SGD-Wiki - User contributions [en]

Historical Systematic Sequence Information

2011-12-22T01:41:32Z

Eurie:

These pages refer to the systematic sequence of S288C prior to Release 64. Before Release 64, there were [[Guidelines_for_changing_systematic_sequence | guidelines for changing systematic sequence]].

=Chromosomal Features=
[http://www.yeastgenome.org/snoRNAtable.shtml snoRNAs in S. cerevisiae]

[http://www.yeastgenome.org/RNAmodTable.shtml Modified Nucleotides within RNAs in S. cerevisiae]

[http://www.yeastgenome.org/archive/newORF-sage.shtml SGD ORF Additions based on SAGE]

[http://www.yeastgenome.org/community/DSB_graphic.shtml Meiotic Double-Stranded Breaks in the Yeast Genome]

[http://www.yeastgenome.org/community/codon_usage.shtml Codon Usage Tables]

=Reagents=
[http://www.yeastgenome.org/community/primerPage.shtml Primer sets for amplifying yeast ORFs]

[http://www.yeastgenome.org/alleletable.shtml Commonly Used Auxotrophic Markers]

Guidelines for changing systematic sequence

2011-12-22T01:35:24Z

Eurie: Created page with "#The complete sequence of S. cerevisiae is that of strain S288C. Therefore, the first step is to be sure that you have sequenced that strain. Data on other strains are interestin..."

#The complete sequence of S. cerevisiae is that of strain S288C. Therefore, the first step is to be sure that you have sequenced that strain. Data on other strains are interesting to remember as notes but cannot result in changing the systematic sequence edition in the yeast databases. If the strain you sequenced is different from S288C, you can submit your piece of sequence to Genbank/EMBL/DDBJ with a clear indication of your strain. Your sequence will then be linked to the locus in SGD although it will not be the systematic sequence stored in the database. It is only by strictly following this principle that we can distinguish sequence errors that need to be corrected from natural polymorphisms that should not be inserted in the sequence.
#Although nucleotide omission is the most frequent type of sequencing error, it is not because the protein reported by an author is longer than the predicted one that it is correct. There are several cases of real in-frame stop codons verified by direct sequencing of the DNA of S288C (B. Dujon, personal communication). Therefore, the second step is to provide the experimental demonstration that the sequence change you propose is real. Sequencing a PCR reaction amplified on S288C DNA and covering the region of interest is the best method.
#After steps 1 and 2 are finished, please [http://www.yeastgenome.org/cgi-bin/suggestion contact SGD] and MIPS with details about the proposed change.

MediaWiki:Sidebar

2011-12-02T20:04:16Z

Eurie:

Meetings

2011-12-01T23:01:31Z

Eurie:

Meetings that may be of interest to the yeast community are listed below. If you would like to add a conference or meeting to list, please log in to the wiki. If you do not have a user account, please contact the [http://www.yeastgenome.org/cgi-bin/suggestion SGD helpdesk] and we will gladly create an account for you.

=Upcoming Conferences & Courses =

[http://www.mohb.org/2012/ Model Organisms to Human Biology: Cancer Genetics] 
Omni Shoreham, Washington, DC 
June 17 - 20, 2012

[http://www.yeast-meet.org/2012/ Yeast Genetics 2012] 
Princeton University, New Jersey, USA 
July 31 - August 5, 2012

[http://conferencing.uwex.edu/conferences/icy2012/index.cfm 13th International Congress on Yeasts] 
Madison, WI, USA 
August 26 - 30, 2012

[http://www.embl.de/training/events/2012/EAE12-01/ Experimental Approaches to Evolution and Ecology using Yeast] 
EMBL Heidelberg, Germany 
October 17 - 21, 2012

[http://www.yeast-2013.org/ YEAST 2013: 26th International Conference on Yeast Genetics and Molecular Biology] 
Frankfurt University, Frankfurt, Germany 
August 29 - September 3, 2013

=Past Yeast Meetings=
International Conference on Yeast Genetics and Molecular Biology 
:Browse or search abstracts: 
:[http://www.yeast-2011.org/ 2011] (XXV) | 2009 (XXIV) | [http://www.yeastgenome.org/community/meetings/yeast07/ 2007] (XXIII) | [http://www.yeastgenome.org/community/meetings/yeast05/ 2005] (XXII) | [http://www.yeastgenome.org/community/meetings/yeast03/ 2003] (XXI) | [http://www.yeastgenome.org/community/meetings/yeast01/ 2001] (XX)

Yeast Genetics & Molecular Biology Meeting 
:Browse or search abstracts; view participant lists and photos: 
:[http://www.yeast-meet.org/2010/ 2010] | [http://www.yeast-meet.org/2008 2008] | [http://www.yeastgenome.org/community/meetings/yeast06/ 2006] | [http://www.yeastgenome.org/community/meetings/yeast04/ 2004] | [http://www.yeastgenome.org/community/meetings/yeast02/ 2002] | [http://www.yeastgenome.org/community/meetings/yeast00/ 2000] | [http://www.yeastgenome.org/community/meetings/yeast98/ 1998] | [http://www.yeastgenome.org/community/meetings/yeast96/ 1996]

Historical Systematic Sequence Information

2011-10-12T22:48:50Z

Eurie:

These pages refer to the systematic sequence of S288C prior to Release 64. Before Release 64, there were [http://www.yeastgenome.org/help/howtoseq.shtml guidelines for changing systematic sequence].

=Chromosomal Features=
[http://www.yeastgenome.org/snoRNAtable.shtml snoRNAs in S. cerevisiae]

[http://www.yeastgenome.org/RNAmodTable.shtml Modified Nucleotides within RNAs in S. cerevisiae]

[http://www.yeastgenome.org/archive/newORF-sage.shtml SGD ORF Additions based on SAGE]

[http://www.yeastgenome.org/community/DSB_graphic.shtml Meiotic Double-Stranded Breaks in the Yeast Genome]

[http://www.yeastgenome.org/community/codon_usage.shtml Codon Usage Tables]

=Reagents=
[http://www.yeastgenome.org/community/primerPage.shtml Primer sets for amplifying yeast ORFs]

[http://www.yeastgenome.org/alleletable.shtml Commonly Used Auxotrophic Markers]

Historical Systematic Sequence Information

2011-10-12T22:43:48Z

Eurie:

[http://www.yeastgenome.org/help/howtoseq.shtml Guidelines for changing Systematic Sequence]

[http://www.yeastgenome.org/community/codon_usage.shtml Codon Usage Tables]

[http://www.yeastgenome.org/snoRNAtable.shtml snoRNAs in S. cerevisiae]

[http://www.yeastgenome.org/RNAmodTable.shtml Modified Nucleotides within RNAs in S. cerevisiae]

[http://www.yeastgenome.org/archive/newORF-sage.shtml SGD ORF Additions based on SAGE]

[http://www.yeastgenome.org/community/DSB_graphic.shtml Meiotic Double-Stranded Breaks in the Yeast Genome]

=Reagents=
[http://www.yeastgenome.org/community/primerPage.shtml Primer sets for amplifying yeast ORFs]

[http://www.yeastgenome.org/alleletable.shtml Commonly Used Auxotrophic Markers]

Historical Systematic Sequence Information

2011-10-12T22:41:49Z

Eurie: Created page with "[http://www.yeastgenome.org/community/codon_usage.shtml Codon Usage Tables] [http://www.yeastgenome.org/community/primerPage.shtml Primer sets for amplifying yeast ORFs] [http:..."

[http://www.yeastgenome.org/community/codon_usage.shtml Codon Usage Tables]

[http://www.yeastgenome.org/community/primerPage.shtml Primer sets for amplifying yeast ORFs]

[http://www.yeastgenome.org/alleletable.shtml Commonly Used Auxotrophic Markers]

[http://www.yeastgenome.org/community/DSB_graphic.shtml Meiotic Double-Stranded Breaks in the Yeast Genome]

[http://www.yeastgenome.org/snoRNAtable.shtml snoRNAs in S. cerevisiae]

[http://www.yeastgenome.org/RNAmodTable.shtml Modified Nucleotides within RNAs in S. cerevisiae]

[http://www.yeastgenome.org/archive/newORF-sage.shtml SGD ORF Additions based on SAGE]

[http://www.yeastgenome.org/help/howtoseq.shtml Guidelines for changing Systematic Sequence]

Meetings

2011-09-30T21:52:08Z

Eurie: /* Upcoming Conferences & Courses */

Meetings that may be of interest to the yeast community are listed below. If you would like to add a conference or meeting to list, please log in to the wiki. If you do not have a user account, please contact the [http://www.yeastgenome.org/cgi-bin/suggestion SGD helpdesk] and we will gladly create an account for you.

=Upcoming Conferences & Courses =

[http://events.embo.org/11-comparative-genomics/ Comparative genomics of eukaryotic microorganisms: understanding the complexity of diversity] 
Sant Feliux, Spain 
October 15-20, 2011

[http://www.pasteur.edu.uy/ysbc Yeast Systems Biology Course and Symposium] 
Institut Pasteur de Montevideo, Montevideo, Uruguay 
November 7-22, 2011

[http://www.yeast-meet.org/2012/ Yeast Genetics 2012] 
Princeton University, New Jersey, USA 
July 31 - August 5, 2012

=Past Yeast Meetings=
International Conference on Yeast Genetics and Molecular Biology 
:Browse or search abstracts: 
:[http://www.yeast-2011.org/ 2011] (XXV) | 2009 (XXIV) | [http://www.yeastgenome.org/community/meetings/yeast07/ 2007] (XXIII) | [http://www.yeastgenome.org/community/meetings/yeast05/ 2005] (XXII) | [http://www.yeastgenome.org/community/meetings/yeast03/ 2003] (XXI) | [http://www.yeastgenome.org/community/meetings/yeast01/ 2001] (XX)

Yeast Genetics & Molecular Biology Meeting 
:Browse or search abstracts; view participant lists and photos: 
:[http://www.yeast-meet.org/2010/ 2010] | [http://www.yeast-meet.org/2008 2008] | [http://www.yeastgenome.org/community/meetings/yeast06/ 2006] | [http://www.yeastgenome.org/community/meetings/yeast04/ 2004] | [http://www.yeastgenome.org/community/meetings/yeast02/ 2002] | [http://www.yeastgenome.org/community/meetings/yeast00/ 2000] | [http://www.yeastgenome.org/community/meetings/yeast98/ 1998] | [http://www.yeastgenome.org/community/meetings/yeast96/ 1996]

Meetings

2011-09-30T21:48:10Z

Eurie: /* Past Yeast Meetings */

Meetings that may be of interest to the yeast community are listed below. If you would like to add a conference or meeting to list, please log in to the wiki. If you do not have a user account, please contact the [http://www.yeastgenome.org/cgi-bin/suggestion SGD helpdesk] and we will gladly create an account for you.

=Upcoming Conferences & Courses =

[http://events.embo.org/11-comparative-genomics/ Comparative genomics of eukaryotic microorganisms: understanding the complexity of diversity] 
Sant Feliux, Spain 
October 15-20, 2011

[http://www.pasteur.edu.uy/ysbc Yeast Systems Biology Course and Symposium] 
Institut Pasteur de Montevideo, Montevideo, Uruguay 
November 7-22, 2011

[http://www.yeast-meet.org/2012/ Yeast Genetics 2012] 
Princeton University, New Jersey, USA 
July 31 - August 5, 2012

=Past Yeast Meetings=
International Conference on Yeast Genetics and Molecular Biology 
:Browse or search abstracts: 
:[http://www.yeast-2011.org/ 2011] (XXV) | 2009 (XXIV) | [http://www.yeastgenome.org/community/meetings/yeast07/ 2007] (XXIII) | [http://www.yeastgenome.org/community/meetings/yeast05/ 2005] (XXII) | [http://www.yeastgenome.org/community/meetings/yeast03/ 2003] (XXI) | [http://www.yeastgenome.org/community/meetings/yeast01/ 2001] (XX)

Yeast Genetics & Molecular Biology Meeting 
:Browse or search abstracts; view participant lists and photos: 
:[http://www.yeast-meet.org/2010/ 2010] | [http://www.yeast-meet.org/2008 2008] | [http://www.yeastgenome.org/community/meetings/yeast06/ 2006] | [http://www.yeastgenome.org/community/meetings/yeast04/ 2004] | [http://www.yeastgenome.org/community/meetings/yeast02/ 2002] | [http://www.yeastgenome.org/community/meetings/yeast00/ 2000] | [http://www.yeastgenome.org/community/meetings/yeast98/ 1998] | [http://www.yeastgenome.org/community/meetings/yeast96/ 1996]

Meetings

2011-09-30T20:59:28Z

Eurie: Created page with "Meetings that may be of interest to the yeast community are listed below. If you would like to add a conference or meeting to list, please log in to the wiki. If you do not hav..."

General Topics

2011-02-06T04:53:55Z

Eurie: /* Schizosaccharomyces pombe information */

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

*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
**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.

=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://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

2010-12-16T23:19:53Z

Eurie:

This page describes some of the most commonly used yeast lab strains. Much of the information is taken from [http://dbb.urmc.rochester.edu/labs/sherman_f/StartedYeast.html 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?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]

=Sigma 1278B=

'''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.

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+'']

'''Notes:''' W303 also contains 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].

'''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]

=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.

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

Methods

2010-09-22T15:49:58Z

Eurie:

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

*[http://labs.fhcrc.org/gottschling/Yeast%20Protocols/index.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://www.umanitoba.ca/faculties/medicine/biochem/gietz/Trafo.html 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://www.fccc.edu/research/labs/golemis/InteractionTrapInWork.html Interaction Trap at Work] information page from Erica Golemis's laboratory at the Fox Chase Cancer Center.

*[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)

*The [http://depts.washington.edu/yeastrc/ 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.

*Full text of the paper (Erdeniz et al. (1997) Genome Res. 7:1174-1183) describing [http://www.genome.org/cgi/content/full/7/12/1174 PCR-Based Allele Replacement]. 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 Bartsch for the W303 strain used in the study'').

*[http://genomics.princeton.edu/dunham/chemostat.html Chemostat Manual] from Maitreya Dunham's lab, Princeton University. See her [http://genomics.princeton.edu/dunham/protocols.shtml other protocols].

*[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]] 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://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://wiki.yeastgenome.org/index.php/Software Software tools] created by members of the scientific community.

Methods

2010-09-22T15:44:43Z

Eurie: Reverted edits by Eurie (Talk) to last revision by Gail

Methods

2010-09-22T15:43:21Z

Eurie: Reverted edits by Gail (Talk) to last revision by Qqq

from the Breeden Lab, Fred Hutchinson Cancer Research Center.

from the Gottschling Lab, Fred Hutchinson Cancer Research Center.

from the Gasch Lab, University of Wisconsin-Madison.

from the University of Manitoba.

from the Fangman and Brewer Labs, University of Washington.

information page from Erica Golemis's laboratory at the Fox Chase Cancer Center.

, a complete guide to microarraying for the molecular biologist, from the Brown Lab, Stanford University.

, by Audrey Gasch, from Guide to Yeast Genetics and Molecular and Cellular Biology, Methods in Enzymology (2002)

*The 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.

*Full text of the paper (Erdeniz et al. (1997) Genome Res. 7:1174-1183) describing . 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]][http://www.mightystudents.com essay topics] from RR and Stephan Bartsch for the W303 strain used in the study'').

* from Maitreya Dunham's lab, Princeton University. See her .

*A Classroom Guide To Yeast Experiments] from The GENE project at Kansas State University based on .

* from the RNA Decay Resource, a resource for the sharing of information, know-how, and wisdom among researchers who study mRNA decay.

*[[SGA]] SGA protocols and scoring software.

* from Life in Research, LLC. Also life sciences databases, online tools, software, and powerpoints. For example

* created by members of the scientific community.

Strains

2010-09-20T04:55:54Z

Eurie: /* Strain Backgrounds */

=Strain Backgrounds=
*View genotypes and descriptions of [[Commonly_used_strains|commonly used strains]].
*View [http://gbrowse.princeton.edu/cgi-bin/gbrowse/yeast_strains_snps/ SNPs] in S. cerevisiae strains

=Stock Centers=
*[http://www.atcc.org/ American Type Culture Collection] (ATCC) maintains yeast stocks and clones.

*[http://web.uni-frankfurt.de/fb15/mikro/euroscarf/ EUROSCARF], the EUROpean Saccharomyces Cerevisiae ARchive for Functional analysis, maintains a collection of systematic deletion strains [http://cgi.server.uni-frankfurt.de/fb15/rose/index.html searchable] by gene name.

*[http://www.ncyc.co.uk/ National Collection of Yeast Cultures (NCYC)] maintains over 3,100 non-pathogenic yeasts, including type strains, strains of general interest for education and research, strains of industrial importance, and genetically marked strains.

*[http://www.cabri.org/ Common Access to Biological Resources and Information] (CABRI) includes catalogs from European culture collections for yeast and other organisms.

*[http://www.addgene.org Addgene] is a non-profit plasmid repository that distributes many plasmids for yeast research. In particular, Addgene is distributing a collection of [http://www.addgene.org/yeast_gateway Yeast Advanced Gateway Destination Vectors] created by Dr. Susan Lindquist's laboratory.

*[http://yeast.lab.nig.ac.jp/nig/index_en.html Yeast Genetic Resource Center (YGRC)] maintains over 4,800 S. pombe strains and over 9,000 S. cerevisiae strains.

*[http://www.agr.unipg.it/dbvpg/ Industrial Yeasts Collection DBVPG]. The Industrial Yeasts Collection DBVPG, an academic biological resource centre (BRC) specialized in yeasts and yeast-like microorganisms, offers biological products and services to the international scientific community and to other private Institutions.

=Strain Collections=

*[http://clones.invitrogen.com/cloneinfo.php?clone=yeastgfp Yeast-GFP Clone Collection] from Dr. Erin O'Shea and Dr. Jonathan Weissman at UCSF, consisting of C-terminal tagged open reading frames (ORFs). Hosted by [http://www.invitrogen.com Invitrogen].

*[http://www.openbiosystems.com/GeneExpression/Yeast/GST/ Yeast GST-Tagged Collection] for inducible overexpression of yeast ORFs, developed in the Andrews lab at the University of Toronto. Hosted by [http://www.openbiosystems.com/ Open Biosystems].

*[http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Yeast Knockout (YKO) Collection] from the [http://www-sequence.stanford.edu/group/yeast_deletion_project/member.html Saccharomyces Genome Deletion Consortium].
**[http://www-sequence.stanford.edu/group/yeast_deletion_project/ykocpadd.html Submit] a comment to the Community Posting page.
**[http://www-sequence.stanford.edu/group/yeast_deletion_project/gb/ykocp.html Read] all comments.

*[http://www.openbiosystems.com/GeneExpression/Yeast/TAP/ Yeast-TAP Fusion Library] from Dr. Erin O'Shea and Dr. Jonathan Weissman at UCSF, containing open reading frames (ORFs) tagged with a high-affinity epitope and expressed from their natural chromosomal locations. Hosted by [http://www.openbiosystems.com Open Biosystems].

*[http://www.openbiosystems.com/GeneExpression/Yeast/Tet-Promoters/ Yeast Tet-promoters Hughes Collection] containing 800 essential yeast genes for which expression is regulated by doxycycline. Hosted by [http://www.openbiosystems.com Open Biosystems].

*[http://ygac.med.yale.edu/mtn/insertion_libraries.stm Yeast Transposon Insertion Library Collection], derived by using mini-transposons (mTns) to mutagenize a yeast genomic DNA library, from the [http://ygac.med.yale.edu/default.stm Yale Genome Analysis Center].

General Topics

2010-09-09T20:37:05Z

Eurie: /* General S. cerevisiae information */

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

*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
**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 wine making, 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 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, wine making, 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.

=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://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

2010-09-09T20:29:57Z

Eurie: /* General S. cerevisiae information */

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

*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
**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 wine making, 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 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, wine making, brewing.

=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.

=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://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

2010-09-09T20:07:45Z

Eurie: /* General S. cerevisiae information */

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

*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
**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 wine making, 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 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]

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

=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.

=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://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.

MediaWiki:Sidebar

2010-06-18T22:29:20Z

Eurie:

Positions in yeast labs

2009-04-29T23:03:55Z

Eurie:

=Postdoctoral Position at Rutgers University=

A postdoctoral position is available at the Biotech Center at Rutgers University in the laboratory of Dr. Nilgun E. Tumer to investigate the mechanisms of uptake, transport and cytotoxicity of ricin and Shiga-like toxins. The Tumer lab works on elucidating the basic mechanisms of action of ricin and Shiga-like toxins using Saccharomyces cerevisae and C. elegans as model systems. Both toxins depurinate the sarcin/ricin loop of the large rRNA and inhibit translation. Our goal is to identify the targets of these toxins to understand the mechanism by which they kill cells and to develop therapeutic intervention strategies. The successful candidate will use genetic, cell biology and chemical genomic approaches to investigate the mechanism of uptake and transport of the toxins in yeast and C. elegans and use chemical genomics approaches to identify the cellular pathways affected by these toxins. The ideal candidate should have a Ph.D. in a related field, experience with yeast and/or C.elegans genetics and cell biology and familiarity with chemical biology approaches. The Biotech Center is located in New Brunswick, New Jersey near New York City and Philadelphia and is equipped with state-of-the-art facilities and instrumentation. Rutgers University is an equal opportunity employer that strongly encourages underrepresented groups to apply for open positions.

Interested applicants should send their CV and names and addresses of three references to Dr. Nilgun E. Tumer (tumer@aesop.rutgers.edu). Information on our research can be found at: http://biotech.rutgers.edu/faculty/tumer.html, http://aesop.rutgers.edu/~plantbiopath/faculty/tumer/TUMER.HTML, http://lifesci.rutgers.edu/~molbiosci/faculty/tumer.html
Contact: Nilgun Tumer, Foran Hall, Biotech Center, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901-8520. Tel: 732-932-8165 X215.

=Postdoctoral Position, Chemical Genomics=

Research Department: Molecular Ligand Target Research Team, Chemical Genomics Research Group, RIKEN Advanced Science Institute
Dr. Charles Boone, Visiting Scientist
Dr. Minoru Yoshida, Team Leader

Location: RIKEN Advanced Science Institute, RIKEN Wako Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan

Area of Research: Chemical genetics and chemical genomics

Job Description: A postdoctoral researcher position is open in the field of chemical genomics. We have constructed a unique chemical library based on natural products in the Department of Chemical Biology, RIKAN Advanced Science Institute. The successful candidate will carry out original research on global analysis of drug-target interaction using the chemical library and various yeast mutants or transformants.

Selection Process: Candidates will be selected based on research results, publications, letters of recommendation (preferably in English), etc. The CV (preferably detailed and complete) and publications must be in English.

Application Deadline: Applications are now being accepted. Position will be closed after a suitable candidate is found.

Start of Employment: Immediately

Contract Conditions: Full-time employment with the contract shall be for one year, renewable annually upon evaluation until the end of the project (March 2012). Salary will be commensurate with qualifications and experience. Commuting and housing allowances will be provided. Moving expenses to RIKEN will be reimbursed. Social insurance will also be applicable. Days off include public holidays, New Year's holidays (Dec. 29-Jan 3), summer holidays and RIKEN Foundation Day. These and other employment provisions are in accordance with RIKEN regulations.

Information at Web: Information on our team can be found on our website (http://www.riken.go.jp/engn/r-world/research/lab/asi/chemical/index.html)

Applications: Electronic copies of your curriculum vitae/résumé, a list of publications, two or three representative publications, and two reference letters should be sent to the address below or via e-mail to "charlie.boone" (add @utoronto.ca" to complete the address):
Charles Boone
Professor, University of Toronto, Donnelly CCBR
160 College St, Rm 1306
Toronto, ON
M5S 3E1

Notes: The documents you submit will be handled with the utmost care in accordance with RIKEN's rules for the protection of personal data and will be used only for employment screening purposes. This information will not be divulged, assigned, or loaned to a third party without legitimate reason.

=Postdoctoral Position: Engineering sea lamprey antibodies=

A vacant postdoctoral position at the Center of Marine Biotechnology in Baltimore to characterize antigen binding properties of VLR, the unique variable lymphocyte receptors of sea lamprey. The successful candidate will join a study with the goal to explore biotechnology applications for these novel antibodies (Pancer & Mariuzza, Nat. Biotechnol., 2008; Rogozin et al., Nat. Immunol., 2007; Alder et al., Science 2005; Pancer et al., Nature 2004). Our research platform includes yeast displayed recombinant VLR libraries that are screened with various antigens. Biochemical and structural properties of monoclonal VLRs are then characterized.

Candidates must have a PhD with solid background in protein biochemistry and molecular biology, experience in recombinant protein expression and characterization, and relevant peer-reviewed publications.

To apply for position #300957 please submit a letter describing your research interests and experience, an updated curriculum vitae and names of three references via http://www.cytiva.com/umbi/ext/detail.asp?jobid=umbi300957

Contact: Zeev Pancer, PhD
Center of Marine Biotechnology, UMBI
Columbus Center, Suite 236
701 East Pratt St. Baltimore, MD 21202, USA
Office: 410-234-8834; Fax: 410-234-8896
Email: pancer@comb.umbi.umd.edu

=Epigenetic Postdoctoral Fellow Posting=

'''Postdoctoral positions''' are available at Massachusetts General Hospital Cancer Center. My laboratory is focused on understanding the impact that both methylation and acetylation dynamics has in both human cell culture and C. elegans. In particular, the laboratory is investigating the impact that the histone 3 lysine 9/36 tri-demethylases [JMJD2A-D; Whetstine et al., (2007) Cell 125: 467-81] have on tumorigenesis, transcriptional regulation, and genomic integrity. The laboratory will interrogate the role of these enzymes by using genomic, proteomic, cytological and genetic approaches. Similar approaches allowed an important link to be established for histone deacetylase 1 (HDAC-1) and the regulation of extra-cellular matrix biology in both human and C. elegans, which has direct implications in cancer chemotherapy [Whetstine et al., (2005) Mol. Cell 18:483-90]. The laboratory will continue to investigate the functional overlap or unique pathways that the C. elegans class I histone deacetylases regulate by using the same type of approaches. Overall, the laboratory will integrate a number of approaches and systems to determine the important biological pathways regulated by histone demethylases and histone deacetylases.

The laboratory is looking for highly motivated, tenacious scientists that are enthusiastic, team players and love science. The laboratory is looking for researchers with documented proficiency in any of the following areas (basic molecular biology, protein biochemistry, genomics, epigenetics, C. elegans, cytology, development biology, DNA damage and repair) but interested in learning new approaches or systems to answer the exciting questions before us.

Requirements:
For these positions a Ph.D. and/or M.D. is required. These positions require enthusiastic, self motivated, independent thinkers with strong interpersonal skills, and the ability to communicate with laboratory members, national and international collaborators. Please have three letters of recommendation sent to the below address and/or e-mail.

Johnathan R. Whetstine, Ph.D.
Assistant Professor of Medicine
Harvard Medical School and
Massachusetts General Hospital Cancer Center
Building 149, 13th Street , Room 7-213
Charlestown, MA 02129, USA
Office Phone: 617-643-4374
jwhetstine@hms.harvard.edu

= INDIANAPOLIS, Indiana University-Purdue University, Indianapolis. Postdoctoral position in DNA repair and genomic stability. =

'A postdoctoral position is available for qualified graduates to pursue further training in genetics/molecular biology. We use molecular and classic genetics approaches to examine the mechanisms of DNA repair and recombination in yeast Saccharomyces cerevisiae – a model eukaryotic organism. The successful candidate will investigate genetic and environmental factors that channel repair of double-strand DNA breaks into dangerous repair pathways (break-induced replication, single-strand annealing, and breakage-fusion-bridge cycles) leading to genomic instabilities.

Applicants should hold a Ph.D. in Biology, Molecular Biology or a related life science discipline. The ideal applicant should have experience in genetics and molecular biology.
The laboratory is located on the campus of Indiana University Purdue University – Indianapolis. This campus is in downtown Indianapolis, the Indiana state capital and a city of over 1 million people with outstanding resources and a low cost of living. The campus is the major academic research location in the state. Postdocs at IUPUI receive competitive compensation and benefits packages. IUPUI also offers extensive career development opportunities for our postdoctoral fellows, including a Preparing Future Faculty program.
Interested persons should send curriculum vitae and the names and contact information of three references by e-mail to amalkova@iupui.edu (Dr.Anna Malkova) with "Postdoc Opening 2008" in the message title.
'''

= EVOLVA SA. Basel, Switzerland =
''''''Yeast cell biologist ''''

Key words: Yeast (S. cerevisiae) genetics, physiology, cell biology and biochemistry

Evolva is an early/mid stage biotech and drug discovery company using its proprietary platform technology to produce small molecular weight, active compounds. We rely on genetic engineering of both yeast and E. coli, to create novel “genetic chemistry” for in-house screening in pharmaceutically relevant, cell based assays.

To help in the further development of our core technologies we now wish to employ an experienced yeast cell biologist, with special qualifications and interest in the areas of yeast genetics and physiology, including cell cycle progression, mitotic and meiotic division, genome stability, homologous recombination, DNA double strand break repair etc.

Preferably you have a PhD in life science plus some years of post doctoral work, maybe even industrial experience. In addition to a solid theoretic foundation we expect you to have hands-on experience with standard procedures for handling end engineering yeast, since a major part of the job will involve working in the wet lab.

We are currently around 30 people working in modern facilities in Basel, Switzerland. We are hard working but, nonetheless, the atmosphere is relaxed and flexible. We appreciate good collaboration skills and a sense of humor.

For more information please look at our website (www.evolva.com) or contact Michael Naesby at Evolva: +41 61 485 2016. If you wish to send an application, please direct it to elodief@evolva.com with the subject “yeast biologist”.

= Seattle, Wa Fred Hutchinson Cancer Research Center =
''''''STAFF SCIENTIST/ POSTDOCTORAL RESEARCH FELLOW ''''#KSW-21860

The overarching goal of the Paulovich laboratory at the Fred Hutchinson Cancer Research Center is to characterize human phenotypic variation and translate this variation into clinically useful diagnostics. The laboratory is a highly interdisciplinary collaborative setting in which chemists, biochemists, statisticians, computer scientists, biologists, and geneticists work closely together on projects ranging from basic yeast genetics to the mammalian cell DNA damage response to mass spectrometry and biomarker discovery.

Job Description:
This is an upper-level, flexible position for an experienced yeast geneticist to lead a new Project in the laboratory. This position is funded off of a new R01 grant aimed to characterize cellular networks that buffer the phenotypic effects of defects in the DNA damage response pathway, using the yeast S. cerevisiae as a model system.

This position can be adapted to suit a variety of career goals, including:

• a new postdoctoral fellow (with graduate training in yeast genetics) interested in developing technical and leadership skills for a future academic position

• a Staff Scientist- or Postdoctoral-level applicant who would like a long-term position in the group and the opportunity to develop a research project

• a Staff Scientist- or Postdoctoral-level applicant who has chosen not to develop his/her own laboratory at this time, but would like the opportunity to lead a small research group within our laboratory and to co-author NIH grants. This is a unique opportunity for a go-getter who wants to take his/her career to the next level but does not plan to have an independent laboratory in the next 4-5 years. Highly motivated recent graduates are encouraged to apply.

Major duties:

Scientific:
• Build new yeast strains and libraries
• Perform genetic screens for mutants sensitive to DNA damage
• Characterize mutants that buffer defects in the DNA damage response
• Carry out yeast genetics and physiology experiments: kill curves, mutation rates, recombination rates, crosses, tetrad analysis, transformation, and genotyping

Managerial:
• Assume primary responsibility for day-to-day management of the project, its budget, and its milestones
• Read relevant technical literature and play a lead role in strategic planning for the project
• Assist in hiring and managing staff for the project
• Write manuscripts for publication
• Prepare progress reports for funding agencies
• Assist in / serve as PI on future grant applications
• Present work at local and national meetings
• Provide mentorship for junior members of the team

Qualifications:
A Ph.D. and extensive experience with molecular and cellular biology techniques, as well as with YEAST MOLECULAR GENETICS, including cell mating, tetrad analysis, and physiology experiments with S. cerevisiae, are required. The successful candidate must be a highly confident self-starter who is productive when working with minimal supervision, able to read the literature critically, capable of designing experiments independently, capable of contributing intellectually to the project, and must be an effective collaborator and leader of a team.

Job Type: Full time position

Compensation: Salary DOE (or based on NIH scale for postdoctoral level) + excellent benefits

OPENING DATE: June 25, 2008; description revised 7-9-08

To apply for this position, please send cover letter, curriculum vitae, and the contact information for three professional references to:

Käthe Watanabe
Human Resources Specialist
Fred Hutchinson Cancer Research Center
Human Resources, J1-105
P.O. Box 19024
Seattle, WA 98109-1024
Email: kwatanab@fhcrc.org
Fax: 206-667-4051
Web site: http://www.fhcrc.org

=University of New Mexico =

Post doctoral position available now at the University of New Mexico, Albuquerque to study differentiation of quiescent and non-quiescent cells in yeast stationary phase cultures. This position is for a beginning post doc and applicants should have a strong background in yeast genetics, genomics, or flow cytometry. For recent work see Mol. Biol. Cell 2008 19: 1271-1280; and http://biology.unm.edu/biology/maggieww/public_html/Maggieww.html.

Applicants should email their cv and names/email address of three references to Maggie Werner-Washburne, maggieww@unm.edu.

=Duke University Medical Center=

NIH-funded postdoctoral positions are available at Duke University Medical Center to study quantitative (complex) traits in “S. cerevisiae”; for example, see Nature 416:326-330 (2002) and PLoS Genetics 2(2):e13 (2006).

Applicants should have 0 to (at most) 2 years of post-doctoral experience and a strong background in at least one of three areas – yeast genetics, quantitative/population genetics and/or genomics/informatics – and a desire to expand into the other listed areas. Start dates are flexible.

See the [http://www.duke.edu/web/microlabs/mccusker/ lab website] for more information and publications. Applicants should email their curriculum vitae and the names/email addresses of three references to John McCusker.
Email: mccus001@mc.duke.edu

= Carnegie Institution for Science, Stanford, California, USA =

Highly qualified and motivated individuals are invited to send applications for
a Postdoc Position
in the Research Group of Wolf B. Frommer
on the topic

'''Regulatory circuits controlling sugar flux in yeast grown on ethanol'''

HT screen of the yeast knock out collection using FRET sensors for glucose, sucrose and maltose, follow-up analysis of hits and reconstruction of networks

Our lab has developed a wide range of FRET sensors for metabolites. These sensors have so far been used mainly in mammalian cells to study glutamate release from neurons, glucose transport across the ER membrane or tryptophan/kynurenine exchange.

We have now been able to functionally express the FRET sensors also in the cytoplasm of yeast and to establish a high throughput screening platform. Our goal is to identify novel regulatory pathways involved in the control of glucose flux in yeast. As a first step, the kinase k.o. collection has been screened for altered glucose flux and several hits have been identified and verified.

Next steps will be to verify the hits using a new microfluidic platform, to test the effect on other sugar fluxes using FRET sensors for sucrose, maltose and ribose and to place the kinases into signaling networks. The screen can be expanded to include the whole genome at a later stage. Focus points are regulatory effects on glucose transporters and hexokinases. Due to the advanced stage, it is expected that the work will lead to high profile publications within less than a year.

Start date asap

Send your application with CV and the names of three references to:

Wolf B. Frommer
Carnegie Institution for Science
260 Panama St, Stanford CA 94305 USA.
Website[http://carnegiedpb.stanford.edu]
E-mail: wfrommer@stanford.edu

Positions in yeast labs

2009-04-29T23:02:56Z

Eurie:

=Postdoctoral Position at Rutgers University=

A postdoctoral position is available at the Biotech Center at Rutgers University in the laboratory of Dr. Nilgun E. Tumer to investigate the mechanisms of uptake, transport and cytotoxicity of ricin and Shiga-like toxins. The Tumer lab works on elucidating the basic mechanisms of action of ricin and Shiga-like toxins using Saccharomyces cerevisae and C. elegans as model systems. Both toxins depurinate the sarcin/ricin loop of the large rRNA and inhibit translation. Our goal is to identify the targets of these toxins to understand the mechanism by which they kill cells and to develop therapeutic intervention strategies. The successful candidate will use genetic, cell biology and chemical genomic approaches to investigate the mechanism of uptake and transport of the toxins in yeast and C. elegans and use chemical genomics approaches to identify the cellular pathways affected by these toxins. The ideal candidate should have a Ph.D. in a related field, experience with yeast and/or C.elegans genetics and cell biology and familiarity with chemical biology approaches. The Biotech Center is located in New Brunswick, New Jersey near New York City and Philadelphia and is equipped with state-of-the-art facilities and instrumentation. Rutgers University is an equal opportunity employer that strongly encourages underrepresented groups to apply for open positions.

Interested applicants should send their CV and names and addresses of three references to Dr. Nilgun E. Tumer (tumer@aesop.rutgers.edu). Information on our research can be found at: http://biotech.rutgers.edu/faculty/tumer.html, http://aesop.rutgers.edu/~plantbiopath/faculty/tumer/TUMER.HTML, http://lifesci.rutgers.edu/~molbiosci/faculty/tumer.html
Contact: Nilgun Tumer, Foran Hall, Biotech Center, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901-8520. Tel: 732-932-8165 X215.
__________________________________________________________________________________________

=Postdoctoral Position, Chemical Genomics=

Research Department: Molecular Ligand Target Research Team, Chemical Genomics Research Group, RIKEN Advanced Science Institute
Dr. Charles Boone, Visiting Scientist
Dr. Minoru Yoshida, Team Leader

Location: RIKEN Advanced Science Institute, RIKEN Wako Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan

Area of Research: Chemical genetics and chemical genomics

Job Description: A postdoctoral researcher position is open in the field of chemical genomics. We have constructed a unique chemical library based on natural products in the Department of Chemical Biology, RIKAN Advanced Science Institute. The successful candidate will carry out original research on global analysis of drug-target interaction using the chemical library and various yeast mutants or transformants.

Selection Process: Candidates will be selected based on research results, publications, letters of recommendation (preferably in English), etc. The CV (preferably detailed and complete) and publications must be in English.

Application Deadline: Applications are now being accepted. Position will be closed after a suitable candidate is found.

Start of Employment: Immediately

Contract Conditions: Full-time employment with the contract shall be for one year, renewable annually upon evaluation until the end of the project (March 2012). Salary will be commensurate with qualifications and experience. Commuting and housing allowances will be provided. Moving expenses to RIKEN will be reimbursed. Social insurance will also be applicable. Days off include public holidays, New Year's holidays (Dec. 29-Jan 3), summer holidays and RIKEN Foundation Day. These and other employment provisions are in accordance with RIKEN regulations.

Information at Web: Information on our team can be found on our website (http://www.riken.go.jp/engn/r-world/research/lab/asi/chemical/index.html)

Applications: Electronic copies of your curriculum vitae/résumé, a list of publications, two or three representative publications, and two reference letters should be sent to the address below or via e-mail to "charlie.boone" (add @utoronto.ca" to complete the address):
Charles Boone
Professor, University of Toronto, Donnelly CCBR
160 College St, Rm 1306
Toronto, ON
M5S 3E1

Notes: The documents you submit will be handled with the utmost care in accordance with RIKEN's rules for the protection of personal data and will be used only for employment screening purposes. This information will not be divulged, assigned, or loaned to a third party without legitimate reason.

__________________________________________________________________

=Postdoctoral Position: Engineering sea lamprey antibodies=

A vacant postdoctoral position at the Center of Marine Biotechnology in Baltimore to characterize antigen binding properties of VLR, the unique variable lymphocyte receptors of sea lamprey. The successful candidate will join a study with the goal to explore biotechnology applications for these novel antibodies (Pancer & Mariuzza, Nat. Biotechnol., 2008; Rogozin et al., Nat. Immunol., 2007; Alder et al., Science 2005; Pancer et al., Nature 2004). Our research platform includes yeast displayed recombinant VLR libraries that are screened with various antigens. Biochemical and structural properties of monoclonal VLRs are then characterized.

Candidates must have a PhD with solid background in protein biochemistry and molecular biology, experience in recombinant protein expression and characterization, and relevant peer-reviewed publications.

To apply for position #300957 please submit a letter describing your research interests and experience, an updated curriculum vitae and names of three references via http://www.cytiva.com/umbi/ext/detail.asp?jobid=umbi300957

Contact: Zeev Pancer, PhD
Center of Marine Biotechnology, UMBI
Columbus Center, Suite 236
701 East Pratt St. Baltimore, MD 21202, USA
Office: 410-234-8834; Fax: 410-234-8896
Email: pancer@comb.umbi.umd.edu

__________________________________________________________________

=Epigenetic Postdoctoral Fellow Posting=

'''Postdoctoral positions''' are available at Massachusetts General Hospital Cancer Center. My laboratory is focused on understanding the impact that both methylation and acetylation dynamics has in both human cell culture and C. elegans. In particular, the laboratory is investigating the impact that the histone 3 lysine 9/36 tri-demethylases [JMJD2A-D; Whetstine et al., (2007) Cell 125: 467-81] have on tumorigenesis, transcriptional regulation, and genomic integrity. The laboratory will interrogate the role of these enzymes by using genomic, proteomic, cytological and genetic approaches. Similar approaches allowed an important link to be established for histone deacetylase 1 (HDAC-1) and the regulation of extra-cellular matrix biology in both human and C. elegans, which has direct implications in cancer chemotherapy [Whetstine et al., (2005) Mol. Cell 18:483-90]. The laboratory will continue to investigate the functional overlap or unique pathways that the C. elegans class I histone deacetylases regulate by using the same type of approaches. Overall, the laboratory will integrate a number of approaches and systems to determine the important biological pathways regulated by histone demethylases and histone deacetylases.

The laboratory is looking for highly motivated, tenacious scientists that are enthusiastic, team players and love science. The laboratory is looking for researchers with documented proficiency in any of the following areas (basic molecular biology, protein biochemistry, genomics, epigenetics, C. elegans, cytology, development biology, DNA damage and repair) but interested in learning new approaches or systems to answer the exciting questions before us.

Requirements:
For these positions a Ph.D. and/or M.D. is required. These positions require enthusiastic, self motivated, independent thinkers with strong interpersonal skills, and the ability to communicate with laboratory members, national and international collaborators. Please have three letters of recommendation sent to the below address and/or e-mail.

Johnathan R. Whetstine, Ph.D.
Assistant Professor of Medicine
Harvard Medical School and
Massachusetts General Hospital Cancer Center
Building 149, 13th Street , Room 7-213
Charlestown, MA 02129, USA
Office Phone: 617-643-4374
jwhetstine@hms.harvard.edu

__________________________________________________________________

= INDIANAPOLIS, Indiana University-Purdue University, Indianapolis. Postdoctoral position in DNA repair and genomic stability. =

'A postdoctoral position is available for qualified graduates to pursue further training in genetics/molecular biology. We use molecular and classic genetics approaches to examine the mechanisms of DNA repair and recombination in yeast Saccharomyces cerevisiae – a model eukaryotic organism. The successful candidate will investigate genetic and environmental factors that channel repair of double-strand DNA breaks into dangerous repair pathways (break-induced replication, single-strand annealing, and breakage-fusion-bridge cycles) leading to genomic instabilities.

Applicants should hold a Ph.D. in Biology, Molecular Biology or a related life science discipline. The ideal applicant should have experience in genetics and molecular biology.
The laboratory is located on the campus of Indiana University Purdue University – Indianapolis. This campus is in downtown Indianapolis, the Indiana state capital and a city of over 1 million people with outstanding resources and a low cost of living. The campus is the major academic research location in the state. Postdocs at IUPUI receive competitive compensation and benefits packages. IUPUI also offers extensive career development opportunities for our postdoctoral fellows, including a Preparing Future Faculty program.
Interested persons should send curriculum vitae and the names and contact information of three references by e-mail to amalkova@iupui.edu (Dr.Anna Malkova) with "Postdoc Opening 2008" in the message title.
'''

= EVOLVA SA. Basel, Switzerland =
''''''Yeast cell biologist ''''

Key words: Yeast (S. cerevisiae) genetics, physiology, cell biology and biochemistry

Evolva is an early/mid stage biotech and drug discovery company using its proprietary platform technology to produce small molecular weight, active compounds. We rely on genetic engineering of both yeast and E. coli, to create novel “genetic chemistry” for in-house screening in pharmaceutically relevant, cell based assays.

To help in the further development of our core technologies we now wish to employ an experienced yeast cell biologist, with special qualifications and interest in the areas of yeast genetics and physiology, including cell cycle progression, mitotic and meiotic division, genome stability, homologous recombination, DNA double strand break repair etc.

Preferably you have a PhD in life science plus some years of post doctoral work, maybe even industrial experience. In addition to a solid theoretic foundation we expect you to have hands-on experience with standard procedures for handling end engineering yeast, since a major part of the job will involve working in the wet lab.

We are currently around 30 people working in modern facilities in Basel, Switzerland. We are hard working but, nonetheless, the atmosphere is relaxed and flexible. We appreciate good collaboration skills and a sense of humor.

For more information please look at our website (www.evolva.com) or contact Michael Naesby at Evolva: +41 61 485 2016. If you wish to send an application, please direct it to elodief@evolva.com with the subject “yeast biologist”.

= Seattle, Wa Fred Hutchinson Cancer Research Center =
''''''STAFF SCIENTIST/ POSTDOCTORAL RESEARCH FELLOW ''''#KSW-21860

The overarching goal of the Paulovich laboratory at the Fred Hutchinson Cancer Research Center is to characterize human phenotypic variation and translate this variation into clinically useful diagnostics. The laboratory is a highly interdisciplinary collaborative setting in which chemists, biochemists, statisticians, computer scientists, biologists, and geneticists work closely together on projects ranging from basic yeast genetics to the mammalian cell DNA damage response to mass spectrometry and biomarker discovery.

Job Description:
This is an upper-level, flexible position for an experienced yeast geneticist to lead a new Project in the laboratory. This position is funded off of a new R01 grant aimed to characterize cellular networks that buffer the phenotypic effects of defects in the DNA damage response pathway, using the yeast S. cerevisiae as a model system.

This position can be adapted to suit a variety of career goals, including:

• a new postdoctoral fellow (with graduate training in yeast genetics) interested in developing technical and leadership skills for a future academic position

• a Staff Scientist- or Postdoctoral-level applicant who would like a long-term position in the group and the opportunity to develop a research project

• a Staff Scientist- or Postdoctoral-level applicant who has chosen not to develop his/her own laboratory at this time, but would like the opportunity to lead a small research group within our laboratory and to co-author NIH grants. This is a unique opportunity for a go-getter who wants to take his/her career to the next level but does not plan to have an independent laboratory in the next 4-5 years. Highly motivated recent graduates are encouraged to apply.

Major duties:

Scientific:
• Build new yeast strains and libraries
• Perform genetic screens for mutants sensitive to DNA damage
• Characterize mutants that buffer defects in the DNA damage response
• Carry out yeast genetics and physiology experiments: kill curves, mutation rates, recombination rates, crosses, tetrad analysis, transformation, and genotyping

Managerial:
• Assume primary responsibility for day-to-day management of the project, its budget, and its milestones
• Read relevant technical literature and play a lead role in strategic planning for the project
• Assist in hiring and managing staff for the project
• Write manuscripts for publication
• Prepare progress reports for funding agencies
• Assist in / serve as PI on future grant applications
• Present work at local and national meetings
• Provide mentorship for junior members of the team

Qualifications:
A Ph.D. and extensive experience with molecular and cellular biology techniques, as well as with YEAST MOLECULAR GENETICS, including cell mating, tetrad analysis, and physiology experiments with S. cerevisiae, are required. The successful candidate must be a highly confident self-starter who is productive when working with minimal supervision, able to read the literature critically, capable of designing experiments independently, capable of contributing intellectually to the project, and must be an effective collaborator and leader of a team.

Job Type: Full time position

Compensation: Salary DOE (or based on NIH scale for postdoctoral level) + excellent benefits

OPENING DATE: June 25, 2008; description revised 7-9-08

To apply for this position, please send cover letter, curriculum vitae, and the contact information for three professional references to:

Käthe Watanabe
Human Resources Specialist
Fred Hutchinson Cancer Research Center
Human Resources, J1-105
P.O. Box 19024
Seattle, WA 98109-1024
Email: kwatanab@fhcrc.org
Fax: 206-667-4051
Web site: http://www.fhcrc.org

=University of New Mexico =

Post doctoral position available now at the University of New Mexico, Albuquerque to study differentiation of quiescent and non-quiescent cells in yeast stationary phase cultures. This position is for a beginning post doc and applicants should have a strong background in yeast genetics, genomics, or flow cytometry. For recent work see Mol. Biol. Cell 2008 19: 1271-1280; and http://biology.unm.edu/biology/maggieww/public_html/Maggieww.html.

Applicants should email their cv and names/email address of three references to Maggie Werner-Washburne, maggieww@unm.edu.

=Duke University Medical Center=

NIH-funded postdoctoral positions are available at Duke University Medical Center to study quantitative (complex) traits in “S. cerevisiae”; for example, see Nature 416:326-330 (2002) and PLoS Genetics 2(2):e13 (2006).

Applicants should have 0 to (at most) 2 years of post-doctoral experience and a strong background in at least one of three areas – yeast genetics, quantitative/population genetics and/or genomics/informatics – and a desire to expand into the other listed areas. Start dates are flexible.

See the [http://www.duke.edu/web/microlabs/mccusker/ lab website] for more information and publications. Applicants should email their curriculum vitae and the names/email addresses of three references to John McCusker.
Email: mccus001@mc.duke.edu

= Carnegie Institution for Science, Stanford, California, USA =

Highly qualified and motivated individuals are invited to send applications for
a Postdoc Position
in the Research Group of Wolf B. Frommer
on the topic

'''Regulatory circuits controlling sugar flux in yeast grown on ethanol'''

HT screen of the yeast knock out collection using FRET sensors for glucose, sucrose and maltose, follow-up analysis of hits and reconstruction of networks

Our lab has developed a wide range of FRET sensors for metabolites. These sensors have so far been used mainly in mammalian cells to study glutamate release from neurons, glucose transport across the ER membrane or tryptophan/kynurenine exchange.

We have now been able to functionally express the FRET sensors also in the cytoplasm of yeast and to establish a high throughput screening platform. Our goal is to identify novel regulatory pathways involved in the control of glucose flux in yeast. As a first step, the kinase k.o. collection has been screened for altered glucose flux and several hits have been identified and verified.

Next steps will be to verify the hits using a new microfluidic platform, to test the effect on other sugar fluxes using FRET sensors for sucrose, maltose and ribose and to place the kinases into signaling networks. The screen can be expanded to include the whole genome at a later stage. Focus points are regulatory effects on glucose transporters and hexokinases. Due to the advanced stage, it is expected that the work will lead to high profile publications within less than a year.

Start date asap

Send your application with CV and the names of three references to:

Wolf B. Frommer
Carnegie Institution for Science
260 Panama St, Stanford CA 94305 USA.
Website[http://carnegiedpb.stanford.edu]
E-mail: wfrommer@stanford.edu

File:Wiki-invite3.jpg

2009-04-27T15:23:24Z

Eurie: Removing all content from page

Main Page

2009-04-01T15:56:20Z

Eurie:

<protect>
<big>'''Welcome to the Yeast Wiki'''</big>

[[Image:Wiki-invite3.jpg|right]]
* Use the search box in left-hand navigation bar to find or create specific wiki pages.
* Find already existing gene pages pre-filled with basic info from SGD by entering an ORF or gene name into the search box.
* Use these wiki pages as a place to enter your observations or notes for a gene or ORF.
* It's easy to add info! Just create an account via the "Log in/Create an account" link in the upper right-hand corner of this page.

 

==Table of Contents==

[[Methods|Protocols and Methods]]: Includes useful yeast protocols and methods posted by researchers.

[[Reagents|Reagents]]: Includes links to plasmid collections and other useful reagents, such as antibodies.

[[Strains|Strains]]: Includes information about strain collections and the major yeast strain backgrounds.

[[General_Topics|General Topics]]: A collection of information about the general biology of S. cerevisiae and other fungi, including educational resources.

[[Career_Resources|Career Resources]]: Includes links to job opportunities posted by researchers.

== Useful SGD Links ==

[http://www.yeastgenome.org SGD Home] | [http://db.yeastgenome.org/cgi-bin/suggestion Contact SGD]

[http://www.openhelix.com/sgd Online SGD Tutorial] developed by [http://www.openhelix.com/ OpenHelix]: describes navigation of SGD and many features of the database.

[[Specification for New Interactions and Phenotype FTP files]]

== Useful Wiki Links ==

[http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide] | [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ] | [http://meta.wikimedia.org/wiki/Help:Wikitext Quick Guide to Editing Wiki Text]
</protect>

Main Page

2009-03-31T19:39:20Z

Eurie:

<protect>
<big>'''Welcome to the Yeast Wiki'''</big>

[[Image:Wiki-invite3.jpg|right]]
* Use the search box in left-hand navigation bar to find or create specific wiki pages.
* Find already existing gene pages pre-filled with basic info from SGD by entering an ORF or gene name into the search box.
* Use these wiki pages as a place to enter your observations or notes for a gene or ORF.
* It's easy to add info! Just create an account via the "Log in/Create an account" link in the upper right-hand corner of this page.

 

==Table of Contents==

[[Methods|Protocols and Methods]]: Includes useful yeast protocols and methods posted by researchers.

[[Reagents|Reagents]]: Includes links to plasmid collections and other useful reagents, such as antibodies.

[[Strains|Strains]]: Includes information about strain collections and the major yeast strain backgrounds.

[[General_Topics|General Topics]]: A collection of information about the general biology of S. cerevisiae and other fungi, including educational resources.

[[Career_Resources|Career Resources]]: Includes links to job opportunities posted by researchers.

== Useful SGD Links ==

[http://www.yeastgenome.org SGD Home] | [http://db.yeastgenome.org/cgi-bin/suggestion Contact SGD]

[http://www.openhelix.com/sgd Online SGD Tutorial] developed by [http://www.openhelix.com/ Open Helix]: describes navigation of SGD and many features of the database.

[[Specification for New Interactions and Phenotype FTP files]]

== Useful Wiki Links ==

[http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide] | [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ] | [http://meta.wikimedia.org/wiki/Help:Wikitext Quick Guide to Editing Wiki Text]
</protect>

General Topics

2009-03-12T18:32:49Z

Eurie:

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

*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
**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 wine making, 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 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.

*[http://www.yeastgenome.org/ SGD] maintains a [http://www.yeastgenome.org/ExternalContents.shtml 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]

=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://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].

=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]

=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://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.

Main Page

2008-07-30T20:43:32Z

Eurie: /* Table of Contents */

<protect>
<big>'''Welcome to the Yeast Wiki'''</big>

[[Image:Wiki-invite3.jpg|right]]
* Use the search box in left-hand navigation bar to find or create specific wiki pages.
* Find already existing gene pages pre-filled with basic info from SGD by entering an ORF or gene name into the search box.
* Use these wiki pages as a place to enter your observations or notes for a gene or ORF.
* It's easy to add info! Just create an account via the "Log in/Create an account" link in the upper right-hand corner of this page.

 

==Table of Contents==

[[Methods|Protocols and Methods]]: Includes useful yeast protocols and methods posted by researchers.

[[Reagents|Reagents]]: Includes links to plasmid collections and other useful reagents, such as antibodies.

[[Strains|Strains]]: Includes information about strain collections and the major yeast strain backgrounds.

[[General_Topics|General Topics]]: A collection of information about the general biology of S. cerevisiae and other fungi, including educational resources.

[[Career_Resources|Career Resources]]: Includes links to job opportunities posted by researchers.

== Useful SGD Links ==

[http://www.yeastgenome.org SGD Home] | [http://db.yeastgenome.org/cgi-bin/suggestion Contact SGD]

[[Specification for New Interactions and Phenotype FTP files]]

== Useful Wiki Links ==

[http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide] | [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ] | [http://meta.wikimedia.org/wiki/Help:Wikitext Quick Guide to Editing Wiki Text]
</protect>

MediaWiki:Sidebar

2008-07-30T20:28:01Z

Eurie:

Main Page

2008-07-30T20:25:51Z

Eurie:

MediaWiki:Sidebar

2008-07-30T20:19:29Z

Eurie:

Specification for New Interactions and Phenotype FTP files

2008-07-17T04:00:41Z

Eurie:

SGD has released new interfaces to view physical and genetic interactions as well as new interfaces to view newly curated phenotype data. In order to provide these data in a convenient format to the scientific community, SGD has made two new FTP files to replace the current FTP files.

=Phenotype=

The new file is available in this directory:

[ftp://genome-ftp.stanford.edu/pub/yeast/literature_curation/phenotype_data.tab| ftp://genome-ftp.stanford.edu/pub/yeast/literature_curation/phenotype_data.tab]

And will replace this file:

<pre>
ftp://ftp.yeastgenome.org/yeast/literature_curation/phenotypes.tab
</pre>

==Time frame==
The new '''phenotype_data.tab''' file is now available.

The old '''phenotypes.tab''' file will no longer be updated after July 14, 2008. It will be removed from the FTP directory October 31, 2008.

==Column specifications==
{|width="100%" border="1"
|- bgcolor="#CCCCFF"
! Column number
! Type of data
! Contents
! Required or Optional
|-
|1
|Feature Name
|The feature name of the gene
|Required
|-
|2
|Feature Type
|The feature type of the gene
|Required
|-
|3
|Gene Name
|The standard name of the gene
|Optional
|-
|4
|SGDID
|The SGDID of the gene
|Required
|-
|5
|Reference
|PMID: #### SGD_REF: #### (separated by pipe)(one reference per row)
|SGD_REF Required, PMID optional
|-
|6
|Experiment Type
|experiment_type (experiment_comment)
|experiment_type required, experiment_comment optional
|-
|7
|Mutant Type
|mutant_type
|Required
|-
|8
|Allele
|property_value (property_description) where property_type='Allele'
|Optional
|-
|9
|Strain Background
|property_value where property_type='strain_background'
|Optional
|-
|10
|Phenotype
|observable: qualifier
|Required
|-
|11
|Chemical
|property_value (property_description) where property_type='Chemical_pending' or 'chebi_ontology'; multiple properties separated by pipes
|Optional
|-
|12
|Condition
|property_value (property_description) where property_type='Condition'; multiple properties separated by pipes
|Optional
|-
|13
|Details
|property_value (property_description) where property_type='Details'; multiple properties separated by pipes
|Optional
|-
|14
|Reporter
|property_value (property_description) where property_type='Reporter'
|Optional
|-
|}

=Interactions=

The new file will be located in the following directory:

[ftp://ftp.yeastgenome.org/yeast/literature_curation/interactions_data.tab| ftp://ftp.yeastgenome.org/yeast/literature_curation/interactions_data.tab]

And will replace this file:

<pre>
ftp://ftp.yeastgenome.org/yeast/literature_curation/interactions.tab
</pre>

==Time frame==
The new '''interactions_data.tab''' file is now available.

The old '''interactions.tab''' file will no longer be updated after July 14, 2008. It will be removed from the FTP directory October 31, 2008.

==Column specifications==
{|width="100%" border="1"
|- bgcolor="#CCCCFF"
! Column number
! Type of data
! Contents
! Required or Optional
|-
|1
|Feature Name (Bait)
|The feature name of the gene used as the bait
|Required
|-
|2
|Standard Gene Name (Bait)
| The standard gene name of the gene used as the bait
| Optional
|-
|3
|Feature Name (Hit)
| The feature name of the gene that interacts with the bait
| Required
|-
|4
|Standard Gene Name (Hit)
| The standard gene name of the gene that interacts with the bait
| Optional
|-
|5
|Experiment Type
| A description of the experimental used to identify the interaction
| Required
|-
|6
|Genetic or Physical Interaction
| Indicates whether the experimental method is a genetic or physical interaction
| Required
|-
| 7
| Source
| Lists the database source for the interaction
| Required
|-
|8
| Manually curated or High-throughput
| Lists whether the interaction was manually curated from a publication or added as part of a high-throughput dataset
| Required
|-
|9
| Notes
| Free text field that contains additional information about the interaction
| Optional
|-
|10
| Phenotype
| Contains the phenotype of the interaction
| Optional
|-
|11
| Reference
| Lists the identifiers for the reference as an SGDID (SGD_REF:) or a PubMed ID (PMID:)
| Required
|-
|12
| Citation
| Lists the citation for the reference
| Required
|}

Specification for New Interactions and Phenotype FTP files

2008-07-01T20:50:52Z

Eurie:

SGD is planning on releasing new interfaces to view physical and genetic interactions as well as new interfaces to view newly curated phenotype data. In order to provide these data in a convenient format to the scientific community, SGD is proposing two new FTP files to replace the current FTP files.

=Phenotype=

=Interactions=

The new file will be located in the following directory:

<pre>
ftp://ftp.yeastgenome.org/yeast/literature_curation/interactions_data.tab
</pre>

And will replace this file:

<pre>
ftp://ftp.yeastgenome.org/yeast/literature_curation/interactions.tab
</pre>

==Time frame==
The new '''interactions_data.tab''' file will be available the week of July 14, 2008.

The old '''interactions.tab''' file will no longer be updated after July 14, 2008. It will be removed from the FTP directory October 31, 2008.

==Column specifications==
{|width="100%" border="1"
|- bgcolor="#CCCCFF"
! Column number
! Type of data
! Contents
! Required or Optional
|-
|1
|Feature Name (Bait)
|The feature name of the gene used as the bait
|Required
|-
|2
|Standard Gene Name (Bait)
| The standard gene name of the gene used as the bait
| Optional
|-
|3
|Feature Name (Hit)
| The feature name of the gene that interacts with the bait
| Required
|-
|4
|Standard Gene Name (Hit)
| The standard gene name of the gene that interacts with the bait
| Optional
|-
|5
|Experiment Type
| A description of the experimental used to identify the interaction
| Required
|-
|6
|Genetic or Physical Interaction
| Indicates whether the experimental method is a genetic or physical interaction
| Required
|-
| 7
| Source
| Lists the database source for the interaction
| Required
|-
|8
| Manually curated or High-throughput
| Lists whether the interaction was manually curated from a publication or added as part of a high-throughput dataset
| Required
|-
|9
| Notes
| Free text field that contains additional information about the interaction
| Optional
|-
|10
| Phenotype
| Contains the phenotype of the interaction
| Optional
|-
|11
| Reference
| Lists the identifiers for the reference as an SGDID (SGD_REF:) or a PubMed ID (PMID:)
| Required
|-
|12
| Citation
| Lists the citation for the reference
| Required
|}

Specification for New Interactions and Phenotype FTP files

2008-07-01T20:48:17Z

Eurie: New page: SGD is planning on releasing new interfaces to view physical and genetic interactions as well as new interfaces to view newly curated phenotype data. In order to provide these data in a c...

SGD is planning on releasing new interfaces to view physical and genetic interactions as well as new interfaces to view newly curated phenotype data. In order to provide these data in a convenient format to the scientific community, SGD is proposing two new FTP files to replace the current FTP files.

=Interactions=

The new file will be located in the following directory:

<pre>
ftp://ftp.yeastgenome.org/yeast/literature_curation/interactions_data.tab
</pre>

And will replace this file:

<pre>
ftp://ftp.yeastgenome.org/yeast/literature_curation/interactions.tab
</pre>

==Time frame==
The new '''interactions_data.tab''' file will be available the week of July 14, 2008.

The old '''interactions.tab''' file will no longer be updated after July 14, 2008. It will be removed from the FTP directory October 31, 2008.

==Column specifications==
{|width="100%" border="1"
|- bgcolor="#CCCCFF"
! Column number
! Type of data
! Contents
! Required or Optional
|-
|1
|Feature Name (Bait)
|The feature name of the gene used as the bait
|Required
|-
|2
|Standard Gene Name (Bait)
| The standard gene name of the gene used as the bait
| Optional
|-
|3
|Feature Name (Hit)
| The feature name of the gene that interacts with the bait
| Required
|-
|4
|Standard Gene Name (Hit)
| The standard gene name of the gene that interacts with the bait
| Optional
|-
|5
|Experiment Type
| A description of the experimental used to identify the interaction
| Required
|-
|6
|Genetic or Physical Interaction
| Indicates whether the experimental method is a genetic or physical interaction
| Required
|-
| 7
| Source
| Lists the database source for the interaction
| Required
|-
|8
| Manually curated or High-throughput
| Lists whether the interaction was manually curated from a publication or added as part of a high-throughput dataset
| Required
|-
|9
| Notes
| Free text field that contains additional information about the interaction
| Optional
|-
|10
| Phenotype
| Contains the phenotype of the interaction
| Optional
|-
|11
| Reference
| Lists the identifiers for the reference as an SGDID (SGD_REF:) or a PubMed ID (PMID:)
| Required
|-
|12
| Citation
| Lists the citation for the reference
| Required
|}

=Phenotype=

Main Page

2008-07-01T20:20:06Z

Eurie: /* Useful SGD Links */

<protect>
<big>'''Welcome to the Yeast Wiki'''</big>

* Use the search box in left-hand navigation bar to find or create specific wiki pages.
* Find already existing gene pages pre-filled with basic info from SGD by entering an ORF or gene name into the search box.
* Use these wiki pages as a place to enter your observations or notes for a gene or ORF.
* It's easy to add info! Just create an account via the "Log in/Create an account" link in the upper right-hand corner of this page.

[[Image:Wiki-invite3.jpg]]
 

== Useful SGD Links ==

[http://www.yeastgenome.org SGD Home] | [http://db.yeastgenome.org/cgi-bin/suggestion Contact SGD]

[[Specification for New Interactions and Phenotype FTP files]]

== Useful Wiki Links ==

[http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide] | [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ] | [http://meta.wikimedia.org/wiki/Help:Wikitext Quick Guide to Editing Wiki Text]
</protect>

Career Resources

2008-04-02T18:52:37Z

Eurie: New page: 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 s...

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.

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

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

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

*[http://www.healthecareers.com/site_templates/ASM/index.asp?aff=ASM&SPLD=ASM ASM Career Connections] offered by [http://www.asm.org/index.asp American Society for Microbiology]

*[http://www.faseb.org/careers/careerresources.htm Career Resources] offered by [http://www.faseb.org FASEB]

*[http://www.sdbonline.org/career/jobs.php Job Openings] offered by [http://www.sdbonline.org Society for Developmental Biology]

*[http://recruit.sciencemag.org Science Careers] and [http://nextwave.sciencemag.org Science Next Wave] offered by [http://www.scienceonline.org Science Magazine Online]

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

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

MediaWiki:Sidebar

2008-04-02T18:52:07Z

Eurie:

General Topics

2008-04-02T18:50:37Z

Eurie: /* Biology related career resources */

=General S. cerevisiae information=

*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
**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 wine making, 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 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.

*[http://www.yeastgenome.org/ SGD] maintains a [http://www.yeastgenome.org/ExternalContents.shtml 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]

=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://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.

=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]

=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. ''grubbii'' 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://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.

MediaWiki:Sidebar

2008-04-02T18:40:59Z

Eurie:

MediaWiki:Sidebar

2008-04-02T18:40:02Z

Eurie:

MediaWiki:Sidebar

2008-04-02T18:36:21Z

Eurie:

MediaWiki:Sidebar

2008-04-02T18:36:03Z

Eurie:

MediaWiki:Sidebar

2008-04-02T18:35:15Z

Eurie:

General Topics

2008-04-02T18:19:33Z

Eurie: /* Biology related career resources */

Positions in yeast labs

2008-04-01T15:23:03Z

Eurie: New page: == Carnegie Institution for Science, Stanford, California, USA == Highly qualified and motivated individuals are invited to send applications for a Postdoc Position in the Research Group ...

== Carnegie Institution for Science, Stanford, California, USA ==

Highly qualified and motivated individuals are invited to send applications for
a Postdoc Position
in the Research Group of Wolf B. Frommer
on the topic

'''Regulatory circuits controlling sugar flux in yeast grown on ethanol'''

HT screen of the yeast knock out collection using FRET sensors for glucose, sucrose and maltose, follow-up analysis of hits and reconstruction of networks

Our lab has developed a wide range of FRET sensors for metabolites. These sensors have so far been used mainly in mammalian cells to study glutamate release from neurons, glucose transport across the ER membrane or tryptophan/kynurenine exchange.

We have now been able to functionally express the FRET sensors also in the cytoplasm of yeast and to establish a high throughput screening platform. Our goal is to identify novel regulatory pathways involved in the control of glucose flux in yeast. As a first step, the kinase k.o. collection has been screened for altered glucose flux and several hits have been identified and verified.

Next steps will be to verify the hits using a new microfluidic platform, to test the effect on other sugar fluxes using FRET sensors for sucrose, maltose and ribose and to place the kinases into signaling networks. The screen can be expanded to include the whole genome at a later stage. Focus points are regulatory effects on glucose transporters and hexokinases. Due to the advanced stage, it is expected that the work will lead to high profile publications within less than a year.

Start date asap

Send your application with CV and the names of three references to:

Wolf B. Frommer
Carnegie Institution for Science
260 Panama St, Stanford CA 94305 USA.
Website[http://carnegiedpb.stanford.edu]
E-mail: wfrommer@stanford.edu

General Topics

2008-04-01T00:13:36Z

Eurie: /* Biology related career resources */

Commonly used strains

2007-12-17T22:58:35Z

Eurie: /* SK1 */

Commonly used strains

2007-12-17T22:52:37Z

Eurie: /* S288C */

Commonly used strains

2007-12-17T22:52:19Z

Eurie: /* A364A */

Commonly used strains

2007-12-17T22:48:05Z

Eurie: /* A364A */

Main Page

2007-08-16T19:04:48Z

Eurie:

<protect>
<big>'''Welcome to the Yeast Wiki'''</big>

* Use the search box in left-hand navigation bar to find or create specific wiki pages.
* Find already existing gene pages pre-filled with basic info from SGD by entering an ORF or gene name into the search box.
* Use these wiki pages as a place to enter your observations or notes for a gene or ORF.
* It's easy to add info! Just create an account via the "Log in/Create an account" link in the upper right-hand corner of this page.

[[Image:Wiki-invite3.jpg]]
 

== Useful SGD Links ==

[http://www.yeastgenome.org SGD Home] | [http://db.yeastgenome.org/cgi-bin/suggestion Contact SGD]

== Useful Wiki Links ==

[http://meta.wikimedia.org/wiki/Help:Contents MediaWiki User's Guide] | [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ] | [http://meta.wikimedia.org/wiki/Help:Wikitext Quick Guide to Editing Wiki Text]
</protect>