SGD-Wiki - User contributions [en]

Methods

2014-06-19T23:10:52Z

Plloyd:

*[http://labs.fhcrc.org/breeden/Methods/index.html Yeast Lab Protocols] from the Breeden Lab, Fred Hutchinson Cancer Research Center.

*[http://research.fhcrc.org/gottschling/en/protocols/yeast-protocols.html Yeast Lab Protocols] from the Gottschling Lab, Fred Hutchinson Cancer Research Center.

*[http://gasch.genetics.wisc.edu/protocols.html Yeast & Microarray Protocols] from the Gasch Lab, University of Wisconsin-Madison.

*[http://home.cc.umanitoba.ca/~gietz/ The Definitive Yeast Transformation Homepage] from the University of Manitoba.

*[http://fangman-brewer.genetics.washington.edu/index.html DNA Replication Protocols] from the Fangman and Brewer Labs, University of Washington.

*[http://cmgm.stanford.edu/pbrown/mguide/index.html The MGuide. Version 2.0], a complete guide to microarraying for the molecular biologist, from the Brown Lab, Stanford University.

*[http://gasch.genetics.wisc.edu/protocols/Gasch_MethEnzym.pdf Guide to Yeast Microarray Experiments], by Audrey Gasch, from Guide to Yeast Genetics and Molecular and Cellular Biology, Methods in Enzymology (2002)

*[http://depts.washington.edu/yeastrc/ The NCRR Yeast Resource Center] at the University of Washington facilitates the study of yeast protein complexes by providing access to techniques such as mass spectrometry, two-hybrid arrays, deconvolution fluorescence microscopy and protein structure prediction.

* [http://genome.cshlp.org/content/7/12/1174.full PCR-Based Allele Replacement] (Erdeniz et al. (1997) Genome Res. 7:1174-1183). Available to the public without password restriction and at no charge, through a special arrangement with Genome Research arranged by Rodney Rothstein (''see [[CommunityW303.html|detailed notes]] from RR and Stephan Bärtsch on the W303 strain; derivatives were used in the study'').

*[http://dunham.gs.washington.edu/home.shtml Chemostat Manual] from Maitreya Dunham's lab, University of Washington.

*[http://www.phys.ksu.edu/gene/chapters.html A Classroom Guide To Yeast Experiments] from The GENE project at Kansas State University based on [http://www.rushessay.com essay writing].

*[http://openwetware.org/wiki/The_mRNA_Decay_Resource:Protocols_and_Resources Protocols and Resources] from the RNA Decay Resource, a resource for the sharing of information, know-how, and wisdom among researchers who study mRNA decay.

*[[SGA]] protocols and scoring software.

*[http://Vadlo.com/ Molecular Biology Protocols Search Engine] from Life in Research, LLC. Also life sciences databases, online tools, software, and powerpoints. For example [http://www.vadlo.com/b/q?k=Yeast+Protocols&rel=0 Yeast protocols], [http://www.vadlo.com/b/q?k=Yeast&rel=3 Yeast databases]

*[http://wiki.yeastgenome.org/index.php/Software Software tools] created by members of the scientific community.
*[http://sbs.umkc.edu/yeastcommunity/ Yeast Community Site] from Honigberg Lab, University of Missouri Kansas City.

*[http://www.magusto.com/ Concours Site] from concours Lab, University of Mousseaux sur seine (protocol in French).

*[[Yeast_Cell_Micromanipulation|Yeast Cell Micromanipulation]] Protocol for Making Support Rod with Fiber Optic Needle Attached from Cora Styles

*[http://yeastgenome.org/cgi-bin/geneticData/displayTwoPoint? Genetic Mapping (Two-Point) Data] for yeast genes.

Career Resources

2014-04-15T22:57:04Z

Plloyd:

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

* Fermentation Instructor/Advisor, Oregon State University, Corvallis, Oregon; View Job Announcement: [[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.

* 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]

Positions in yeast labs

2014-04-15T22:49:46Z

Plloyd:

=='''Postdoctoral position in Cell Biology, Univ. of Miami, Florida (posted April 2014)'''==

A Postdoctoral position is available in the lab of Dr. Sandra Lemmon, University of Miami, Miller School of Medicine. Research focuses on regulation of membrane dynamics in the yeast S. cerevisiae. Particular interests include the role of phosphorylation, the actin cytoskeleton, and lipids in endocytosis and the function of clathrin in endocytosis and sorting to the lysosome/vacuole. For information on research interests check: <http://biomed.miami.edu/?p=482&pid=208&m=facultyph&mid=0&item=9>.

Qualifications: Candidates should have a PhD in chemistry, biology, genetics or a related life science. Applicants with a background in cell biology, yeast genetics and molecular biology, fluorescence microscopy and/or lipid biochemistry are especially encouraged to apply. Please submit a curriculum vitae, publications, summary of past research experiences, research interests, and the names of three references to: Dr. Sandra Lemmon at <slemmon[at]miami[dot]edu>.

=='''Postdoctoral Fellowship in yeast evolutionary genomics at Stanford University'''==

The Fraser Lab in the Department of Biology is seeking a postdoctoral fellow to work on the evolution of gene expression in Saccharomyces yeast. The exact subject is flexible, but will likely involve using RNA-seq to answer fundamental questions about the mechanisms and consequences of gene expression evolution- especially in cases of evolutionary adaptations. The ideal candidate would have experience in yeast molecular biology techniques, as well as some familiarity with computational and/or evolutionary analysis. Salary and benefits are both above the NIH standards for postdocs. Please email a cover letter and CV to hbfraser[at]stanford[dot]edu.

=='''Research Associate position (Ph.D. level) at Stanford University'''==

The Fraser Lab in the Department of Biology is seeking a Basic Life Science Research Associate (Ph.D. level). We apply the exciting tools of genomics and high-throughput sequencing to study the evolution of gene expression in a variety of species, but primarily budding yeast. Duties will include:

• Performing a wide range of experiments with the yeast S. cerevisiae. These will focus on a revolutionary new tool in molecular biology: genetic engineering via the CRISPR/Cas system. Other experiments will include gene knockout/replacement, chromatin immunoprecipitation, and high-throughput sequencing of mRNA.
• Teaching experimental protocols to others in the lab
• Keeping the lab's yeast strains/chemicals organized
• Overseeing an undergraduate student for dishwashing/media preparation

A Ph.D. in a Biology-related field is required, with at least 2 years spent working with S. cerevisiae. Also desirable (but not required) is experience with: mammalian cell culture, chromatin immunoprecipitation, and/or high-throughput sequencing. Please email a cover letter and CV to hbfraser[at]stanford[dot]edu.

=='''Postdoctoral fellowship in cell cycle evolution at the Institute of Genetics and Development of Rennes, France'''==

A three-year post-doctoral position supported by a starting grant from the European Research Council (ERC) is available in the group of Dr. Damien Coudreuse at the Institute of Genetics and Development of Rennes (IGDR), France (http://igdr.univ-rennes1.fr/english/). Research in this laboratory takes a synthetic biology approach in fission yeast to study the architecture and evolution of cell cycle regulation. The proposed project aims at understanding fundamental aspects of the evolution of cell proliferation, from how cells overcome external challenges to common features of independent evolutionary processes. It will be based on the use of fission yeast cells operating with various minimal cell cycle control circuits as starting points for experimental evolution approaches. Candidates should contact Dr. Damien Coudreuse at damien.coudreuse@univ-rennes1.fr and send a Curriculum Vitae, including past research experiences and publication records, as well as a letter detailing their motivation and interest in our work. Applicants should also request recommendation letters to be directly sent by two or three references.

=='''Postdoctoral Fellowship in Cell Fate and Gene Regulation (POS00123), LRI/Crick Institute, London, UK'''==

We seek a talented and motivated Postdoc to join the Cell Fate and Gene Regulation Laboratory in London, UK. The Cell Fate and Gene Regulation laboratory headed by Dr Folkert van Werven will be opened in the fall of this year. It will be a small, highly interactive, international research group that focuses on understanding the molecular mechanisms of how cell fate decisions are controlled. Initially we will use budding yeast as a model system, and take molecular, systematic and quantitative approaches (including single-molecule, proteomic, and genomic techniques) to study this problem. For more information please send an email (Folkert.vanWerven at cancer.org.uk) or go to:
https://cruk.taleo.net/careersection/cruk_corporate/jobdetail.ftl?lang=en&job=POS00123&view=rss

=='''Postdoctoral Position in Biology of Yeast Colonies at Charles University in Prague, Czech Republic'''==

Postdoctoral positions are available in the lab of Zdena Palkova (http://www.natur.cuni.cz/~zdenap). The Research Group is interested in different aspects of yeast multicellularity including questions related to topics of yeast cell differentiation, ageing, stress defense, adaptation and longevity that are crucial in any organism, including humans.

Selected recent references:
• Cap M, Stepanek L, Harant K, Vachova L, Palkova Z. (2012) Cell differentiation within a yeast colony: metabolic and regulatory parallels with a tumor-affected organism. Mol Cell 46: 436-448
• Vachova L, Stovicek V, Hlavacek O, Chernyavskiy O, Stepanek L, Kubinová L, Palkova Z. (2011) Flo11p, drug efflux pumps, and the extracellular matrix cooperate to form biofilm yeast colonies. J Cell Biol. 194: 679-87.

Candidates should have experience in molecular and cellular biology and methodical knowledge in techniques of yeast cell growth and manipulation. In addition, candidates should have high motivation and ability to work independently and take responsibility for his/her own project as well as to work in a team.

The applicants should have (i) a recent PhD (the degree obtained no earlier than on 28th of March 2008), (ii) promising publication record and be able to speak fluent English (or Czech). Please send your motivation letter (<500 words), CV, list of publications (including IF and the number of citations) and contact information of three references directly to the group leader Zdena Palkova, mailto:zdenap@natur.cuni.cz (please combine all documents into single PDF file). Applications will be considered until suitable candidates are found. The positions include additional funds for the international mobility (3 months).

=='''PhD student in Molecular Biology (Marie Curie Early Stage Researcher)at the University of Gothenburg, Sweden'''==
A PhD student position in Molecular Biology/Systems Biology is available in the lab of Prof. Stefan Hohmann, Dept of Cell and Molecular Biology, University of Gothenburg, Sweden.

The research project “Experimental investigation of the yeast Hxk2/Snf1/Mig1 network” aims to understand the dynamic control of the Hxk2/Snf1/Mig1 glucose signalling pathway employing single cell technology developed in the ISOLATE project. Here the experimental platform generated in the project will be optimized, especially the formation of cell arrays of synchronized cells as well as image analysis. Using in parallel Mig1 and Msn2 reporters, response thresholds under different glucose levels will be establish and effects on cell-to-cell variability and bistability will be determined.

Requested Background(advantageous but not required): Yeast biology, yeast genetics, glucose signalling, use of microfluidic devices, microscopy, image analysis, application of nano-sensor technology, ‘systems’ thinking.

The Marie Curie project ISOLATE is a collaborative research and training network between eight partners, incl. in different European countries. The PhD students and postdocs in the project will perform top-notch research and will additionally benefit from an excellent training network offered by the project partners. Research stays during the PhD projects in other partners’ labs are strongly encouraged. Primarily recruitment of researchers from EC Member States and associated countries, but also open to researchers from third countries. Researchers are normally required to move from one country to another when taking up the appointment.

Please send an application including (1) a max. one-page cover letter containing a justification why this position was chosen as well as a career vision statement, (2) a complete CV with details on education, previous research activities and a list of publications (if any,)(3) a copy of the passport or ID with picture, (4) two letters of recommendation, to maria.enge@gu.se (Project Manager in Prof. Hohmann's group).

=='''PhD student in Systems Biology (Marie Curie Early Stage Researcher)at the University of Gothenburg, Sweden'''==

A PhD student position in Systems Biology is available in the lab of Prof. Stefan Hohmann, Dept of Cell and Molecular Biology, University of Gothenburg, Sweden.

The research project “Theoretical investigation of the yeast Hxk2/Snf1/Mig1 network” aims to understand the dynamic control of the Hxk2/Snf1/Mig1 glucose signalling pathway employing single cell technology developed in the ISOLATE project. Data generated in the project will be interpreted by mathematical modelling together with other project partners to understand feedback and feed-forward mechanisms of signalling. Mutants and inhibitory compounds will be used to test how those affect thresholds and bistability. The analysis will reveal the genetic determination of the system properties, how they are regulated and how robustness against perturbation is established.

Requested Background(advantageous but not required): Yeast biology, yeast genetics, glucose signaling, microscopy, image analysis, development of mathematical models, ‘systems’ thinking.

The Marie Curie project ISOLATE is a collaborative research and training network between eight partners, incl. in different European countries. The PhD students and postdocs in the project will perform top-notch research and will additionally benefit from an excellent training network offered by the project partners. Research stays during the PhD projects in other partners’ labs are strongly encouraged. Primarily recruitment of researchers from EC Member States and associated countries, but also open to researchers from third countries. Researchers are normally required to move from one country to another when taking up the appointment.

Please send an application including (1) a max. one-page cover letter containing a justification why this position was chosen as well as a career vision statement, (2) a complete CV with details on education, previous research activities and a list of publications (if any,)(3) a copy of the passport or ID with picture, (4) two letters of recommendation, to maria.enge@gu.se (Project Manager in Prof. Hohmann's group).

=='''Postdoctoral position to study Ty1 retrotransposition at the University of Georgia''' ==

A postdoctoral position is available in the lab of David J. Garfinkel, Department of Biochemistry and Molecular Biology, University of Georgia, Athens GA to work on the retrovirus-like transposon Ty1 of ''Saccharomyces''. Specifically, we are investigating a new form of RNA-interference based on Ty1 antisense RNAs that acts posttranslationally and targets Ty1 proteins in the absence of the conserved RNAi pathways.

Experience in molecular genetics, protein/nucleic acid interactions or cytology would be helpful.

Also see our website for further information [http://www.bmb.uga.edu/home/people/people.php?fname=David&lname=Garfinkel]

Please send resume or inquiries to:
David J. Garfinkel
Department of Biochemistry and Molecular Biology
A130 Life Sciences
120 Green St.
University of Georgia
Athens, GA 30622

tel: 706-542-9403
djgarf@bmb.uga.edu

==Yeast Systems Biology Position at Virginia Tech (Research Associate or Sr Research Associate)==
The Synthetic Biology group at Virginia Bioinformatics Institute (VBI) is involved in two collaborative research projects focused on the development of mathematical models of gene-protein regulatory networks controlling cell growth and division. Temporal organization of the budding yeast cell cycle has been studied from two vantage points: bottom-up models emphasize a protein regulatory network centered around cyclin-dependent protein kinases, whereas top-down models focus on a gene regulatory network governed by interrelated transcription factors. The first project is focused on unifying these two perspectives. The second project is focused on the development of stochastic models of the regulatory network controlling the cell cycle. Both projects are performed in close collaboration with experts in computer science, data mining, bioinformatics, and mathematical modeling. The successful candidate will be expected to contribute significantly to these two projects by being responsible for designing and performing experiments used to validate model predictions. These experiments will involve the development of a new collection of cell cycle mutants and their quantitative characterization by time-lapse microscopy. In addition, the successful candidate will be expected to prepare the results for publication and presentation, to help supervise graduate and undergraduate students, and to contribute to grant proposals.

Dependent on the qualifications of the successful candidate, the position will hold the research faculty rank of either Research Associate or Senior Research Associate.

Go to the [http://bit.ly/n4nDUQ position description] for additional information and for submitting applications.

More information about our team can be found by visiting:
* [http://www.vbi.vt.edu/faculty/personal/Jean_Peccoud Jean Peccoud's home page]
* [http://www.biol.vt.edu/faculty/tyson/ John Tyson's home page]
* [https://bioinformatics.cs.vt.edu/~murali/ T.M. Murali's home page]

==Postdoctoral position - Laboratory of Cell Physics - Strasbourg, France==
Postdoctoral position is available in the Laboratory of Cell Physics, ISIS/IGBMC, Strasbourg, France. The project will focus on the dynamics of the cytokinetic ring in the fission yeast S. pombe. The roles of the Rho GTPase, actin polymerisation, and myosin will be studied. The work will involve genetics, cell biology, microscopy, microfabrication and microfluidics; for more information, send a CV and contact information of referees to Dr. Daniel Riveline (riveline@unistra.fr)

==Postdoctoral Position in Quantitative Systems Biology==
A postdoctoral fellow position is immediately available for a highly motivated recent PhD or MD/PhD graduate in biomedical science in the lab of Dr. Gregor Neuert at Vanderbilt University School of Medicine in Nashville, Tennessee.

The main interests of the group focuses on quantitative understanding of signaling and gene regulatory processes of coding and non-coding RNA in single cells at single molecule resolution. Our research methods include a combination of single-cell experimental and computational techniques as well as molecular biology and yeast genetics.

We are seeking highly motivated and curious applicants with strong background in yeast genetics, molecular biology and computational biology. Background in microscopy and computational modeling is also considered a plus but not required.

We offer a highly interactive, international and interdisciplinary research environment with strong mentoring and career development support. Vanderbilt University School of Medicine is ranked #9 in NIH funding and #15 in U.S. News medical school ranking and is equipped with world-class cutting-edge core facilities.

Selected publications:
Neuert, Munsky et al. Science 2013 ; Munsky, Neuert et al. Science 2012; Bumgarner, Neuert et al. Mol.Cell 2012; Van Werven, Neuert et al. Cell 2013

Interested applicants should send curriculum vitae, a summary of research experience and accomplishments, and contact information of 2-3 references to gregor.neuert@vanderbilt.edu.

For more information please visit:
https://www.mc.vanderbilt.edu/root/vumc.php?site=neuertlab

Positions in yeast labs

2014-04-15T22:49:17Z

Plloyd:

=='''Postdoctoral position in Cell Biology, Univ. of Miami, Florida (posted April 2014)'''==

A Postdoctoral position is available in the lab of Dr. Sandra Lemmon, University of Miami, Miller School of Medicine. Research focuses on regulation of membrane dynamics in the yeast S. cerevisiae. Particular interests include the role of phosphorylation, the actin cytoskeleton, and lipids in endocytosis and the function of clathrin in endocytosis and sorting to the lysosome/vacuole. For information on research interests check: <http://biomed.miami.edu/?p=482&pid=208&m=facultyph&mid=0&item=9>.

Qualifications: Candidates should have a PhD in chemistry, biology, genetics or a related life science. Applicants with a background in cell biology, yeast genetics and molecular biology, fluorescence microscopy and/or lipid biochemistry are especially encouraged to apply. Please submit a curriculum vitae, publications, summary of past research experiences, research interests, and the names of three references to: Dr. Sandra Lemmon at <slemmon[at]miami[dot]edu>.

=='''Postdoctoral Fellowship in yeast evolutionary genomics at Stanford University'''==

The Fraser Lab in the Department of Biology is seeking a postdoctoral fellow to work on the evolution of gene expression in Saccharomyces yeast. The exact subject is flexible, but will likely involve using RNA-seq to answer fundamental questions about the mechanisms and consequences of gene expression evolution- especially in cases of evolutionary adaptations. The ideal candidate would have experience in yeast molecular biology techniques, as well as some familiarity with computational and/or evolutionary analysis. Salary and benefits are both above the NIH standards for postdocs. Please email a cover letter and CV to hbfraser[at]stanford[dot]edu.

=='''Research Associate position (Ph.D. level) at Stanford University'''==

The Fraser Lab in the Department of Biology is seeking a Basic Life Science Research Associate (Ph.D. level). We apply the exciting tools of genomics and high-throughput sequencing to study the evolution of gene expression in a variety of species, but primarily budding yeast. Duties will include:

• Performing a wide range of experiments with the yeast S. cerevisiae. These will focus on a revolutionary new tool in molecular biology: genetic engineering via the CRISPR/Cas system. Other experiments will include gene knockout/replacement, chromatin immunoprecipitation, and high-throughput sequencing of mRNA.
• Teaching experimental protocols to others in the lab
• Keeping the lab's yeast strains/chemicals organized
• Overseeing an undergraduate student for dishwashing/media preparation

A Ph.D. in a Biology-related field is required, with at least 2 years spent working with S. cerevisiae. Also desirable (but not required) is experience with: mammalian cell culture, chromatin immunoprecipitation, and/or high-throughput sequencing. Please email a cover letter and CV to hbfraser[at]stanford[dot]edu.

=='''Postdoctoral fellowship in cell cycle evolution at the Institute of Genetics and Development of Rennes, France'''==

A three-year post-doctoral position supported by a starting grant from the European Research Council (ERC) is available in the group of Dr. Damien Coudreuse at the Institute of Genetics and Development of Rennes (IGDR), France (http://igdr.univ-rennes1.fr/english/). Research in this laboratory takes a synthetic biology approach in fission yeast to study the architecture and evolution of cell cycle regulation. The proposed project aims at understanding fundamental aspects of the evolution of cell proliferation, from how cells overcome external challenges to common features of independent evolutionary processes. It will be based on the use of fission yeast cells operating with various minimal cell cycle control circuits as starting points for experimental evolution approaches. Candidates should contact Dr. Damien Coudreuse at damien.coudreuse@univ-rennes1.fr and send a Curriculum Vitae, including past research experiences and publication records, as well as a letter detailing their motivation and interest in our work. Applicants should also request recommendation letters to be directly sent by two or three references.

=='''Postdoctoral Fellowship in Cell Fate and Gene Regulation (POS00123), LRI/Crick Institute, London, UK'''==

We seek a talented and motivated Postdoc to join the Cell Fate and Gene Regulation Laboratory in London, UK. The Cell Fate and Gene Regulation laboratory headed by Dr Folkert van Werven will be opened in the fall of this year. It will be a small, highly interactive, international research group that focuses on understanding the molecular mechanisms of how cell fate decisions are controlled. Initially we will use budding yeast as a model system, and take molecular, systematic and quantitative approaches (including single-molecule, proteomic, and genomic techniques) to study this problem. For more information please send an email (Folkert.vanWerven at cancer.org.uk) or go to:
https://cruk.taleo.net/careersection/cruk_corporate/jobdetail.ftl?lang=en&job=POS00123&view=rss

=='''Postdoctoral Position in Biology of Yeast Colonies at Charles University in Prague, Czech Republic'''==

Postdoctoral positions are available in the lab of Zdena Palkova (http://www.natur.cuni.cz/~zdenap). The Research Group is interested in different aspects of yeast multicellularity including questions related to topics of yeast cell differentiation, ageing, stress defense, adaptation and longevity that are crucial in any organism, including humans.

Selected recent references:
• Cap M, Stepanek L, Harant K, Vachova L, Palkova Z. (2012) Cell differentiation within a yeast colony: metabolic and regulatory parallels with a tumor-affected organism. Mol Cell 46: 436-448
• Vachova L, Stovicek V, Hlavacek O, Chernyavskiy O, Stepanek L, Kubinová L, Palkova Z. (2011) Flo11p, drug efflux pumps, and the extracellular matrix cooperate to form biofilm yeast colonies. J Cell Biol. 194: 679-87.

Candidates should have experience in molecular and cellular biology and methodical knowledge in techniques of yeast cell growth and manipulation. In addition, candidates should have high motivation and ability to work independently and take responsibility for his/her own project as well as to work in a team.

The applicants should have (i) a recent PhD (the degree obtained no earlier than on 28th of March 2008), (ii) promising publication record and be able to speak fluent English (or Czech). Please send your motivation letter (<500 words), CV, list of publications (including IF and the number of citations) and contact information of three references directly to the group leader Zdena Palkova, mailto:zdenap@natur.cuni.cz (please combine all documents into single PDF file). Applications will be considered until suitable candidates are found. The positions include additional funds for the international mobility (3 months).

=='''PhD student in Molecular Biology (Marie Curie Early Stage Researcher)at the University of Gothenburg, Sweden'''==
A PhD student position in Molecular Biology/Systems Biology is available in the lab of Prof. Stefan Hohmann, Dept of Cell and Molecular Biology, University of Gothenburg, Sweden.

The research project “Experimental investigation of the yeast Hxk2/Snf1/Mig1 network” aims to understand the dynamic control of the Hxk2/Snf1/Mig1 glucose signalling pathway employing single cell technology developed in the ISOLATE project. Here the experimental platform generated in the project will be optimized, especially the formation of cell arrays of synchronized cells as well as image analysis. Using in parallel Mig1 and Msn2 reporters, response thresholds under different glucose levels will be establish and effects on cell-to-cell variability and bistability will be determined.

Requested Background(advantageous but not required): Yeast biology, yeast genetics, glucose signalling, use of microfluidic devices, microscopy, image analysis, application of nano-sensor technology, ‘systems’ thinking.

The Marie Curie project ISOLATE is a collaborative research and training network between eight partners, incl. in different European countries. The PhD students and postdocs in the project will perform top-notch research and will additionally benefit from an excellent training network offered by the project partners. Research stays during the PhD projects in other partners’ labs are strongly encouraged. Primarily recruitment of researchers from EC Member States and associated countries, but also open to researchers from third countries. Researchers are normally required to move from one country to another when taking up the appointment.

Please send an application including (1) a max. one-page cover letter containing a justification why this position was chosen as well as a career vision statement, (2) a complete CV with details on education, previous research activities and a list of publications (if any,)(3) a copy of the passport or ID with picture, (4) two letters of recommendation, to maria.enge@gu.se (Project Manager in Prof. Hohmann's group).

=='''PhD student in Systems Biology (Marie Curie Early Stage Researcher)at the University of Gothenburg, Sweden'''==

A PhD student position in Systems Biology is available in the lab of Prof. Stefan Hohmann, Dept of Cell and Molecular Biology, University of Gothenburg, Sweden.

The research project “Theoretical investigation of the yeast Hxk2/Snf1/Mig1 network” aims to understand the dynamic control of the Hxk2/Snf1/Mig1 glucose signalling pathway employing single cell technology developed in the ISOLATE project. Data generated in the project will be interpreted by mathematical modelling together with other project partners to understand feedback and feed-forward mechanisms of signalling. Mutants and inhibitory compounds will be used to test how those affect thresholds and bistability. The analysis will reveal the genetic determination of the system properties, how they are regulated and how robustness against perturbation is established.

Requested Background(advantageous but not required): Yeast biology, yeast genetics, glucose signaling, microscopy, image analysis, development of mathematical models, ‘systems’ thinking.

The Marie Curie project ISOLATE is a collaborative research and training network between eight partners, incl. in different European countries. The PhD students and postdocs in the project will perform top-notch research and will additionally benefit from an excellent training network offered by the project partners. Research stays during the PhD projects in other partners’ labs are strongly encouraged. Primarily recruitment of researchers from EC Member States and associated countries, but also open to researchers from third countries. Researchers are normally required to move from one country to another when taking up the appointment.

Please send an application including (1) a max. one-page cover letter containing a justification why this position was chosen as well as a career vision statement, (2) a complete CV with details on education, previous research activities and a list of publications (if any,)(3) a copy of the passport or ID with picture, (4) two letters of recommendation, to maria.enge@gu.se (Project Manager in Prof. Hohmann's group).

=='''Postdoctoral position to study Ty1 retrotransposition at the University of Georgia''' ==

A postdoctoral position is available in the lab of David J. Garfinkel, Department of Biochemistry and Molecular Biology, University of Georgia, Athens GA to work on the retrovirus-like transposon Ty1 of ''Saccharomyces''. Specifically, we are investigating a new form of RNA-interference based on Ty1 antisense RNAs that acts posttranslationally and targets Ty1 proteins in the absence of the conserved RNAi pathways.

Experience in molecular genetics, protein/nucleic acid interactions or cytology would be helpful.

Also see our website for further information [http://www.bmb.uga.edu/home/people/people.php?fname=David&lname=Garfinkel]

Please send resume or inquiries to:
David J. Garfinkel
Department of Biochemistry and Molecular Biology
A130 Life Sciences
120 Green St.
University of Georgia
Athens, GA 30622

tel: 706-542-9403
djgarf@bmb.uga.edu

==""Yeast Systems Biology Position at Virginia Tech (Research Associate or Sr Research Associate)""==
The Synthetic Biology group at Virginia Bioinformatics Institute (VBI) is involved in two collaborative research projects focused on the development of mathematical models of gene-protein regulatory networks controlling cell growth and division. Temporal organization of the budding yeast cell cycle has been studied from two vantage points: bottom-up models emphasize a protein regulatory network centered around cyclin-dependent protein kinases, whereas top-down models focus on a gene regulatory network governed by interrelated transcription factors. The first project is focused on unifying these two perspectives. The second project is focused on the development of stochastic models of the regulatory network controlling the cell cycle. Both projects are performed in close collaboration with experts in computer science, data mining, bioinformatics, and mathematical modeling. The successful candidate will be expected to contribute significantly to these two projects by being responsible for designing and performing experiments used to validate model predictions. These experiments will involve the development of a new collection of cell cycle mutants and their quantitative characterization by time-lapse microscopy. In addition, the successful candidate will be expected to prepare the results for publication and presentation, to help supervise graduate and undergraduate students, and to contribute to grant proposals.

Dependent on the qualifications of the successful candidate, the position will hold the research faculty rank of either Research Associate or Senior Research Associate.

Go to the [http://bit.ly/n4nDUQ position description] for additional information and for submitting applications.

More information about our team can be found by visiting:
* [http://www.vbi.vt.edu/faculty/personal/Jean_Peccoud Jean Peccoud's home page]
* [http://www.biol.vt.edu/faculty/tyson/ John Tyson's home page]
* [https://bioinformatics.cs.vt.edu/~murali/ T.M. Murali's home page]

==Postdoctoral position - Laboratory of Cell Physics - Strasbourg, France==
Postdoctoral position is available in the Laboratory of Cell Physics, ISIS/IGBMC, Strasbourg, France. The project will focus on the dynamics of the cytokinetic ring in the fission yeast S. pombe. The roles of the Rho GTPase, actin polymerisation, and myosin will be studied. The work will involve genetics, cell biology, microscopy, microfabrication and microfluidics; for more information, send a CV and contact information of referees to Dr. Daniel Riveline (riveline@unistra.fr)

==Postdoctoral Position in Quantitative Systems Biology==
A postdoctoral fellow position is immediately available for a highly motivated recent PhD or MD/PhD graduate in biomedical science in the lab of Dr. Gregor Neuert at Vanderbilt University School of Medicine in Nashville, Tennessee.

The main interests of the group focuses on quantitative understanding of signaling and gene regulatory processes of coding and non-coding RNA in single cells at single molecule resolution. Our research methods include a combination of single-cell experimental and computational techniques as well as molecular biology and yeast genetics.

We are seeking highly motivated and curious applicants with strong background in yeast genetics, molecular biology and computational biology. Background in microscopy and computational modeling is also considered a plus but not required.

We offer a highly interactive, international and interdisciplinary research environment with strong mentoring and career development support. Vanderbilt University School of Medicine is ranked #9 in NIH funding and #15 in U.S. News medical school ranking and is equipped with world-class cutting-edge core facilities.

Selected publications:
Neuert, Munsky et al. Science 2013 ; Munsky, Neuert et al. Science 2012; Bumgarner, Neuert et al. Mol.Cell 2012; Van Werven, Neuert et al. Cell 2013

Interested applicants should send curriculum vitae, a summary of research experience and accomplishments, and contact information of 2-3 references to gregor.neuert@vanderbilt.edu.

For more information please visit:
https://www.mc.vanderbilt.edu/root/vumc.php?site=neuertlab

Positions in yeast labs

2014-04-15T22:48:34Z

Plloyd:

=='''Postdoctoral position in Cell Biology, Univ. of Miami, Florida (posted April 2014)'''==

A Postdoctoral position is available in the lab of Dr. Sandra Lemmon, University of Miami, Miller School of Medicine. Research focuses on regulation of membrane dynamics in the yeast S. cerevisiae. Particular interests include the role of phosphorylation, the actin cytoskeleton, and lipids in endocytosis and the function of clathrin in endocytosis and sorting to the lysosome/vacuole. For information on research interests check: <http://biomed.miami.edu/?p=482&pid=208&m=facultyph&mid=0&item=9>.

Qualifications: Candidates should have a PhD in chemistry, biology, genetics or a related life science. Applicants with a background in cell biology, yeast genetics and molecular biology, fluorescence microscopy and/or lipid biochemistry are especially encouraged to apply. Please submit a curriculum vitae, publications, summary of past research experiences, research interests, and the names of three references to: Dr. Sandra Lemmon at <slemmon[at]miami[dot]edu>.

=='''Postdoctoral Fellowship in yeast evolutionary genomics at Stanford University'''==

The Fraser Lab in the Department of Biology is seeking a postdoctoral fellow to work on the evolution of gene expression in Saccharomyces yeast. The exact subject is flexible, but will likely involve using RNA-seq to answer fundamental questions about the mechanisms and consequences of gene expression evolution- especially in cases of evolutionary adaptations. The ideal candidate would have experience in yeast molecular biology techniques, as well as some familiarity with computational and/or evolutionary analysis. Salary and benefits are both above the NIH standards for postdocs. Please email a cover letter and CV to hbfraser[at]stanford[dot]edu.

=='''Research Associate position (Ph.D. level) at Stanford University'''==

The Fraser Lab in the Department of Biology is seeking a Basic Life Science Research Associate (Ph.D. level). We apply the exciting tools of genomics and high-throughput sequencing to study the evolution of gene expression in a variety of species, but primarily budding yeast. Duties will include:

• Performing a wide range of experiments with the yeast S. cerevisiae. These will focus on a revolutionary new tool in molecular biology: genetic engineering via the CRISPR/Cas system. Other experiments will include gene knockout/replacement, chromatin immunoprecipitation, and high-throughput sequencing of mRNA.
• Teaching experimental protocols to others in the lab
• Keeping the lab's yeast strains/chemicals organized
• Overseeing an undergraduate student for dishwashing/media preparation

A Ph.D. in a Biology-related field is required, with at least 2 years spent working with S. cerevisiae. Also desirable (but not required) is experience with: mammalian cell culture, chromatin immunoprecipitation, and/or high-throughput sequencing. Please email a cover letter and CV to hbfraser[at]stanford[dot]edu.

=='''Postdoctoral fellowship in cell cycle evolution at the Institute of Genetics and Development of Rennes, France'''==

A three-year post-doctoral position supported by a starting grant from the European Research Council (ERC) is available in the group of Dr. Damien Coudreuse at the Institute of Genetics and Development of Rennes (IGDR), France (http://igdr.univ-rennes1.fr/english/). Research in this laboratory takes a synthetic biology approach in fission yeast to study the architecture and evolution of cell cycle regulation. The proposed project aims at understanding fundamental aspects of the evolution of cell proliferation, from how cells overcome external challenges to common features of independent evolutionary processes. It will be based on the use of fission yeast cells operating with various minimal cell cycle control circuits as starting points for experimental evolution approaches. Candidates should contact Dr. Damien Coudreuse at damien.coudreuse@univ-rennes1.fr and send a Curriculum Vitae, including past research experiences and publication records, as well as a letter detailing their motivation and interest in our work. Applicants should also request recommendation letters to be directly sent by two or three references.

=='''Postdoctoral Fellowship in Cell Fate and Gene Regulation (POS00123), LRI/Crick Institute, London, UK'''==

We seek a talented and motivated Postdoc to join the Cell Fate and Gene Regulation Laboratory in London, UK. The Cell Fate and Gene Regulation laboratory headed by Dr Folkert van Werven will be opened in the fall of this year. It will be a small, highly interactive, international research group that focuses on understanding the molecular mechanisms of how cell fate decisions are controlled. Initially we will use budding yeast as a model system, and take molecular, systematic and quantitative approaches (including single-molecule, proteomic, and genomic techniques) to study this problem. For more information please send an email (Folkert.vanWerven at cancer.org.uk) or go to:
https://cruk.taleo.net/careersection/cruk_corporate/jobdetail.ftl?lang=en&job=POS00123&view=rss

=='''Postdoctoral Position in Biology of Yeast Colonies at Charles University in Prague, Czech Republic'''==

Postdoctoral positions are available in the lab of Zdena Palkova (http://www.natur.cuni.cz/~zdenap). The Research Group is interested in different aspects of yeast multicellularity including questions related to topics of yeast cell differentiation, ageing, stress defense, adaptation and longevity that are crucial in any organism, including humans.

Selected recent references:
• Cap M, Stepanek L, Harant K, Vachova L, Palkova Z. (2012) Cell differentiation within a yeast colony: metabolic and regulatory parallels with a tumor-affected organism. Mol Cell 46: 436-448
• Vachova L, Stovicek V, Hlavacek O, Chernyavskiy O, Stepanek L, Kubinová L, Palkova Z. (2011) Flo11p, drug efflux pumps, and the extracellular matrix cooperate to form biofilm yeast colonies. J Cell Biol. 194: 679-87.

Candidates should have experience in molecular and cellular biology and methodical knowledge in techniques of yeast cell growth and manipulation. In addition, candidates should have high motivation and ability to work independently and take responsibility for his/her own project as well as to work in a team.

The applicants should have (i) a recent PhD (the degree obtained no earlier than on 28th of March 2008), (ii) promising publication record and be able to speak fluent English (or Czech). Please send your motivation letter (<500 words), CV, list of publications (including IF and the number of citations) and contact information of three references directly to the group leader Zdena Palkova, mailto:zdenap@natur.cuni.cz (please combine all documents into single PDF file). Applications will be considered until suitable candidates are found. The positions include additional funds for the international mobility (3 months).

=='''PhD student in Molecular Biology (Marie Curie Early Stage Researcher)at the University of Gothenburg, Sweden'''==
A PhD student position in Molecular Biology/Systems Biology is available in the lab of Prof. Stefan Hohmann, Dept of Cell and Molecular Biology, University of Gothenburg, Sweden.

The research project “Experimental investigation of the yeast Hxk2/Snf1/Mig1 network” aims to understand the dynamic control of the Hxk2/Snf1/Mig1 glucose signalling pathway employing single cell technology developed in the ISOLATE project. Here the experimental platform generated in the project will be optimized, especially the formation of cell arrays of synchronized cells as well as image analysis. Using in parallel Mig1 and Msn2 reporters, response thresholds under different glucose levels will be establish and effects on cell-to-cell variability and bistability will be determined.

Requested Background(advantageous but not required): Yeast biology, yeast genetics, glucose signalling, use of microfluidic devices, microscopy, image analysis, application of nano-sensor technology, ‘systems’ thinking.

The Marie Curie project ISOLATE is a collaborative research and training network between eight partners, incl. in different European countries. The PhD students and postdocs in the project will perform top-notch research and will additionally benefit from an excellent training network offered by the project partners. Research stays during the PhD projects in other partners’ labs are strongly encouraged. Primarily recruitment of researchers from EC Member States and associated countries, but also open to researchers from third countries. Researchers are normally required to move from one country to another when taking up the appointment.

Please send an application including (1) a max. one-page cover letter containing a justification why this position was chosen as well as a career vision statement, (2) a complete CV with details on education, previous research activities and a list of publications (if any,)(3) a copy of the passport or ID with picture, (4) two letters of recommendation, to maria.enge@gu.se (Project Manager in Prof. Hohmann's group).

=='''PhD student in Systems Biology (Marie Curie Early Stage Researcher)at the University of Gothenburg, Sweden'''==

A PhD student position in Systems Biology is available in the lab of Prof. Stefan Hohmann, Dept of Cell and Molecular Biology, University of Gothenburg, Sweden.

The research project “Theoretical investigation of the yeast Hxk2/Snf1/Mig1 network” aims to understand the dynamic control of the Hxk2/Snf1/Mig1 glucose signalling pathway employing single cell technology developed in the ISOLATE project. Data generated in the project will be interpreted by mathematical modelling together with other project partners to understand feedback and feed-forward mechanisms of signalling. Mutants and inhibitory compounds will be used to test how those affect thresholds and bistability. The analysis will reveal the genetic determination of the system properties, how they are regulated and how robustness against perturbation is established.

Requested Background(advantageous but not required): Yeast biology, yeast genetics, glucose signaling, microscopy, image analysis, development of mathematical models, ‘systems’ thinking.

The Marie Curie project ISOLATE is a collaborative research and training network between eight partners, incl. in different European countries. The PhD students and postdocs in the project will perform top-notch research and will additionally benefit from an excellent training network offered by the project partners. Research stays during the PhD projects in other partners’ labs are strongly encouraged. Primarily recruitment of researchers from EC Member States and associated countries, but also open to researchers from third countries. Researchers are normally required to move from one country to another when taking up the appointment.

Please send an application including (1) a max. one-page cover letter containing a justification why this position was chosen as well as a career vision statement, (2) a complete CV with details on education, previous research activities and a list of publications (if any,)(3) a copy of the passport or ID with picture, (4) two letters of recommendation, to maria.enge@gu.se (Project Manager in Prof. Hohmann's group).

=='''Postdoctoral position to study Ty1 retrotransposition at the University of Georgia''' ==

A postdoctoral position is available in the lab of David J. Garfinkel, Department of Biochemistry and Molecular Biology, University of Georgia, Athens GA to work on the retrovirus-like transposon Ty1 of ''Saccharomyces''. Specifically, we are investigating a new form of RNA-interference based on Ty1 antisense RNAs that acts posttranslationally and targets Ty1 proteins in the absence of the conserved RNAi pathways.

Experience in molecular genetics, protein/nucleic acid interactions or cytology would be helpful.

Also see our website for further information [http://www.bmb.uga.edu/home/people/people.php?fname=David&lname=Garfinkel]

Please send resume or inquiries to:
David J. Garfinkel
Department of Biochemistry and Molecular Biology
A130 Life Sciences
120 Green St.
University of Georgia
Athens, GA 30622

tel: 706-542-9403
djgarf@bmb.uga.edu

==""Yeast Systems Biology Position at Virginia Tech (Research Associate or Sr Research Associate)""==
The Synthetic Biology group at Virginia Bioinformatics Institute (VBI) is involved in two collaborative research projects focused on the development of mathematical models of gene-protein regulatory networks controlling cell growth and division. Temporal organization of the budding yeast cell cycle has been studied from two vantage points: bottom-up models emphasize a protein regulatory network centered around cyclin-dependent protein kinases, whereas top-down models focus on a gene regulatory network governed by interrelated transcription factors. The first project is focused on unifying these two perspectives. The second project is focused on the development of stochastic models of the regulatory network controlling the cell cycle. Both projects are performed in close collaboration with experts in computer science, data mining, bioinformatics, and mathematical modeling. The successful candidate will be expected to contribute significantly to these two projects by being responsible for designing and performing experiments used to validate model predictions. These experiments will involve the development of a new collection of cell cycle mutants and their quantitative characterization by time-lapse microscopy. In addition, the successful candidate will be expected to prepare the results for publication and presentation, to help supervise graduate and undergraduate students, and to contribute to grant proposals.

Dependent on the qualifications of the successful candidate, the position will hold the research faculty rank of either Research Associate or Senior Research Associate.

Go to the [http://bit.ly/n4nDUQ position description] for additional information and for submitting applications.

More information about our team can be found by visiting:
* [http://www.vbi.vt.edu/faculty/personal/Jean_Peccoud Jean Peccoud's home page]
* [http://www.biol.vt.edu/faculty/tyson/ John Tyson's home page]
* [https://bioinformatics.cs.vt.edu/~murali/ T.M. Murali's home page]

==""Postdoctoral position - Laboratory of Cell Physics - Strasbourg, France""==
Postdoctoral position is available in the Laboratory of Cell Physics, ISIS/IGBMC, Strasbourg, France. The project will focus on the dynamics of the cytokinetic ring in the fission yeast S. pombe. The roles of the Rho GTPase, actin polymerisation, and myosin will be studied. The work will involve genetics, cell biology, microscopy, microfabrication and microfluidics; for more information, send a CV and contact information of referees to Dr. Daniel Riveline (riveline@unistra.fr)

==""Postdoctoral Position in Quantitative Systems Biology""==
A postdoctoral fellow position is immediately available for a highly motivated recent PhD or MD/PhD graduate in biomedical science in the lab of Dr. Gregor Neuert at Vanderbilt University School of Medicine in Nashville, Tennessee.

The main interests of the group focuses on quantitative understanding of signaling and gene regulatory processes of coding and non-coding RNA in single cells at single molecule resolution. Our research methods include a combination of single-cell experimental and computational techniques as well as molecular biology and yeast genetics.

We are seeking highly motivated and curious applicants with strong background in yeast genetics, molecular biology and computational biology. Background in microscopy and computational modeling is also considered a plus but not required.

We offer a highly interactive, international and interdisciplinary research environment with strong mentoring and career development support. Vanderbilt University School of Medicine is ranked #9 in NIH funding and #15 in U.S. News medical school ranking and is equipped with world-class cutting-edge core facilities.

Selected publications:
Neuert, Munsky et al. Science 2013 ; Munsky, Neuert et al. Science 2012; Bumgarner, Neuert et al. Mol.Cell 2012; Van Werven, Neuert et al. Cell 2013

Interested applicants should send curriculum vitae, a summary of research experience and accomplishments, and contact information of 2-3 references to gregor.neuert@vanderbilt.edu.

For more information please visit:
https://www.mc.vanderbilt.edu/root/vumc.php?site=neuertlab

General Topics

2013-05-06T21:17:45Z

Plloyd:

This page has replaced the Virtual Library.
=General S. cerevisiae information=

*Generally speaking:
**[[What_are_yeast?|What are yeast?]]
**Here are some [http://www.yeastgenome.org/yeast_images.shtml pictures] of yeast

*The [http://www.yeastgenome.org/community/ArtOfBrewing.htm Art of Brewing], courtesy of [http://www.millerbrewing.com/ Miller Brewing Company].

*Information about winemaking, from [http://www.wine-oenology.com Wine High School of The Champagne region].

*Information about yeast and bread baking, from [http://www.breadworld.com/ Fleischmann's] and [http://www.redstaryeast.com/ Red Star Yeast] companies.

*Information about the yeast-based foods [http://www.accomodata.co.uk/marmite.htm Marmite] and [http://www.vegemite.com.au/ Vegemite].

*An [http://www.urmc.rochester.edu/labs/Sherman-Lab/publications/pdfs/Saccharomyces-Cerevisiae-Yeast-Intro.pdf introduction to yeast], the most ideal eukaryotic microorganism for biological studies, written by Fred Sherman.

*An updated version of the yeast primer [http://www.urmc.rochester.edu/labs/Sherman-Lab/publications/pdfs/Getting-Started-With-Yeast.pdf Getting Started with Yeast] written by Fred Sherman.

*[http://biochemie.web.med.uni-muenchen.de/Yeast_Biol/ Yeast Molecular Biology: A Short Compendium on Basic Features and Novel Aspects] written by Horst Feldmann at the University of Munich

*Download a [http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf guide to S.cerevisiae nomenclature], published in [http://www.sciencedirect.com/science/journal/01689525 Trends in Genetics].

*A [[Polymerase_targets|table]] describing the gene targets of the different RNA polymerases in S. cerevisiae.

*A [http://www.usask.ca/biology/sgd/sgd1.html tutorial] from the University of Saskatchewan provides an introduction to SGD and to S. cerevisiae molecular biology and genetics.

*A [[External_Links|list]] of websites with relevance to S. cerevisiae molecular biology and genetics and to general molecular biology.

*Search the [http://www.bio.net/hypermail/yeast/ Yeast BioSci] (a.k.a. BioNet) Electronic Conference

*Usenet group on yeast molecular biology: [http://www.bio.net/hypermail/yeast/ bionet.molbio.yeast]

*Curated publications at SGD describing [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Industrial%20Applications industrial uses of yeast], such as biofuels, winemaking, brewing.

*Curated publications at SGD addressing [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Infection%20and%20Antifungals infections and antifungals] and [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Disease%20Gene%20Related genes associated with diseases]

=Educational resources=

*[http://www.phys.ksu.edu/gene/ Genetics Education Network] Tom Manney's (Kansas State University) yeast experiments for undergrads and high school students. A well-done and informative web site for yeast in the classroom.

*[http://faculty.bsc.edu/phanson/yen/ Yeast Education Network] An archive of yeast-based teaching tools for the undergraduate classroom and laboratory. This site also includes most of the Education Workshop talks from YGM 2008.

*[http://www.cur.org/reslink2000.html Research Link 2000] Aimed at undergraduate classrooms, this is an offshoot of Tom Manney's yeast experiments. It also lists other model organisms.

*[http://www.woodrow.org/teachers/bi/1993/using.html Using Yeast As An Ultraviolet Light Measurement Tool.] This is a Tom Manney protocol rewritten by Kevin Conant, a participant in the Woodrow Wilson Biology Institute 1993.

*[http://www.mendelweb.org/ MendelWeb], an educational resource on the origins of classical genetics.

*[http://www.nsta.org National Science Teachers Association.] Resources for all science teachers from kindergarten to college.

*[http://www.nabt.org National Association of Biology Teachers] High school teachers predominate in this organization, but there are resources for post-secondary education as well.

*[http://www.asm.org American Society for Microbiology.] The ASM website lists resources in its education section. The ASM publishes numerous books on microbiology education at various levels.

*[http://www.bio.davidson.edu/courses/genomics/genomics.html Discovering Genomics, Proteomics, and Bioinformatics] This website describes a course and the accompanying textbook written by A. Malcolm Campbell and Laurie J. Heyer.

*[http://www.bio.davidson.edu/projects/GCAT/gcat.html Genome Consortium for Active Teaching (GCAT)] Description of the consortium and how it is working to bring functional genomics methods into the undergraduate biology curriculum.

*[http://www.actionbioscience.org/genomic/index.html Issues in Genomics] ActionBioscience.org lists a number of articles on genomics topics.

*[http://www.bio.davidson.edu/projects/magic/magic.html MicroArray Genome Imaging and Clustering Tool (MAGIC)] Open source software for analysis of large-scale gene expression datasets; developed by Laurie Heyer and her undergraduate students at Davidson College, North Carolina.

*[http://Vadlo.com VADLO Life Sciences Search Engine] from Life in Research, LLC. Provides search for life sciences research methods, databases, online tools, software, and powerpoints. For example [http://search.vadlo.com/b/q?k=Yeast+Protocols&rel=0 Yeast protocols], [http://search.vadlo.com/b/q?k=Yeast&rel=3 Yeast databases], [http://search.vadlo.com/b/q?k=Cerevisiae&rel=2 S. cerevisiae Powerpoints].

*[http://www.nature.com/scitable Scitable] A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.

*[http://www.guidetohealthcareschools.com/library/human-genetics The Human Genetics Education Resource] A general guide to resources in human genomics, inheritance, molecular genetics, genetic interactions, gene expression and evolution.

*[http://genetics.thetech.org/book-titles When Will Broccoli Taste Like Chocolate?: Your Questions on Genetic Traits Answered by Stanford University Scientists] A collection of general genetics questions and answers from the Ask a Geneticist section of [http://www.thetech.org/ The Tech Museum website].

=Schizosaccharomyces pombe information=

*[http://www.nature.com/nature/journal/v415/n6874/abs/nature724.html S. pombe genomic sequence] published by V. Wood et al., [http://www.nature.com Nature] 415, 871-880 (2002)

*[http://www.genedb.org/genedb/pombe/index.jsp PomBase] S. pombe database compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/cgi-bin/blast/submitblast/s_pombe Blast Server] for S. pombe compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/Projects/S_pombe/EUseqgrp.shtml European Schizosaccharomyces genome sequencing project]

*[http://www-rcf.usc.edu/~forsburg/ General information about S. pombe] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/vectors.html S. pombe molecular genetics: plasmids, markers, maps and references] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/genetable.html An S. pombe nomenclature guide]: S. pombe genes mapped to S. cerevisiae genes from the Forsburg Lab

=Candida albicans information=

*[http://candida.bri.nrc.ca/candida/index.cfm Candida albicans pages] at the NRC/BRI

*[http://www.candidagenome.org/ Candida Genome Database] at Stanford

*[http://www-sequence.stanford.edu/group/candida/ Candida information] from the Stanford Genome Technology Center

*[http://genolist.pasteur.fr/CandidaDB/ CandidaDB], a genomic database for C. albicans, part of the Galar Fungail Consortium project

*[http://albicansmap.ahc.umn.edu/ Institute for Candida experimentation] at the University of Minnesota

*[http://www.nlm.nih.gov/medlineplus/candidiasis.html Candidiasis information] at MEDLINE plus

*[http://agabian.ucsf.edu/ Annotation of the C. albicans genome] from the Agabian Lab

=Links to other fungal information=

*[http://botit.botany.wisc.edu/toms_fungi/ Tom Volk's Fungi]

*[http://www.doctorfungus.org/ Doctor Fungus]

*[http://www.fgsc.net/ The Fungal Genetics Stock Center]

=Fungal genome sequencing projects=

==Euascomycota==
*[http://www.tigr.org/tdb/e2k1/afu1/ Aspergillus fumigatus]
*[http://www.broad.mit.edu/annotation/fungi/aspergillus/ Aspergillus nidulans]
*[http://www.broad.mit.edu/annotation/fungi/magnaporthe/ Magnaporthe grisea]
*[http://www.broad.mit.edu/annotation/fungi/neurospora/ Neurospora crassa]

==Basidiomycota==

* ''Cryptococcus''
**[http://sequence-www.stanford.edu/group/C.neoformans/index.html ''Cryptococcus neoformans'' var. ''neoformans'' strain B3501]
** [http://www.tigr.org/tdb/e2k1/cna1/ ''Cryptococcus neoformans'' var. ''neoformans'' strain JEC21]
** ''Cryptococcus neoformans'' var. ''grubii'' H99 - [http://cneo.genetics.duke.edu/ Duke University], [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans Fungal Genome Initiative]
** ''Cryptococcus gattii'' R265 - [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans_b Fungal Genome Initiative]
** ''Cryptococcus gattii'' WM276 - [http://www.bcgsc.ca/project/cryptococcus/ Kronstad Lab/British Columbia Genome Sequencing Centre]

* [http://www.broad.mit.edu/annotation/genome/coprinus_cinereus/ ''Coprinus cinereus'']
* [http://www.broad.mit.edu/annotation/genome/puccinia_graminis ''Puccinia graminis f. sp. tritici'']
* [http://www.broad.mit.edu/annotation/genome/ustilago_maydis/ ''Ustilago maydis''], [http://mips.gsf.de/genre/proj/ustilago/ MIPS resources].

==Archiascomycota==
* [http://pgp.cchmc.org/ ''Pneumocystis carinii'']
* [http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus ''Schizosaccharomyces japonicus'']

==Hemiascomycota==
* The [http://cbi.labri.fr/Genolevures/ Génolevures] project, featuring partial genomic sequence for 13 Hemiascomycete species

==Links==
* There is also [http://fungalgenomes.org/wiki/Fungal_Genome_Links list] of currently sequenced or in progress fungal genome projects with references.

=Fungal genome database projects=

*[http://www.aspgd.org/ Aspergillus Genome Database], a database for A. nidulans, A. fumigatus, A. niger and related species.
* [http://cryptogenome.ucsf.edu/ CryptoBase], a scientific database resource at [http://www.ucsf.edu UCSF] for ''C. neoformans'' var. ''grubii'' (serotype A)
*[http://fungal.genome.duke.edu fungal.genome.duke.edu], a scientific database resource at [http://www.duke.edu Duke University] providing Genome Browser, BLAST, and downloadable genome annotations for many fungal genomes.

General Topics

2013-05-06T21:16:25Z

Plloyd: Undo revision 398052 by Plloyd (talk)

This page has replaced the Virtual Library.
=General S. cerevisiae information=

*Generally speaking:
**[[What_are_yeast?|What are yeast?]]
**Here are some [http://www.yeastgenome.org/yeast_images.shtml pictures] of yeast

*The [http://www.yeastgenome.org/community/ArtOfBrewing.htm Art of Brewing], courtesy of [http://www.millerbrewing.com/ Miller Brewing Company].

*Information about winemaking, from [http://www.wine-oenology.com Wine High School of The Champagne region].

*Information about yeast and bread baking, from [http://www.breadworld.com/ Fleischmann's] and [http://www.redstaryeast.com/ Red Star Yeast] companies.

*Information about the yeast-based foods [http://www.accomodata.co.uk/marmite.htm Marmite] and [http://www.vegemite.com.au/ Vegemite].

*An [http://dbb.urmc.rochester.edu/labs/Sherman_f/yeast/Index.html introduction] to yeast, the most ideal eukaryotic microorganism for biological studies, written by Fred Sherman.

*An updated version of the yeast primer [http://dbb.urmc.rochester.edu/labs/sherman_f/StartedYeast.html Getting Started with Yeast] written by Fred Sherman.

*[http://biochemie.web.med.uni-muenchen.de/Yeast_Biol/ Yeast Molecular Biology: A Short Compendium on Basic Features and Novel Aspects] written by Horst Feldmann at the University of Munich

*Download a [http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf guide to S.cerevisiae nomenclature], published in [http://www.sciencedirect.com/science/journal/01689525 Trends in Genetics].

*A [[Polymerase_targets|table]] describing the gene targets of the different RNA polymerases in S. cerevisiae.

*A [http://www.usask.ca/biology/sgd/sgd1.html tutorial] from the University of Saskatchewan provides an introduction to SGD and to S. cerevisiae molecular biology and genetics.

*A [[External_Links|list]] of websites with relevance to S. cerevisiae molecular biology and genetics and to general molecular biology.

*Search the [http://www.bio.net/hypermail/yeast/ Yeast BioSci] (a.k.a. BioNet) Electronic Conference

*Usenet group on yeast molecular biology: [http://www.bio.net/hypermail/yeast/ bionet.molbio.yeast]

*Curated publications at SGD describing [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Industrial%20Applications industrial uses of yeast], such as biofuels, winemaking, brewing.

*Curated publications at SGD addressing [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Infection%20and%20Antifungals infections and antifungals] and [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Disease%20Gene%20Related genes associated with diseases]

=Educational resources=

*[http://www.phys.ksu.edu/gene/ Genetics Education Network] Tom Manney's (Kansas State University) yeast experiments for undergrads and high school students. A well-done and informative web site for yeast in the classroom.

*[http://faculty.bsc.edu/phanson/yen/ Yeast Education Network] An archive of yeast-based teaching tools for the undergraduate classroom and laboratory. This site also includes most of the Education Workshop talks from YGM 2008.

*[http://www.cur.org/reslink2000.html Research Link 2000] Aimed at undergraduate classrooms, this is an offshoot of Tom Manney's yeast experiments. It also lists other model organisms.

*[http://www.woodrow.org/teachers/bi/1993/using.html Using Yeast As An Ultraviolet Light Measurement Tool.] This is a Tom Manney protocol rewritten by Kevin Conant, a participant in the Woodrow Wilson Biology Institute 1993.

*[http://www.mendelweb.org/ MendelWeb], an educational resource on the origins of classical genetics.

*[http://www.nsta.org National Science Teachers Association.] Resources for all science teachers from kindergarten to college.

*[http://www.nabt.org National Association of Biology Teachers] High school teachers predominate in this organization, but there are resources for post-secondary education as well.

*[http://www.asm.org American Society for Microbiology.] The ASM website lists resources in its education section. The ASM publishes numerous books on microbiology education at various levels.

*[http://www.bio.davidson.edu/courses/genomics/genomics.html Discovering Genomics, Proteomics, and Bioinformatics] This website describes a course and the accompanying textbook written by A. Malcolm Campbell and Laurie J. Heyer.

*[http://www.bio.davidson.edu/projects/GCAT/gcat.html Genome Consortium for Active Teaching (GCAT)] Description of the consortium and how it is working to bring functional genomics methods into the undergraduate biology curriculum.

*[http://www.actionbioscience.org/genomic/index.html Issues in Genomics] ActionBioscience.org lists a number of articles on genomics topics.

*[http://www.bio.davidson.edu/projects/magic/magic.html MicroArray Genome Imaging and Clustering Tool (MAGIC)] Open source software for analysis of large-scale gene expression datasets; developed by Laurie Heyer and her undergraduate students at Davidson College, North Carolina.

*[http://Vadlo.com VADLO Life Sciences Search Engine] from Life in Research, LLC. Provides search for life sciences research methods, databases, online tools, software, and powerpoints. For example [http://search.vadlo.com/b/q?k=Yeast+Protocols&rel=0 Yeast protocols], [http://search.vadlo.com/b/q?k=Yeast&rel=3 Yeast databases], [http://search.vadlo.com/b/q?k=Cerevisiae&rel=2 S. cerevisiae Powerpoints].

*[http://www.nature.com/scitable Scitable] A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.

*[http://www.guidetohealthcareschools.com/library/human-genetics The Human Genetics Education Resource] A general guide to resources in human genomics, inheritance, molecular genetics, genetic interactions, gene expression and evolution.

*[http://genetics.thetech.org/book-titles When Will Broccoli Taste Like Chocolate?: Your Questions on Genetic Traits Answered by Stanford University Scientists] A collection of general genetics questions and answers from the Ask a Geneticist section of [http://www.thetech.org/ The Tech Museum website].

=Schizosaccharomyces pombe information=

*[http://www.nature.com/nature/journal/v415/n6874/abs/nature724.html S. pombe genomic sequence] published by V. Wood et al., [http://www.nature.com Nature] 415, 871-880 (2002)

*[http://www.genedb.org/genedb/pombe/index.jsp PomBase] S. pombe database compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/cgi-bin/blast/submitblast/s_pombe Blast Server] for S. pombe compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/Projects/S_pombe/EUseqgrp.shtml European Schizosaccharomyces genome sequencing project]

*[http://www-rcf.usc.edu/~forsburg/ General information about S. pombe] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/vectors.html S. pombe molecular genetics: plasmids, markers, maps and references] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/genetable.html An S. pombe nomenclature guide]: S. pombe genes mapped to S. cerevisiae genes from the Forsburg Lab

=Candida albicans information=

*[http://candida.bri.nrc.ca/candida/index.cfm Candida albicans pages] at the NRC/BRI

*[http://www.candidagenome.org/ Candida Genome Database] at Stanford

*[http://www-sequence.stanford.edu/group/candida/ Candida information] from the Stanford Genome Technology Center

*[http://genolist.pasteur.fr/CandidaDB/ CandidaDB], a genomic database for C. albicans, part of the Galar Fungail Consortium project

*[http://albicansmap.ahc.umn.edu/ Institute for Candida experimentation] at the University of Minnesota

*[http://www.nlm.nih.gov/medlineplus/candidiasis.html Candidiasis information] at MEDLINE plus

*[http://agabian.ucsf.edu/ Annotation of the C. albicans genome] from the Agabian Lab

=Links to other fungal information=

*[http://botit.botany.wisc.edu/toms_fungi/ Tom Volk's Fungi]

*[http://www.doctorfungus.org/ Doctor Fungus]

*[http://www.fgsc.net/ The Fungal Genetics Stock Center]

=Fungal genome sequencing projects=

==Euascomycota==
*[http://www.tigr.org/tdb/e2k1/afu1/ Aspergillus fumigatus]
*[http://www.broad.mit.edu/annotation/fungi/aspergillus/ Aspergillus nidulans]
*[http://www.broad.mit.edu/annotation/fungi/magnaporthe/ Magnaporthe grisea]
*[http://www.broad.mit.edu/annotation/fungi/neurospora/ Neurospora crassa]

==Basidiomycota==

* ''Cryptococcus''
**[http://sequence-www.stanford.edu/group/C.neoformans/index.html ''Cryptococcus neoformans'' var. ''neoformans'' strain B3501]
** [http://www.tigr.org/tdb/e2k1/cna1/ ''Cryptococcus neoformans'' var. ''neoformans'' strain JEC21]
** ''Cryptococcus neoformans'' var. ''grubii'' H99 - [http://cneo.genetics.duke.edu/ Duke University], [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans Fungal Genome Initiative]
** ''Cryptococcus gattii'' R265 - [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans_b Fungal Genome Initiative]
** ''Cryptococcus gattii'' WM276 - [http://www.bcgsc.ca/project/cryptococcus/ Kronstad Lab/British Columbia Genome Sequencing Centre]

* [http://www.broad.mit.edu/annotation/genome/coprinus_cinereus/ ''Coprinus cinereus'']
* [http://www.broad.mit.edu/annotation/genome/puccinia_graminis ''Puccinia graminis f. sp. tritici'']
* [http://www.broad.mit.edu/annotation/genome/ustilago_maydis/ ''Ustilago maydis''], [http://mips.gsf.de/genre/proj/ustilago/ MIPS resources].

==Archiascomycota==
* [http://pgp.cchmc.org/ ''Pneumocystis carinii'']
* [http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus ''Schizosaccharomyces japonicus'']

==Hemiascomycota==
* The [http://cbi.labri.fr/Genolevures/ Génolevures] project, featuring partial genomic sequence for 13 Hemiascomycete species

==Links==
* There is also [http://fungalgenomes.org/wiki/Fungal_Genome_Links list] of currently sequenced or in progress fungal genome projects with references.

=Fungal genome database projects=

*[http://www.aspgd.org/ Aspergillus Genome Database], a database for A. nidulans, A. fumigatus, A. niger and related species.
* [http://cryptogenome.ucsf.edu/ CryptoBase], a scientific database resource at [http://www.ucsf.edu UCSF] for ''C. neoformans'' var. ''grubii'' (serotype A)
*[http://fungal.genome.duke.edu fungal.genome.duke.edu], a scientific database resource at [http://www.duke.edu Duke University] providing Genome Browser, BLAST, and downloadable genome annotations for many fungal genomes.

General Topics

2013-05-06T21:15:33Z

Plloyd:

This page has replaced the Virtual Library.
=General S. cerevisiae information=

*Generally speaking:
**[[What_are_yeast?|What are yeast?]]
**Here are some [http://www.yeastgenome.org/yeast_images.shtml pictures] of yeast

*The [http://www.yeastgenome.org/community/ArtOfBrewing.htm Art of Brewing], courtesy of [http://www.millerbrewing.com/ Miller Brewing Company].

*Information about winemaking, from [http://www.wine-oenology.com Wine High School of The Champagne region].

*Information about yeast and bread baking, from [http://www.breadworld.com/ Fleischmann's] and [http://www.redstaryeast.com/ Red Star Yeast] companies.

*Information about the yeast-based foods [http://www.accomodata.co.uk/marmite.htm Marmite] and [http://www.vegemite.com.au/ Vegemite].

*An [http://www.urmc.rochester.edu/labs/Sherman-Lab/publications/pdfs/Getting-Started-With-Yeast.pdf introduction] to yeast, the most ideal eukaryotic microorganism for biological studies, written by Fred Sherman.

*An updated version of the yeast primer [http://dbb.urmc.rochester.edu/labs/sherman_f/StartedYeast.html Getting Started with Yeast] written by Fred Sherman.

*[http://biochemie.web.med.uni-muenchen.de/Yeast_Biol/ Yeast Molecular Biology: A Short Compendium on Basic Features and Novel Aspects] written by Horst Feldmann at the University of Munich

*Download a [http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf guide to S.cerevisiae nomenclature], published in [http://www.sciencedirect.com/science/journal/01689525 Trends in Genetics].

*A [[Polymerase_targets|table]] describing the gene targets of the different RNA polymerases in S. cerevisiae.

*A [http://www.usask.ca/biology/sgd/sgd1.html tutorial] from the University of Saskatchewan provides an introduction to SGD and to S. cerevisiae molecular biology and genetics.

*A [[External_Links|list]] of websites with relevance to S. cerevisiae molecular biology and genetics and to general molecular biology.

*Search the [http://www.bio.net/hypermail/yeast/ Yeast BioSci] (a.k.a. BioNet) Electronic Conference

*Usenet group on yeast molecular biology: [http://www.bio.net/hypermail/yeast/ bionet.molbio.yeast]

*Curated publications at SGD describing [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Industrial%20Applications industrial uses of yeast], such as biofuels, winemaking, brewing.

*Curated publications at SGD addressing [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Infection%20and%20Antifungals infections and antifungals] and [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Disease%20Gene%20Related genes associated with diseases]

=Educational resources=

*[http://www.phys.ksu.edu/gene/ Genetics Education Network] Tom Manney's (Kansas State University) yeast experiments for undergrads and high school students. A well-done and informative web site for yeast in the classroom.

*[http://faculty.bsc.edu/phanson/yen/ Yeast Education Network] An archive of yeast-based teaching tools for the undergraduate classroom and laboratory. This site also includes most of the Education Workshop talks from YGM 2008.

*[http://www.cur.org/reslink2000.html Research Link 2000] Aimed at undergraduate classrooms, this is an offshoot of Tom Manney's yeast experiments. It also lists other model organisms.

*[http://www.woodrow.org/teachers/bi/1993/using.html Using Yeast As An Ultraviolet Light Measurement Tool.] This is a Tom Manney protocol rewritten by Kevin Conant, a participant in the Woodrow Wilson Biology Institute 1993.

*[http://www.mendelweb.org/ MendelWeb], an educational resource on the origins of classical genetics.

*[http://www.nsta.org National Science Teachers Association.] Resources for all science teachers from kindergarten to college.

*[http://www.nabt.org National Association of Biology Teachers] High school teachers predominate in this organization, but there are resources for post-secondary education as well.

*[http://www.asm.org American Society for Microbiology.] The ASM website lists resources in its education section. The ASM publishes numerous books on microbiology education at various levels.

*[http://www.bio.davidson.edu/courses/genomics/genomics.html Discovering Genomics, Proteomics, and Bioinformatics] This website describes a course and the accompanying textbook written by A. Malcolm Campbell and Laurie J. Heyer.

*[http://www.bio.davidson.edu/projects/GCAT/gcat.html Genome Consortium for Active Teaching (GCAT)] Description of the consortium and how it is working to bring functional genomics methods into the undergraduate biology curriculum.

*[http://www.actionbioscience.org/genomic/index.html Issues in Genomics] ActionBioscience.org lists a number of articles on genomics topics.

*[http://www.bio.davidson.edu/projects/magic/magic.html MicroArray Genome Imaging and Clustering Tool (MAGIC)] Open source software for analysis of large-scale gene expression datasets; developed by Laurie Heyer and her undergraduate students at Davidson College, North Carolina.

*[http://Vadlo.com VADLO Life Sciences Search Engine] from Life in Research, LLC. Provides search for life sciences research methods, databases, online tools, software, and powerpoints. For example [http://search.vadlo.com/b/q?k=Yeast+Protocols&rel=0 Yeast protocols], [http://search.vadlo.com/b/q?k=Yeast&rel=3 Yeast databases], [http://search.vadlo.com/b/q?k=Cerevisiae&rel=2 S. cerevisiae Powerpoints].

*[http://www.nature.com/scitable Scitable] A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.

*[http://www.guidetohealthcareschools.com/library/human-genetics The Human Genetics Education Resource] A general guide to resources in human genomics, inheritance, molecular genetics, genetic interactions, gene expression and evolution.

*[http://genetics.thetech.org/book-titles When Will Broccoli Taste Like Chocolate?: Your Questions on Genetic Traits Answered by Stanford University Scientists] A collection of general genetics questions and answers from the Ask a Geneticist section of [http://www.thetech.org/ The Tech Museum website].

=Schizosaccharomyces pombe information=

*[http://www.nature.com/nature/journal/v415/n6874/abs/nature724.html S. pombe genomic sequence] published by V. Wood et al., [http://www.nature.com Nature] 415, 871-880 (2002)

*[http://www.genedb.org/genedb/pombe/index.jsp PomBase] S. pombe database compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/cgi-bin/blast/submitblast/s_pombe Blast Server] for S. pombe compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/Projects/S_pombe/EUseqgrp.shtml European Schizosaccharomyces genome sequencing project]

*[http://www-rcf.usc.edu/~forsburg/ General information about S. pombe] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/vectors.html S. pombe molecular genetics: plasmids, markers, maps and references] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/genetable.html An S. pombe nomenclature guide]: S. pombe genes mapped to S. cerevisiae genes from the Forsburg Lab

=Candida albicans information=

*[http://candida.bri.nrc.ca/candida/index.cfm Candida albicans pages] at the NRC/BRI

*[http://www.candidagenome.org/ Candida Genome Database] at Stanford

*[http://www-sequence.stanford.edu/group/candida/ Candida information] from the Stanford Genome Technology Center

*[http://genolist.pasteur.fr/CandidaDB/ CandidaDB], a genomic database for C. albicans, part of the Galar Fungail Consortium project

*[http://albicansmap.ahc.umn.edu/ Institute for Candida experimentation] at the University of Minnesota

*[http://www.nlm.nih.gov/medlineplus/candidiasis.html Candidiasis information] at MEDLINE plus

*[http://agabian.ucsf.edu/ Annotation of the C. albicans genome] from the Agabian Lab

=Links to other fungal information=

*[http://botit.botany.wisc.edu/toms_fungi/ Tom Volk's Fungi]

*[http://www.doctorfungus.org/ Doctor Fungus]

*[http://www.fgsc.net/ The Fungal Genetics Stock Center]

=Fungal genome sequencing projects=

==Euascomycota==
*[http://www.tigr.org/tdb/e2k1/afu1/ Aspergillus fumigatus]
*[http://www.broad.mit.edu/annotation/fungi/aspergillus/ Aspergillus nidulans]
*[http://www.broad.mit.edu/annotation/fungi/magnaporthe/ Magnaporthe grisea]
*[http://www.broad.mit.edu/annotation/fungi/neurospora/ Neurospora crassa]

==Basidiomycota==

* ''Cryptococcus''
**[http://sequence-www.stanford.edu/group/C.neoformans/index.html ''Cryptococcus neoformans'' var. ''neoformans'' strain B3501]
** [http://www.tigr.org/tdb/e2k1/cna1/ ''Cryptococcus neoformans'' var. ''neoformans'' strain JEC21]
** ''Cryptococcus neoformans'' var. ''grubii'' H99 - [http://cneo.genetics.duke.edu/ Duke University], [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans Fungal Genome Initiative]
** ''Cryptococcus gattii'' R265 - [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans_b Fungal Genome Initiative]
** ''Cryptococcus gattii'' WM276 - [http://www.bcgsc.ca/project/cryptococcus/ Kronstad Lab/British Columbia Genome Sequencing Centre]

* [http://www.broad.mit.edu/annotation/genome/coprinus_cinereus/ ''Coprinus cinereus'']
* [http://www.broad.mit.edu/annotation/genome/puccinia_graminis ''Puccinia graminis f. sp. tritici'']
* [http://www.broad.mit.edu/annotation/genome/ustilago_maydis/ ''Ustilago maydis''], [http://mips.gsf.de/genre/proj/ustilago/ MIPS resources].

==Archiascomycota==
* [http://pgp.cchmc.org/ ''Pneumocystis carinii'']
* [http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus ''Schizosaccharomyces japonicus'']

==Hemiascomycota==
* The [http://cbi.labri.fr/Genolevures/ Génolevures] project, featuring partial genomic sequence for 13 Hemiascomycete species

==Links==
* There is also [http://fungalgenomes.org/wiki/Fungal_Genome_Links list] of currently sequenced or in progress fungal genome projects with references.

=Fungal genome database projects=

*[http://www.aspgd.org/ Aspergillus Genome Database], a database for A. nidulans, A. fumigatus, A. niger and related species.
* [http://cryptogenome.ucsf.edu/ CryptoBase], a scientific database resource at [http://www.ucsf.edu UCSF] for ''C. neoformans'' var. ''grubii'' (serotype A)
*[http://fungal.genome.duke.edu fungal.genome.duke.edu], a scientific database resource at [http://www.duke.edu Duke University] providing Genome Browser, BLAST, and downloadable genome annotations for many fungal genomes.

Commonly used strains

2013-05-06T21:12:58Z

Plloyd:

This page describes some of the most commonly used yeast lab strains. Much of the information is taken from [http://www.urmc.rochester.edu/labs/Sherman-Lab/publications/pdfs/Getting-Started-With-Yeast.pdf F. Sherman (2002)] Getting started with yeast, Methods Enzymol. 350, 3-41. Other useful papers for strain background information include:

* [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000050744 Mortimer and Johnston] (1986) Genetics 113:35-43 - thoroughly describes the genealogy of strain S288C
* [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079648 van Dijken et al.] (2000) Enzyme Microb Technol 26:706-714 - compares various characteristics of commonly used lab strains
* [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000080159 Winzeler et al.] (2003) Genetics 163:79-89 - uses SFP (single-feature polymorphisms) analysis to study genetic identity between common lab strains

=S288C=
'''Genotype:''' ''MAT''α ''SUC2 gal2 mal mel flo1 flo8-1 hap1 ho bio1 bio6''

'''Notes:''' Strain used in the systematic sequencing project, the sequence stored in SGD. S288C does not form pseudohyphae. In addition, since it has a mutated copy of [http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000004246 ''HAP1''], it is not a good strain for mitochondrial studies. It has an allelic variant of [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=MIP1 ''MIP1''] which increases petite frequency. S288C strains are ''gal''2- and they do not use galactose anaerobically.

The S288C genome was recently resequenced at the [http://www.sanger.ac.uk/Teams/Team118/sgrp/ Sanger Institute].

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000050744 Mortimer and Johnston] (1986) Genetics 113:35-43.

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=204508&Template=yeastGeneticStock ATCC:204508]

==BY4743==
'''Genotype:''' ''MAT''a/α ''his3''Δ''1/his3''Δ''1 leu2''Δ''0/leu2''Δ''0 LYS2/lys2''Δ''0 met15''Δ''0/MET15 ura3''Δ''0/ura3''Δ''0''

'''Notes:''' Strain used in the [http://www-sequence.stanford.edu/group/yeast_deletion_project/project_desc.html systematic deletion project], generated from a cross between BY4741 and BY4742, which are derived from S288C. As S288c, these strains have an allelic variant of [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=MIP1 ''MIP1''] which increases petite frequency. See Brachmann et al. reference for details.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000041186 Brachmann et al.] (1998) Yeast 14:115-32.

'''Sources:''' [http://www.openbiosystems.com/Query/?i=0&q=YSC1050|Open Biosystems:YSC1050]

==FY4==
'''Genotype:''' ''MAT''a

'''Notes:''' Derived from S288C.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000047446 Winston et al.] (1995) Yeast 11:53-55.

[http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=9483801 Brachmann et al.] (1998) Yeast 14:115-32.

==FY1679==
'''Genotype:''' ''MAT''a/α ''ura3-52/ura3-52 trp1''Δ''63/TRP1 leu2''Δ''1/LEU2 his3''Δ''200/HIS3 GAL2/GAL''

'''Notes:''' Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000047446 Winston et al.] (1995) Yeast 11:53-55.

'''Sources:''' [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/data/fy1679.html EUROSCARF:10000D]

==AB972==
'''Genotype:''' ''MAT''α'' X2180-1B trp10 [rho 0]''

'''Notes:''' Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD. AB972 is an ethidium bromide-induced rho- derivative of the strain X2180-1B-''trp1''.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000057090 Olson MV et al.] (1986) Proc. Natl. Acad. Sci. USA 83:7826-7830.

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=204511&Template=yeastGeneticStock ATCC:204511]

==A364A==
'''Genotype:''' ''MAT''a'' ade1 ade2 ura1 his7 lys2 tyr1 gal1 SUC mal cup BIO''

'''Notes:''' Used in the systematic sequencing project, the sequence stored in SGD.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079649 Hartwell] (1967) J. Bacteriol. 93:1662-1670.

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=208526&Template=yeastGeneticStock ATCC:208526]

==XJ24-24a==
'''Genotype:''' ''MAT''a ''ho HMa HMα ade6 arg4-17 trp1-1 tyr7-1 MAL2''

'''Notes:''' Derived from, but not isogenic to, S288C

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000055409 Strathern et al.] (1979) Cell 18:309-319

==DC5==
'''Genotype:''' ''MAT''a'' leu2-3,112 his3-11,15 can1-11''

'''Notes:''' Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000054242 Broach et al.] (1979) Gene 8:121-133

==X2180-1A==
'''Genotype:''' ''MAT''a'' SUC2 mal mel gal2 CUP1''

'''Notes:'''S288c spontaneously diploidized to give rise to X2180. The haploid segregants X2180-1a and X2180-1b were obtained from sporulated X2180

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000050744 Mortimer and Johnston]

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=204504&Template=yeastGeneticStock ATCC:204504]

=YNN216=
'''Genotype:''' ''MAT''a/α ''ura3-52/ura3-52 lys2-801amber/lys2-801amber ade2-101ochre/ade2-101ochre''

'''Notes:''' Congenic to S288C (see Sikorski and Hieter). Used to derive YSS and CY strains (see Sobel and Wolin).

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski RS and Hieter P] (1989) Genetics 122:19-27. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000042217 Sobel and Wolin] (1999) Mol. Biol. Cell 10:3849-3862.
==YPH499==
'''Genotype:''' ''MAT''a ''ura3-52 lys2-801_amber ade2-101_ochre trp1-''Δ''63 his3-''Δ''200 leu2-''Δ''1''

'''Notes:''' Contains nonrevertible (deletion) auxotrophic mutations that can be used for selection of vectors. Note that ''trp1-''Δ''63'', unlike ''trp1-''Δ''1'', does not delete adjacent ''GAL3'' UAS sequence and retains homology to ''TRP1'' selectable marker. ''gal2-'', does not use galactose anaerobically. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski RS and Hieter P] (1989) Genetics 122:19-27. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000042217 Sobel and Wolin] (1999) Mol. Biol. Cell 10:3849-3862. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=6092912 Johnston M and Davis RW] (1984) Mol Cell Biol 4(8):1440-8.

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=204679&Template=yeastGeneticStock ATCC:204679]

==YPH500==
'''Genotype:''' ''MAT''α ''ura3-52 lys2-801_amber ade2-101_ochre trp1-''Δ''63 his3-''Δ''200 leu2-''Δ''1''

'''Notes:'''''MAT''α strain isogenic to [http://staff.yeastgenome.org/index.php/straintable#yph499 YPH499] except at mating type locus. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski RS and Hieter P] (1989) Genetics 122:19-27. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000042217 Sobel and Wolin] (1999) Mol. Biol. Cell 10:3849-3862. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=6092912 Johnston M and Davis RW] (1984) Mol Cell Biol 4(8):1440-8.

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=204680&Template=yeastGeneticStock ATCC:204680]

==YPH501==
'''Genotype:''' ''MAT''a/''MAT''α ''ura3-52/ura3-52 lys2-801_amber/lys2-801_amber ade2-101_ochre/ade2-101_ochre trp1-''Δ''63/trp1-''Δ''63 his3-''Δ''200/his3-''Δ''200 leu2-''Δ''1/leu2-''Δ''1''

'''Notes:''' a/α diploid isogenic to [http://staff.yeastgenome.org/index.php/straintable#yph499 YPH499] and [http://staff.yeastgenome.org/index.php/straintable#yph500 YPH500]. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski RS and Hieter P] (1989) Genetics 122:19-27. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000042217 Sobel and Wolin] (1999) Mol. Biol. Cell 10:3849-3862. [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=6092912 Johnston M and Davis RW] (1984) Mol Cell Biol 4(8):1440-8.

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=204681&Template=yeastGeneticStock ATCC:204681]

=Sigma1278b=

'''Notes:''' Used in pseudohyphal growth studies. [[History_of_Sigma|Detailed notes]] about the sigma strains have been kindly provided by Cora Styles.

[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000823 Granek and Magwene], PLoS Genet. 2010 Jan 22;6(1):e1000823, established that certain lineages of the Sigma1278B background contain
a nonsense mutation in RIM15, a G-to-T transversion at position 1216 that converts a Gly codon to an opal stop codon. This rim15 mutation interacts epistatically with mutations in certain other genes to affect colony morphology. The Sigma1278b genome is closely related to S288c, and shares some other genomic regions with W303 [http://dx.doi.org/10.1098/rsob.120093].

Annotation of the Sigma1278b genome and information about the systematic deletion collection can be found [http://mcdb.colorado.edu/labs1/dowelllab/pubs/DowellRyan/ here].

=SK1=
'''Genotype:''' ''MAT''a/α'' HO gal2 cupS can1R BIO''

'''Notes:''' Commonly used for studying sporulation or meiosis. Canavanine-resistant derivative.

The SK1 genome was sequenced at the [http://www.sanger.ac.uk/Teams/Team118/sgrp/ Sanger Institute].

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079650 Kane SM and Roth J.] (1974) Bacteriol. 118: 8-14

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=204722&Template=yeastGeneticStock ATCC:204722]

=CEN.PK (aka CEN.PK2)=
'''Genotype:''' ''MAT''a/α'' ura3-52/ura3-52 trp1-289/trp1-289 leu2-3_112/leu2-3_112 his3 ''Δ''1/his3 ''Δ''1 MAL2-8C/MAL2-8C SUC2/SUC2''

'''Notes:''' CEN.PK possesses a mutation in CYR1 (A5627T corresponding to a K1876M substitution near the end of the catalytic domain in adenylate cyclase which eliminates glucose- and acidification-induced cAMP signalling and delays glucose-induced loss of stress resistance ([http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000052724 Vanhalewyn et al., 1999]; [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043601 Dumortier et al., 2000]).

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079648 van Dijken et al.] (2000) Enzyme Microb Technol 26:706-714

'''Sources:''' [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/data/cen.html EUROSCARF:30000D]

=W303=
'''Genotype:''' ''MAT''a/''MAT''α {''leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15''} [''phi+'']

<table style="text-align: left; width: 526px; height: 174px;" border="1"
cellpadding="2" cellspacing="2">
<tr>
<td style="vertical-align: top; font-weight: bold;">allele 
</td>
<td style="vertical-align: top; font-weight: bold;">locus 
</td>
<td style="vertical-align: top; font-weight: bold;">mutation [http://dx.doi.org/10.1098/rsob.120093 (1)] 
</td>
</tr>
<tr>
<td style="vertical-align: top; font-style: italic;">ade2-1 
</td>
<td style="vertical-align: top;"> YOR128C</td>
<td style="vertical-align: top;">nonsense, glu64STOP 
</td>
</tr>
<tr>
<td style="vertical-align: top; font-style: italic;">trp1-1 
</td>
<td style="vertical-align: top;">YDR007W</td>
<td style="vertical-align: top;">nonsense, glu83STOP</td>
</tr>
<tr>
<td style="vertical-align: top; font-style: italic;">can1-100 
</td>
<td style="vertical-align: top;"> YEL063C</td>
<td style="vertical-align: top;">frameshift, lys47</td>
</tr>
<tr>
<td style="vertical-align: top; font-style: italic;">leu2-3,112 
</td>
<td style="vertical-align: top;">YCL018W 
</td>
<td style="vertical-align: top;">frameshift, gly83</td>
</tr>
<tr>
<td style="vertical-align: top; font-style: italic;">his3-11,15 
</td>
<td style="vertical-align: top;">YOR202W</td>
<td style="vertical-align: top;"> 2x frameshifts, ala70 and glu106</td>
</tr>
</table>

'''Notes:''' The W303 genome is to 85.4% derived from S288c, part of the other regions are similar to non-S288c regions of Sigma1278b. In total, some 800 CDS differ between W303 and S288c, but in most cases only one or two residues differ [http://dx.doi.org/10.1098/rsob.120093]. These include a ''bud4'' mutation that causes haploids to bud with a mixture of axial and bipolar budding
patterns. In addition, the original W303 strain contains the
''rad5-535'' allele. As S288c, W303 has an allelic variant of [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=MIP1 ''MIP1''] which increases petite frequency.

The W303 genome was sequenced at the [http://www.sanger.ac.uk/Teams/Team118/sgrp/ Sanger Institute] and by Ralser et al Open Biol 2: 120093.
[http://dx.doi.org/10.1098/rsob.120093 1] (DDBJ/EMBL/GenBank ALAV00000000).

'''References:''' W303 constructed by Rodney Rothstein (''see [[CommunityW303.html|detailed notes]] from RR and Stephan Bartsch''). ''bud4'' info: [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000120449 Voth et al.] (2005) Eukaryotic Cell, 4:1018-28. ''rad5-535'' info: Fan et al. (1996) Genetics 142:749

'''Sources:''' [http://www.openbiosystems.com/Query/?i=0&q=YSC1058|Open Biosystems:YSC1058]

==W303-1A==
'''Genotype:''' ''MAT''a {''leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15''}

'''Notes:''' W303-1A possesses a ''ybp1-1'' mutation (I7L, F328V, K343E, N571D) which abolishes Ybp1p function, increasing sensitivity to oxidative stress.

'''References:''' W303 constructed by Rodney Rothstein (''see [[CommunityW303.html|detailed notes]] from RR and Stephan Bartsch''). ''ybp1-1'' info: [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000073844 Veal et al.] (2003) J. Biol. Chem. 278:30896-904. 

'''Sources:''' [http://www.openbiosystems.com/Query/?i=0&q=YSC1058|Open Biosystems:YSC1058]

==W303-1B==
'''Genotype:''' ''MAT''α {''leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15''}

'''References:''' W303 constructed by Rodney Rothstein (''see [[CommunityW303.html|detailed notes]] from RR and Stephan Bartsch'').

'''Sources:''' [http://www.openbiosystems.com/Query/?i=0&q=YSC1058|Open Biosystems:YSC1058]

==W303-K6001==

'''Genotype:''' ''MAT''a; {''ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, GAL, psi+, ho::HO::CDC6 (at HO), cdc6::hisG, ura3::URA3 GAL-ubiR-CDC6 (at URA3)''}

'''References:''' K6001 was created in Kim Nasmyth's lab ''Piatti at al'' (PMID: 7641697) and ''Bobola et al'' (PMID: 8625408). K6001 has become a popular model in yeast aging research, as it allows a replicative aging assay based on microcolonies (PMID: 15489200). Its genome has been sequenced by Timmermann et al (PMID: 20729566), Ralser et al [http://dx.doi.org/10.1098/rsob.120093].

=D273-10B=
'''Genotype:''' ''MAT''α ''mal''

'''Notes:''' Normal cytochrome content and respiration; low frequency of rho-. This strain and its auxotrophic derivatives were used in numerious laboratories for mitochondrial and related studies and for mutant screens. Good respirer that's relatively resistant to glucose repression.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000080158 Sherman, F.] (1963) Genetics 48:375-385.

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=24657&Template=fungiYeast ATCC:24657]

=FL100=
'''Genotype:''' ''MAT''a

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000065623 Lacroute, F.] (1968) J. Bacteriol. 95:824-832.

Sources: ATCC: 28383

=SEY6210/SEY6211=
'''Genotype:''' ''MAT''a/''MAT''α ''leu2-3,112/leu2-3,112 ura3-52/ura3-52 his3-''Δ''200/his3-''Δ''200 trp1-''Δ''901/trp1-''Δ''901 ade2/ADE2 suc2-''Δ''9/suc2-''Δ''9 GAL/GAL LYS2/lys2-801''

'''Notes:''' SEY6210/SEY6211, also known as SEY6210.5, was constructed by Scott Emr and has been used in studies of autophagy, protein sorting etc. It is the product of crossing with strains from 5 different labs (Gerry Fink, Ron Davis, David Botstein, Fred Sherman, Randy Schekman). It has several selectable markers, good growth properties and good sporulation.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000045321 Robinson et al.] (1988) Mol Cell Biol 8(11):4936-48

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=201392&Template=fungiYeast ATCC:201392]

==SEY6210==
'''Genotype:''' ''MAT''α ''leu2-3,112 ura3-52 his3-''Δ''200 trp1-''Δ''901 suc2-''Δ''9 lys2-801; GAL''

'''Notes:''' SEY6210 is a MATalpha haploid constructed by Scott Emr and has been used in studies of autophagy, protein sorting etc. It is the product of crossing with strains from 5 different labs (Gerry Fink, Ron Davis, David Botstein, Fred Sherman, Randy Schekman). It has several selectable markers and good growth properties.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000045321 Robinson et al.] (1988) Mol Cell Biol 8(11):4936-48

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=96099&Template=fungiYeast ATCC:96099]

==SEY6211==
'''Genotype:''' ''MAT''a ''leu2-3,112 ura3-52 his3-''Δ''200 trp1-''Δ''901 ade2-101 suc2-''Δ''9; GAL''

'''Notes:''' SEY6211 is a MATa haploid constructed by Scott Emr and has been used in studies of autophagy, protein sorting etc. It is the product of crossing with strains from 5 different labs (Gerry Fink, Ron Davis, David Botstein, Fred Sherman, Randy Schekman). It has several selectable markers and good growth properties.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000045321 Robinson et al.] (1988) Mol Cell Biol 8(11):4936-48

'''Sources:''' [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=96100&Template=fungiYeast ATCC:96100]

=JK9-3d=

There are a, alpha and a/alpha diploids of JK9-3d with the following genotypes:

'''Genotypes:''' JK9-3da ''MAT''a ''leu2-3,112 ura3-52 rme1 trp1 his4''

JK9-3dα has the same genotype as JK9-3da with the exception of the MAT locus

JK9-3da/α is homozygous for all markers except mating type

'''Notes:''' JK9-3d was constructed by Jeanette Kunz while in Mike Hall's lab. She made the original strain while Joe Heitman isolated isogenic strains of opposite mating type and
derived the a/alpha isogenic diploid by mating type switching. It has in its background S288c, a strain from the Oshima lab, and a strain from the Herskowitz lab. It was chosen because of its robust growth and sporulation, as well as good growth on galactose (GAL+) (so that genes under control of the galactose promoter could be induced). It may also have a SUP mutation that allows translation through premature STOP codons and therefore produces functional alleles with many point mutations.

'''References:''' [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000054286 Heitman et al.] (1991a) Science 253(5022):905-9 and [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000054822 Heitman et al.] (1991b) Proc Natl Acad Sci U S A 88(5):1948-52

=RM11-1a=

'''Genotype:''' ''MAT''a ''leu2''Δ'' ura3''Δ'' ho::Kan

'''Notes:''' RM11-1a is a haploid derivative of Bb32(3), a natural isolate collected by Robert Mortimer from a California vineyard, as in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000041556 Mortimer et al., 1994]. It has high spore viability (80–90%) and has been extensively characterized phenotypically under a wide range of conditions. It has a significantly longer life span than typical lab yeast strains and accumulates age-associated abnormalities at a lower rate. It displays approximately 0.5–1% sequence divergence relative to S288c. More information is available at the [http://www.broad.mit.edu/annotation/genome/saccharomyces_cerevisiae.3/Home.html Broad Institute website].

'''References:''' [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000069875 Brem et al.] (2002) Science 296(5568):752-5

=Y55=

'''Genotype:''' ''MAT''a /''MAT''alpha ''HO''/''HO''

'''Notes:''' Y55 is a prototrophic, homothallic diploid strain that was originally isolated by Dennis Winge. Many auxotrophic mutant derivatives have been created by John McCusker by using ethidium bromide treatment to eliminate non-auxotrophs. Y55 background strains have been used to study the timing of meiotic recombination ([http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000148282 Borts et al. 1984]); to isolate almost all the subunits of the proteasome ([http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=3294104 McCusker and Haber 1988a], [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=3294103 1988b]); to get mutations in PMA1 and related genes ([http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=2963211 McCusker 1986]); and to do meiotic mapping and interference experiments ([http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15454526 Malkova et al. 2004]).