org/yeast/2014/ Yeast Genetics Meeting] *
:University of Washington, Seattle, Washington
:July 29 - August 3, 2014

*EMBL Conference
:[http://www.embl.de/training/events/2014/FUN14-01/index.html Frontiers in Fungal Systems Biology]
:EMBL Heidelberg, Germany
:September 28-30, 2014

*[http://www.issy31.com/ 31st International Specialised Symposium on Yeast (ISSY)]
:Vipava and Nova Gorica, Slovenia
:October 9-12, 2014

*EMBL Conference
:[http://www.embl.de/training/events/2014/EAE14-01/index.html Experimental Approaches to Evolution and Ecolgy using Yeast & other Model Systems]
:EMBL Heidelberg, Germany
:October 12-15, 2014

 *asterisks indicate attendance by SGD

''Note: If you no longer wish to receive this newsletter, please contact the SGD Help Desk at [mailto:sgd-helpdesk@lists.stanford.edu sgd-helpdesk@lists.stanford.edu].''

SGD Quarterly Newsletter, Spring 2014

2014-04-17T21:24:39Z

Selinad:

[[Category:Newsletter]]
 '''About this newsletter:''' 
 This is the Spring 2014 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 
==Human Disease & Fungal Homologs in YeastMine==
You can now use SGD's advanced search tool, [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine], to find the human homolog(s) of your favorite yeast gene and their corresponding disease associations. Or, begin with your favorite human gene or disease keyword and retrieve the yeast counterparts of the relevant gene(s). As an example, you can search for the ''S. cerevisiae'' homologs of all human genes associated with disorders that contain the keyword “diabetes” ([http://yeastmine.yeastgenome.org/yeastmine/template.doname=Disease_Human_Yeast&scope=global view search]). 

We have recently loaded data from [http://omim.org/ OMIM (Online Mendelian Inheritance in Man)] into our fast, flexible search resource, YeastMine, and provided 3 predefined queries (templates) that make it simple to perform the above searches. Newly updated HomoloGene, Ensembl, TreeFam, and Panther data sets are used to define the homology between ''S. cerevisiae'' and human genes. The results table provides identifiers and standard names for the yeast and human genes, as well as OMIM gene and disease identifiers and names. As with other YeastMine templates, results can be saved as lists and analyzed further. You can also now create a list of human names and/or identifiers using the updated [http://yeastmine.yeastgenome.org/yeastmine/bag.do Create Lists] feature that allows you to specify the organism representing the genes in your list. The query for yeast homologs can then be made against this list. 

In addition to human disease homologs, we have incorporated fungal homolog data for 24 additional species of fungi. You can now query for the fungal homologs of a given ''S. cerevisiae'' gene using the template [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_FungalHomologs&scope=global Gene--> Fungal Homologs]. This fungal homology data comes from various sources including [http://fungidb.org/fungidb/ FungiDB], the [http://cgob.ucd.ie/"> Candida Gene Order Browser (CGOB)] and [http://www.pombase.org/ PomBase], and the results link directly to the corresponding gene pages in the relevant databases, including [http://www.candidagenome.org/ Candida Genome Database (CGD)] and [http://www.aspgd.org/ Aspergillus Genome Database (AspGD)]. 
All of the new templates that query human and fungal homolog data can be found on the YeastMine Home page under the new tab "Homology." These templates complement the template [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Homologs&scope=global Gene--> Non-Fungal] and ''S. cerevisiae'' Homologs] that retrieves homologs of ''S. cerevisiae'' genes in human, rat, mouse, worm, fly, mosquito, and zebrafish.

==Transcriptome Data in YeastMine==
Towards the goal of compiling datasets to produce a complete transcriptome of yeast (the set of all RNA molecules produced in a single cell or population of cells), we have loaded a defined set of transcripts, based primarily on data from [http://www.yeastgenome.org/reference/S000153368/overview Pelechano, et al], but supported by other datasets, into SGD's flexible search tool, [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine]. The representative set includes transcripts that Pelechano et al. identified by simultaneous determination of the 5’ and 3’ ends of mRNA molecules whose end coordinates are supported by datasets from other laboratories. 

The transcript data can be accessed in YeastMine using the [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Transcript&scope=all Gene -> Transcripts] template, which allows you to specify a gene name or list of gene names and return the list of all associated transcripts based on the collection of data described above. The results include the start and end coordinates for each transcript, the number of counts observed for each transcript in glucose and galactose, notes, and references for the relevant datasets.

==Explore a Large New Chemogenomics Dataset Via SGD==
What happens when you cross two comprehensive deletion mutant collections with a library of more than 1800 structurally diverse chemicals? HIP HOP happens. Not the music, but a whole lot of very informative phenotype data - over 40 million data points! 

The response of ''S. cerevisiae'' mutant strains to a chemical can tell us a lot about which pathways or processes the chemical affects. This is not only interesting for yeast biologists, but also has important implications for human molecular biology and disease research. So a group at [href="http://www.nibr.com/ The Novartis Institutes of Biomedical Research] decided to test the sensitivity of nearly 6,000 mutant yeast strains to a panel of about 1,800 compounds. 

[http://www.yeastgenome.org/reference/S000156575/overview Hoepfner and colleagues] have published these results and have also generously offered them to SGD. They used the [http://www.yeastgenome.org/reference/20946813/overview HIP and HOP methods] (HIP, '''H'''aplo'''I'''nsufficiency '''P'''rofiling, using diploid heterozygous deletion mutant strains; HOP, '''HO'''mozygous deletion '''P'''rofiling, using diploid homozygous deletion mutant strains) that have proven very useful in yeast since the creation of the systematic deletion mutant collections. 

To do this mammoth series of experiments they obviously needed to set up an automated pipeline. These sorts of experiments have been done before, but in this study Hoepfner et al. improved on existing procedures in many ways: the physical techniques, the controls and replicates included, and the methods for data analysis. 

'''Phenotype annotations in SGD'''. We’ve incorporated a subset of these results into SGD as mutant phenotype annotations. Why a subset? Some of the chemicals that were used in these experiments are un-named proprietary compounds, so the individual phenotypes would not be very informative in the context of SGD. We've added the phenotypes that involve named chemicals to SGD - more than 5,500 annotations. These may be viewed on Phenotype Details pages for individual genes ([http://www.yeastgenome.org/locus/S000000396/phenotype see example]), retrieved as a set using [http://yeastmine.yeastgenome.org/yeastmine/loadTemplate.do?name=Literature_Phenotype&constraint1=Gene.phenotypes.publications&op1=LOOKUP&method=results&value1=24360837 YeastMine], or downloaded along with all SGD mutant phenotype annotations in our [http://www.yeastgenome.org/download-data/curation phenotype data download file]. 

'''Easy access to the full dataset and analyses'''. We've also added a new set of links to SGD that take you directly from your favorite gene to the authors' [http://www.fmi.ch/hiphop/index website], which provides full access to all of the data and interesting ways to look at it (see below). When you click on a [http://www.fmi.ch/hiphop/profile/gene?ID=YML008C "HIP HOP Profile" link] from the Locus Summary page or the Phenotype Details page of a gene in SGD, the landing page at the authors' website allows you to explore data for mutants in that gene or for chemicals affecting that mutant strain. You can see which chemicals had the greatest effects, which other mutant strains have a similar range of phenotypes, and much more. And if a chemical that has interesting effects is proprietary, don’t worry; Hoepfner and colleagues have stated that they "encourage future academic collaborations around individual compounds used in this study." 

'''Information about mutant strains'''. In the course of this study, the authors also generated some very useful data about particular mutant strains in the deletion collection. Some of them were hypersensitive to more than 100 different chemicals. Others turned out to be carrying additional background mutations that could affect the phenotypes of the mutant strain. We are planning to display this kind of information (from this and other studies) directly on SGD Phenotype Details pages in the future. 

We thank Dominic Hoepfner and colleagues for sharing these data with SGD and for helping us to incorporate the data. And we encourage you to explore this new resource and [http://www.yeastgenome.org/cgi-bin/suggestion contact us] with any questions or suggestions.

==Educational Resources on the SGD Community Wiki==
Did you know you can find and contribute teaching and other educational resources to SGD? We have updated our [http://wiki.yeastgenome.org/index.php/Educational_Resources Educational Resources] page, found on the [http://wiki.yeastgenome.org/index.php/Main_Page SGD Community Wiki]. There are links to teaching resources such as classroom materials, courses, and fun sites, as well as pointers to books, dedicated learning sites, and tutorials that can help you learn more about basic genetics. Many thanks to Dr. Erin Strome and Dr. Bethany Bowling of Northern Kentucky University for being the first to contribute to this updated site by providing a series of Bioinformatics Project Modules designed to introduce undergraduates to using SGD and other bioinformatics resources. 

We would like to encourage others to contribute additional teaching or general educational resources to this page. To do so, just request a wiki account by contacting us at the [mailto:sgd-helpdesk@lists.stanford.edu SGD Help Desk] - you will then be able to edit the SGD Community Wiki. If you prefer, we would also be happy to assist you directly with these edits. 

Note that there are many other types of information you can add to the SGD Community Wiki, including information about your favorite genes, protocols, upcoming meetings, and job postings. The Community Wiki can be accessed from most SGD pages by clicking on "Community" on the main menu bar and selecting "Wiki." The Educational Resources page is linked from the left menu bar under "Resources" from all the SGD Community Wiki pages. For more information on this newly updated page, please view the video [http://youtu.be/hvi0mb4kjEc Educational Resources on the SGD Community Wiki].

==Yeast Researchers Take the Lion's Share of GSA 2014 Awards==
Congratulations to fellow yeasties Angelika Amon, Charlie Boone, and Robin Wright for winning three of the five annual [http://www.genetics-gsa.org/awards/ Genetics Society of America] awards for 2014! Just another confirmation that the awesome power of yeast genetics attracts excellent researchers... 

Angelika Amon, of MIT and the Howard Hughes Medical Institute, has been awarded the Genetics Society of America Medal for outstanding contributions to the field of genetics during the past 15 years. Charlie Boone, of the University of Toronto and a longstanding member of SGD’s [http://www.yeastgenome.org/about/scientific-advisory-board Scientific Advisory Board], received the Edward Novitski Prize for his extraordinary level of creativity and intellectual ingenuity in solving significant problems in genetics research. Robin Wright, of the University of Minnesota, has been awarded the Elizabeth W. Jones Award for Excellence in Education, which recognizes significant and sustained impact in genetics education. Find full details about the awards and recipients at the [http://www.genetics-gsa.org/ GSA website].

==GO Annotation Extension Data, Redesigned GO and Phenotype Pages==
Annotation Extension data for select GO annotations are now available at SGD. The [http://www.geneontology.org/GO.annotation.extension.shtml] Annotation Extension field] (also referred to as column 16 after its position in the gene_association file of GO annotations) was introduced by the Gene Ontology Consortium (GOC) to capture details such as substrates of a protein kinase, targets of regulators, or spatial/temporal aspects of processes. The information in this field serves to provide more biological context to the GO annotation. At SGD, these data are accessible for select GO annotations via the small blue 'i' icon on the newly redesigned GO Details pages. See, for example, the substrate information for MEK1 kinase (image below). Currently, a limited number of GO annotations contain data in this field because we have only recently begun to capture this information; more will be added in the future. 

We have also redesigned the GO Details and Phenotype Details tab pages to make it easier to understand and make connections within the data. In addition to all of the annotations that were previously displayed, these pages now include graphical summaries, interactive network diagrams displaying relationships between genes and tables that can be sorted, filtered, or downloaded. In addition, SGD Paper pages, each focusing on a particular reference that has been curated in SGD, now show all of the various types of data that are derived from that paper in addition to the list of genes covered in the paper ([http://www.yeastgenome.org/reference/S000069091/overview example]). These pages provide seamless access to other tools at SGD such as GO Term Finder, GO Slim Mapper, and YeastMine. Please explore all of these new features from your favorite Locus Summary page and send us your feedback.

==Changes to the SGD GAF File of Gene Ontology Annotations==
The SGD Gene Associations file (GAF; gene_association.sgd) contains Gene Ontology (GO) annotations for all yeast genes, in a [http://www.geneontology.org/GO.format.gaf-2_0.shtml standard file format] specified by the [http://www.geneontology.org/ GO Consortium]. We are changing the taxon identifier in this file to be consistent with the reference genome sequence at GenBank and protein entries at UniProt. 

Until now, the taxon identifier in column 13 of SGD's GAF has been [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4932 4932], which refers to ''Saccharomyces cerevisiae'' in general rather than to a specific ''S. cerevisiae'' strain. Starting March 8th, 2014, we have changed this to taxon ID [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=559292 559292], which is specific to the S288C strain used for the ''S. cerevisiae''reference genome sequence. 

Please note that the taxon ID 559292 merely reflects the sequence (genome) to which the geneIDs in column 2 are mapped. SGD will continue to capture gene functions (GO annotations) for all strains of ''S. cerevisiae''. Please [http://www.yeastgenome.org/cgi-bin/suggestion contact us] if you have any questions. 

The S. cerevisiae GO annotations (GAF) can be downloaded from [http://www.yeastgenome.org/download-data/curation SGD's Download site].

==Upcoming Meetings==

SGD Quarterly Newsletter, Spring 2014

2014-04-17T21:15:51Z

Selinad: /* Educational Resources on the SGD Community Wiki */

SGD Quarterly Newsletter, Spring 2014

2014-04-17T21:12:14Z

Selinad: /* Educational Resources on the SGD Community Wiki */

2014-03-28T17:56:41Z

Selinad:

Following is a list of sites that post biology related job openings. Please note that this is not a comprehensive list. Some of these sites may be free (may require registration) for job seekers, job posters or both.

'''Note''': ''Please include posting date with your entry and try to remember to remove your entry once the position has been filled; old entries with broken links will be periodically cleaned up.''

*[[Positions in yeast labs]] posted by members of the research community

* Fermentation Instructor/Advisor, Oregon State University. [ [https://jobs.oregonstate.edu/applicants/jsp/shared/position/JobDetails_css.jsp?postingId=354906 Online posting] ] [ [[File:OSU-Fermentation_Instructor-Advisor.pdf]] ] ''Posted: March 28, 2014''

* Postdoctoral Position Available in Systems Biology at E&J Gallo Winery, Modesto, CA [http://hrsjobs.gallo.com/psp/ert/EJGAPP/PSFT_HR/c/HRS_HRAM.HRS_CE.GBL?Page=HRS_CE_JOB_DTL&Action=A&JobOpeningId=6210&SiteId=1&PostingSeq=1]

* Computational and Systems Biology at Memorial Sloan-Kettering Cancer Center - [http://cbio.mskcc.org/jobs Faculty] and [http://cbio.mskcc.org/jobs/postdoc.html Postdoc] Recruitment. Also, see the announcement at http://cbio.mskcc.org/jobs/ads/faculty.pdf.

* Technical Director, Enzymes position available through CPL Executive Search http://www.cplsearch.com/technical-director-enzymes/

* R+D Scientist Synthetic Biology, Agilent Laboratories, Santa Clara CA http://wiki.yeastgenome.org/index.php/User:Agilent_Recruiter

== Links to other Career Resources ==

*[http://careers.genetics-gsa.org/ Open positions] offered by [http://www.genetics-gsa.org/ Genetics Society of America]

*[http://jobboard.ascb.org/ Career Services] offered by [http://www.ascb.org/ American Society for Cell Biology]

*[http://www.asmcareerconnections.org/home/index.cfm?site_id=756 ASM Career Connections] offered by [http://www.asm.org/ American Society for Microbiology]

*[http://careers.faseb.org/home/index.cfm?site_id=521 Career Resources] offered by [http://www.faseb.org/#sthash.NzYbAjmD.dpbs FASEB]

*[http://www.sdbonline.org/index.php?option=com_jobs&Itemid=36 Job Openings] offered by [http://www.sdbonline.org Society for Developmental Biology]

*[http://sciencecareers.sciencemag.org/ Science Careers] offered by [http://www.sciencemag.org/ Science Magazine Online]

*[http://www.nature.com/naturejobs/science/ Nature Jobs] offered by [http://www.nature.com Nature Online]

*[http://www.biospace.com Career Center] offered by [http://www.biospace.com Biospace.com]

File:OSU-Fermentation Instructor-Advisor.pdf

2014-03-28T17:50:32Z

Selinad:

Educational Resources

2014-02-07T19:20:26Z

2012-04-20T19:51:48Z

Selinad:

2012-04-17T17:40:01Z

Selinad: /* Suggested Reading */

[[File:Fungi.jpeg|thumb|left|'''Introduction to Fungi''' Credit: ''Kandis Elliot, Mo Fayyaz, University of Wisconsin, Madison'']]

====General Information====
[http://en.wikipedia.org/wiki/Yeast Yeast] are single-celled eukaryotic microorganisms that are classified, along with molds and mushrooms, as members of the kingdom [http://en.wikipedia.org/wiki/Fungus Fungi]. Yeasts are phylogenetically diverse, and as such are classified in two separate phyla, the [http://en.wikipedia.org/wiki/Ascomycota ''Ascomycota''] and the [http://en.wikipedia.org/wiki/Basidiomycota ''Basidiomycota'']. Budding yeast (also called “true yeasts”), such as the well-known species [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae ''Saccharomyces cerevisiae''], are classified in the order [http://en.wikipedia.org/wiki/Saccharomycetales ''Saccharomycetales''] under the phylum ''Ascomycota''. Such classifications are based on characteristics of the cell, ascospore, and colony, as well as on physiology. One of the most well known characteristics of yeast is its ability to ferment sugars for the production of ethanol and carbon dioxide.
[[File:Candida albicans.jpeg|thumb|right|130px|''C. albicans'', Credit: ''E. Gueho/Science Photo Library'']]

Yeast are characterized by a wide dispersion of natural habitats. They are common on plant leaves, flowers, and fruits, as well as in soil. Yeast are also found on the skin surfaces and in the intestinal tracts of
warm-blooded animals, where they may live symbiotically or as parasites. The common "yeast infection" [http://en.wikipedia.org/wiki/Candidiasis ''Candidiasis'']
is typically caused by [http://en.wikipedia.org/wiki/Candida_albicans ''Candida albicans'']. In addition to being the causative agent in vaginal yeast infections ''Candida'' is also a cause of diaper rash and
thrush of the mouth and throat.

[[File:EM yeast.jpeg|thumb|left|150px|'''EM image of ''S. cerevisiae''''' Credit: ''UC Berkeley'']]

[[File:Pombe cerevisiae.jpg|thumb|right|175px|'''Fission (''S. pombe'') and budding (''S. cerevisiae'') yeasts''' Credit: ''Susan L. Forsberg, Nat Rev Gen '''2''':659'']]
Yeast reproduce asexually by an asymmetric division process called budding (eg. [http://en.wikipedia.org/wiki/Saccharomyces ''Saccharomyces'']), by a symmetric division process called fission (eg. [http://en.wikipedia.org/wiki/Schizosaccharomyces ''Schizosaccharomyces'']), or they can grow as simple irregular filaments (mycelium). In budding, a small bud emerges from the surface of the parent cell and enlarges until it is almost the size of the parent, while in fission the rod shaped cell grows at the cell's tips and then divides in half to produce two daughter cells of equal size. Yeast can also reproduce sexually, and most do so my forming asci,
which contain up to eight haploid ascospores. These ascospores may
fuse with adjoining nuclei and multiply through vegetative division
or, as with certain yeast, fuse with other ascospores.

====Commercial Applications====
''Saccharomyces cerevisiae'' are one of the most well-known and commercially significant species of yeast. These organisms have long been utilized to ferment the sugars of rice, wheat, barley, and corn to produce alcoholic beverages, and to expand and raise dough to make bread.

[[File:Hansen-emil-christian.jpeg|thumb|x150px|left|'''Dr. Emil Christian Hansen''', ''1842-1909'']]
In brewing, ''Saccharomyces carlsbergensis'', named after the Carlsberg Brewery in Copenhagen, where it was first isolated in pure culture by Dr. Emil Christian Hansen (1842-1909) in 1883, is used in the production of several types of beers including lagers. ''S. carlsbergensis'' is used for bottom fermentation. ''S. cerevisiae'' is used for the production of ales and conducts top fermentation, in which the yeast rise to the surface of the brewing vessel. In modern brewing many of the original top fermentation strains have been modified to be bottom fermenters. Currently the ''S. carlsbergensis'' designation is not used, the ''S. cerevisiae'' classification is used instead.

[[File:Sourdough-bread.jpeg|thumb|right|x100px|'''Wild yeast and acid-generating bacteria are used in making sourdough bread''']]
The yeast's function in baking is to ferment sugars present in the flour or added to the dough. This fermentation gives off carbon dioxide and ethanol. The carbon dioxide is trapped within tiny bubbles and results in the dough expanding, or rising. Sourdough bread, is not produced with baker's yeast, rather a combination of wild yeast (often [http://en.wikipedia.org/wiki/Candida_milleri ''Candida milleri'']) and an acid-generating bacteria ([http://en.wikipedia.org/wiki/Lactobacillus_sanfranciscensis ''Lactobacillus sanfranciscensis''] sp. nov). It has been reported that the ratio of wild yeast to bacteria in San Francisco sourdough cultures is about 1:100. The ''C. milleri'' strengthens the gluten and the ''L. sanfrancisco'' ferments the maltose.

[[File:Bunches of grapes on vines at Trinity Hill vineyard in the Gimblett Gravels region Hawkes Bay NZ 13-15Feb08.jpg|thumb|150px|left|'''Bunches of grapes on vines at Trinity Hill vineyard in Hawkes Bay NZ''']]
The fermentation of wine is initiated by naturally occurring yeast present in the vineyards. Many wineries still use natural strains, however many use modern methods of strain maintenance and isolation. The bubbles in sparkling wines is trapped carbon dioxide, the result of yeast fermenting sugars in the grape juice. One yeast cell can ferment approximately its own weight of glucose per hour. Under optimal conditions ''S. cerevisiae'' can produce up to 18 percent, by volume, ethanol with 15 to 16 percent being the norm. The sulfur dioxide present in commercially produced wine is actually added just
after the grapes are crushed to kill the naturally present bacteria, mold, and yeast.

In addition to playing a major role in baking, brewing, and wine making, the in-depth knowledge of ''S. cerevisiae'' and it's ability to be metabolically engineered has made it an important organism in the production of specialty chemicals, such as biofuels, industrial lubricants, detergents, and biopharmaceuticals.

====Yeast as a Model Organism====
Yeast, particularly ''S. cerevisiae'', became a model organism for studying cell biology and genetics because it is a single-celled eukaryote that is fairly easy to manipulate and grow, and the basic cellular mechanics of replication, recombination, cell division and metabolism are generally conserved between it and more complex eukaryotes, including humans. As a result it is one of the most thoroughly researched eukaryotic organisms. Several significant scientific discoveries have been made by studying ''S. cerevisiae''.

====Resources====

[http://www.yeastgenome.org/ ''Saccharomyces'' Genome Database (SGD)] provides comprehensive integrated biological information for the budding yeast ''Saccharomyces cerevisiae'' along with search and analysis tools to explore these data.

[http://www.candidagenome.org/ ''Candida'' Genome Database (CGD)], a resource for genomic sequence data and gene and protein information for Candida albicans.

[http://www.pombase.org/ PomBase], a comprehensive database for the fission yeast ''Schizosaccharomyces pombe'', providing structural and functional annotation, literature curation and access to large-scale data sets.

[http://www.ncbi.nlm.nih.gov/projects/genome/guide/fungi/ Fungal Genomes Central], a portal to information and resources about fungi and fungal sequencing projects from NCBI and the fungi research community.

==Suggested Reading==

* [http://www.genetics.org/content/189/3/695.full.pdf+html Yeast: An Experimental Organism for 21st Century Biology]. (2011) David Botstein & Gerald R Fink, Genetics. 2011 Nov;189(3):695-704.

* [http://www.genetics.org/site/misc/yeastbook.xhtml YeastBook]. (2011) ''A comprehensive compendium of reviews that presents the current state of knowledge of the molecular biology, cellular biology, and genetics of the yeast Saccharomyces cerevisiae'', Genetics

* [http://books.google.com/books/about/From_a_to_alpha.html?id=79hO0A08odkC From a to alpha: Yeast as a Model for Cellular Differentiation]. (2007) Hitan D. Madhani, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

* [http://www.cshlpress.com/default.tpl?action=full&cart=133468404249500843&--eqskudatarq=449&newtitle=Landmark%20Papers%20in%20Yeast%20Biology Landmark Papers in Yeast Biology]. (2006), edited by Patrick Linder, David Shore, and Michael N. Hall, Cold Spring Harbor Press, Cold Spring Harbor, New York.

* [http://www.cshlpress.com/default.tpl?action=full&cart=133468404249500843&--eqskudatarq=526&newtitle=Methods%20in%20Yeast%20Genetics%3A%20A%20Cold%20Spring%20%20Harbor%20Laboratory%20Course%20Manual%2C%202005%20Edition Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual]. (2005) David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern. Cold Spring Laboratory Press, Cold Spring Harbor, New York.

* [http://www.cshlpress.com/default.tpl?cart=133468183249354789&fromlink=T&linkaction=full&linksortby=oop_title&--eqSKUdatarq=676 The Early Days of Yeast Genetics]. (1993) edited by Michael N. Hall and Patrick Linder. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

* [http://www.cshlpress.com/default.tpl?action=full&cart=133468299549480865&--eqskudatarq=189&newtitle=The%20Yeast%20Saccharomyces%3A%20Gene%20Expression The Molecular and Cellular Biology of the Yeast ''Saccharomyces cerevisiae'': Gene Expression]. (1992) edited by Elizabeth W. Jones, John R. Pringle, and James R. Broach. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

* Mortimer, R.K., Contopoulou, C.R. and J.S. King (1992) [http://www.ncbi.nlm.nih.gov/pubmed/1413997 Genetic and physical maps of ''Saccharomyces cerevisiae''], Edition 11. Yeast '''8''':817-902.

* [http://www.cshlpress.com/default.tpl?action=full&--eqskudatarq=190 The Molecular and Cellular Biology of the Yeast ''Saccharomyces cerevisiae'': Genome Dynamics, Protein Synthesis, and Energetics]. (1991) edited by James R. Broach, John R. Pringle, and Elizabeth W. Jones. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

* [http://books.google.com/books/about/Yeast.html?id=-GkHRQAACAAJ Yeast: A Practical Approach]. (1988) edited by I. Campbell and , and John H. Duffus, IRL Press, Ithaca, New York.

* The Life of Yeasts. (1978) H.J. Phaff, M.W. Miller, and E. M. Mrak, Harvard University Press, Cambridge, Massachussetts.