SGD-Wiki - User contributions [en]

Bay Area Yeast Meeting

2013-12-10T19:22:27Z

Fisk: /* Key Note Speaker */

=Spring Bay Area Yeast Meeting Information=

* Venue: Li Ka Shing Center (http://lksc.stanford.edu/)
* Location: Stanford University, CA
* Date: April 19th, 2014

==Key Note Speaker==
Randy Schekman (Nobel Prize in Physiology or Medicine, 2013)
UC Berkeley

==Maps & Parking==
[http://maps.stanford.edu/maps_library Stanford University maps]

==Campus Shuttle (Marguerite)==

Free campus shuttle from downtown Palo Alto is available. The Palo Alto Train Station is the closest stop to Stanford University.
A variety of maps for the [http://transportation.stanford.edu/marguerite/MargueriteSched.shtml Marguerite Shuttle] are available.

Realtime [http://lbre-apps.stanford.edu/transportation/stanford_ivl/ Shuttle Bus Service]. The Stanford Marguerite Shuttle is free.

==Registration==
Coming soon!

==Sponsors==

Reagents

2013-06-13T21:59:52Z

Fisk:

*[http://www.corastyles.com/ Cora Styles Lab Supplies] - Simple, high-quality yeast dissection and replica plating tools, including yeast dissection needle kits, velveteens, and replica plating blocks.

*[[Antibodies]] made to ''S. cerevisiae'' proteins

*Custom Oligos and Primers - Several companies provide custom oligo synthesis, including but not limited to, those listed here:
**[http://www.geneworks.com.au/Content.aspx?p=84 GeneWorks]
**[http://www.idtdna.com/pages/products?adwords=oligo&gclid=CMT0tsS9_pMCFRwvagodWhd3WA Integrated DNA Technologies]
**[http://www.invitrogen.com/site/us/en/home/brands/Invitrogen.html Invitrogen]
**Find other companies by searching [http://www.google.com/search?client=safari&rls=en&q=order+oligos+primers&ie=UTF-8&oe=UTF-8 Google]

*[http://wiki.yeastgenome.org/index.php/Primer_Set_Sequences Primer Set Sequences] Links to download the sequences of primer sets from ResGen/Invitrogen and from the Yeast Knockout (YKO) Consortium

*[http://www.thermoscientificbio.com/non-mammalian-cdna-and-orf/yeast-orf-collection/ MORF collection] is a moveable ORF library which enables protein expression and purification for more than 4900 S. cerevisiae genes, as described in [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000113921 Gelperin DM, et al. (2005)].

*[http://www.addgene.org/yeast-gateway/ pAG Vectors] is a collection of 288 yeast Gateway expression vectors. These "Advanced Gateway" vectors are modifications of the pRS series plasmids and allow for inducible or constitutive expression, as well as fusion to a number of protein tags and fluorescent proteins. We have made all of these vectors available through the non-profit plasmid repository [http://www.addgene.org/ Addgene]. Clones were created by the [http://lindquistlab.wi.mit.edu/ Lindquist Lab] at the [http://wi.mit.edu/ Whitehead Institute]. "A suite of Gateway vectors for high-throughput genetic analysis in Saccharomyces cerevisiae". Simon Alberti, Aaron D. Gitler, and Susan Lindquist. 2007. Yeast. In Press.

*The [http://plasmid.med.harvard.edu/PLASMID/ PlasmID] repository distributes over 5,200 fully sequence-verified S. cerevisiae genes in Gateway entry vectors and expression vectors. The PlasmID repository is part of the DF/HCC DNA Resource Core at the [http://harlow.hms.harvard.edu/ Harvard Institute of Proteomics] at [http://hms.harvard.edu/ Harvard Medical School].

*The [http://dnasu.asu.edu/DNASU/Home.jsp DNASU Plasmid Repository] stores and distributes nearly 100,000 plasmids including over 35,000 human and mouse plasmids, full genome collections of numerous organisms including S. cerevisiae, the protein expression plasmids from the Protein Structure Initiative Material Repository (PSI-MR), and both small and large collections from individual researchers. DNASU accepts plasmid contributions from individual researchers and will distribute them to the community.

*[http://www.tritechresearch.com/index.html?research_type=yeast Tritech Research] maintains a list of links to S. cerevisiae information and protocols, and sells reagents and equipment for S. cerevisiae research.

*[http://genome-www.stanford.edu/vectordb/ VectorDB], collected sequences of cloning vectors for use in a variety of organisms.

*[http://www.addgene.org/ Addgene]: A Better Way to Share Plasmids. Addgene is a non-profit plasmid repository dedicated to helping academic scientists around the world share high-quality plasmids.

*[[Microarray methods for profiling the Yeast Knockout (YKO) Collection]]

Strains

2013-06-11T17:58:21Z

Fisk: /* Strain Collections */

=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
*Table of [[Commonly_used_auxotrophic_markers|commonly used auxotrophic markers]], with sequence information where known.

=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/site/us/en/home/brands/Invitrogen.html Invitrogen].

*[http://www.thermoscientificbio.com/non-mammalian-cdna-and-orf/yeast-gst-tagged-orfs/ Yeast GST-Tagged Collection] for inducible overexpression of yeast ORFs, developed in the Andrews lab at the University of Toronto. Hosted by [http://www.thermoscientificbio.com/openbiosystems/?redirect=true 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.thermoscientificbio.com/non-mammalian-cdna-and-orf/yeast-tap-tagged-orfs/ 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.thermoscientificbio.com/openbiosystems/?redirect=true 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].

*The Yeast Transposon Insertion Library Collection, derived by using mini-transposons (mTns) to mutagenize a yeast genomic DNA library, is available from the [http://snyderlab.stanford.edu/ Mike Snyder lab] at Stanford University. Please contact Minyi Shi (minyishi at stanford dot edu) with requests.

Commonly used strains

2013-05-07T20:08:36Z

Fisk:

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

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

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

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

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

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

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

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

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

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

'''Sources:''' [http://www.thermoscientificbio.com/search/?term=YSC1050 Thermo Scientific:YSC1050]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

=Sigma1278b=

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'''Sources:''' [http://www.thermoscientificbio.com/search/?term=YSC1058 Thermo Scientific: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.thermoscientificbio.com/search/?term=YSC1058 Thermo Scientific: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.thermoscientificbio.com/search/?term=YSC1058 Thermo Scientific:YSC1058]

==W303-K6001==

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

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

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

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

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

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

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

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

Sources: ATCC: 28383

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

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

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

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

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

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

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

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

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

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

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

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

=JK9-3d=

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

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

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

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

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

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

=RM11-1a=

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

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

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

=Y55=

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

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

External Links

2013-05-06T16:32:35Z

Fisk:

=General Yeast Resources=
* Information about [[General_S._cerevisiae_Information|Saccharomyces cerevisiae ]] (budding, bakers', and sometimes brewers')
* Information about [[Other_Fungi|Schizosaccharomyces pombe (fission), Candida albicans and other fungi]]
* [[Educational_Resources| Educational resources]] contains information for non-specialists and teachers

*[http://www.bio.net/hypermail/yeast/ BioSci Yeast Archives] search the Yeast Biosci Newsgroup

=Nucleic Acid Data Resources=

*[http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html GenBank] sequence repository at the [http://www.ncbi.nlm.nih.gov/ NCBI], Bethesda, Maryland, USA

*[http://www.ebi.ac.uk/embl/index.html EMBL] sequence repository at the [http://www.ebi.ac.uk/ EBI], Hinxton Hall, Cambridge, UK

*[http://www.nig.ac.jp/index-e.html DDBJ] sequence repository at Mishima, Japan

*[http://www.genepalette.org/index.html GenePalette] software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences

*[http://www.oridb.org OriDB] catalog of confirmed and predicted DNA replication origin sites, currently limited to S. cerevisiae

*[http://seq.cbrc.jp/~wataru/PROSPECT/ PROSPECT: Promoter Inspection Tool] explore promoter regions by searching for genes or a sequence. Also contains a list of yeast transcription factor binding sites.

*[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools] search for regulatory signals in the non-coding sequences of S. cerevisiae, S. pombe, and other organisms

*[http://rulai.cshl.edu/SCPD/ SCPD: The Promoter Database of Saccharomyces cerevisiae] explore the promoter regions of all ORFs in the yeast genome. Note that this web site is not exhaustive, and some of the information is outdated.

*[http://www2.imtech.res.in/anand/sacch_prom_pat.html Search for conserved patterns in Saccharomyces spp.] search tool for identification and analysis of conserved patterns in Saccharomyces promoters. Formore information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079651 Kohli DK, et al (2004) In Silico Biol 4(3):0034]]

*[http://www.cse.ucsc.edu/research/compbio/yeast_introns.html Yeast Introns] yeast intron data from the Ares Lab, U.C. Santa Cruz

*[http://people.biochem.umass.edu/fournierlab/snornadb/main.php Yeast snoRNAs] yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts

*[http://lowelab.cse.ucsc.edu/GtRNAdb/Sacc_cere/ Yeast tRNAs] yeast tRNA information from Todd Lowe, UC-Santa Cruz

=Genome and Protein Resources=

*[http://www.uniprot.org/ UniProt] comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

*[http://www.ebi.ac.uk/interpro/ InterPro] functional analysis of proteins through classification into families and predicting domains and important sites.

*[http://www.ncbi.nlm.nih.gov/homologene HomoloGene] a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.

*[http://ygob.ucd.ie/ Yeast Gene Order Browser (YGOB)] an online tool for visualising the syntenic context of any gene from several yeast genomes.

*[http://www.yeastgenome.org/community/nature_genome_dir_pdf/ Yeast Genome Directory] A collection of papers describing the sequencing of each chromosome of the S. cerevisiae genome

*[http://supfam.org/SUPERFAMILY/index.html Structural assignments of proteins] This website provides structural assignments to protein sequences at the superfamily level. You can browse an [http://supfam.org/SUPERFAMILY/cgi-bin/gen_list.cgi?genome=sc overview] of all the superfamilies currently identified in S. cerevisiae; the site also provides several different ways to search this information. See [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11697912&dopt=Abstract Gough et al.] for more information.

*[http://genome.wustl.edu/tools/blast/ Genome Sequence Center: BLAST Server]at the Washington University GSC in St. Louis. BLAST searches may be performed against genomic sequences from five Saccharomyces species: S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri.

*[http://mips.gsf.de/proj/yeast/CYGD/db/index.html Yeast Project at MIPS] yeast information from the Munich Information Center for Protein Sequences ([http://mips.gsf.de/ MIPS])

*[http://www.incyte.com/control/tools/proteome Yeast Proteome Database (YPD)] yeast protein information from Incyte Genomics, Inc. Access to this resource requires a subscription.

*[http://www.doe-mbi.ucla.edu/Services/GPofYPF/index.html Genome-Wide Protein Function Prediction] Links between functionally related yeast proteins are used to predict functions for about two thirds of all predicted yeast proteins in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044838 Marcotte et al. (1999) Nature 402:83-86.]

*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES - a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu Yale Genome Analysis Center.]

*[http://depts.washington.edu/~sfields/yp_interactions/index.html Yeast Protein Linkage Map] The Fields lab's systematic Two-Hybrid project. Results are described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043128 Uetz et al. (2000) Nature 403:623-627.]

*[http://www.thebiogrid.org/ General Repository for Interaction Datasets (BioGRID)] a database of genetic and physical interactions. BioGRID, developed in Mike Tyers group, contains interaction data from many sources, including both small-scale and genome/proteome-wide studies, the [http://mips.gsf.de/proj/yeast/CYGD/db/index.html MIPS] database, and BIND.

*[http://biodata.mshri.on.ca/osprey/servlet/Index Osprey: A Network Visualization System] a powerful application for graphically representing physical and genetic biological interactions. It provides many features that are helpful in analysis of interaction data. Osprey is also coupled with the [http://www.thebiogrid.org/ General Repository of Interaction Datasets (BioGRID)] and as a result brings a large dataset of interactions to your fingertips.

*[http://www.yeastrc.org/pdr/ Yeast Resource Center Public Data Repository] provides protein searching from multiple yeast databases and provides experimental data from mass spectrometry, yeast two-hybrid, fluorescence microscopy, protein structure prediction and protein complex predictions for S. cerevisiae proteins. Please see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15608220 Riffle et al. (2005) Nucleic Acids Res 33(Database issue):D378-82] for more information.

*[http://gpmdb.thegpm.org/gpmdb_help.html The Global Proteome Machine Database (GPMDB)] a database of mass spectrometry based proteomics information, populated by the general proteomics community.

*[http://wolfe.gen.tcd.ie/ygob/ Yeast Gene Order Browser] a tool used to visualize the syntenic context of any gene from S. cerevisiae, S. castellii, C. glabrata, A. gossypii, K. lactis, K. waltii, and S. kluyveri. This tool was developed by Kevin Byrne and Ken Wolfe (Trinity College, Dublin, Ireland), as described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000113653 Byrne and Wolfe].

*[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/index.shtml YOGY:eukarYotic OrtholoGY] a tool to view orthologous proteins from eukaryotic orgranisms (Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe, and Saccharomyces cerevisiae). This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL and manually curated orthologs between S. cerevisiae and S. pombe. This tool was developed by [http://www.sanger.ac.uk/PostGenomics/S_pombe/ Penkett CJ, Morris JA, Wood V, and Bahler J] (Wellcome Trust Sanger Institute, Cambridge, UK).

*[http://www.binofo.com/en/bioinformatics/iproto/ iProto Yeast] an iPhone application containing proteome information for several different Saccharomyces and Schizosaccharomyces strains

*[http://refnucl.atlas.bx.psu.edu/ Yeast Nucleosome Positions] a compiled and systematic reference map of nucleosome positions across the S. cerevisiae genome

*[http://interologfinder.org/simpleIfWS?operation=doStart InterologFinder] A database of conserved and predicted novel protein-protein interactions (interologs or interologues) in human, mouse, fly, worm, and yeast based on interaction of orthologous proteins found in the other organisms. For more information please see [http://www.ncbi.nlm.nih.gov/pubmed/20353594 Wiles et al., (2010) BMC Syst Biol. Mar 30;4:36.].

=Expression Data Resources=

*[http://www.yeastract.com/ YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking)] A curated database of regulatory associations between transcription factors and their target genes, and information on transcription factor binding sites (see [http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D132 Monteiro et al.</a], (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136).

*[http://sceptrans.org/ SCEPTRANS] A website for visualizing and studying periodic transcription in yeast (see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000122214 Kudlicki et al. (2007) Bioinformatics])

*[http://genome-www.stanford.edu/cellcycle/ Yeast Cell Cycle Analysis Projects] Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman et al. (1998) Mol Cell Biol 9:3273-3297.] These data were re-analyzed in: (1) [http://www.pnas.org/cgi/content/full/98/10/5631 Zhao LP, et al. (2001)] Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc Natl Acad Sci U S A 98(10):5631-6. [http://www.fhcrc.org/science/labs/breeden/spm/ View data], and (2) [http://www.yeasgenome.org/cgi-bin/reference/reference.pl?dbid=S000060075 Alter O, Brown PO, Botstein D (2000)] Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 97(18):10101-6. [http://genome-www.stanford.edu/SVD/ View data].

*[http://www.fhcrc.org/science/labs/breeden/cellcycle/ Periodic Genes of the Yeast Saccharomyces cerevisiae] A combined analysis of five cell cycle microarray data sets, has been published in G&D by Pramila et al. (in press). This includes access to three new expression data sets generated using spotted cDNA arrays after sampling alpha factor synchronized cells across a time-course. Two of these data sets and three additional data sets from the public domain have been analyzed using a permutation based method published by [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15513999&dopt=Abstract de Lichtenberg et al. (2005) Bioinformatics 21:1164-71] to calculate a weighted average peak time base. This interactive resource allows users to sort and filter data, as well as access expression plots and heat maps.

*[http://www.transcriptome.ens.fr/ymgv/ Yeast Microarray Global Viewer] a database containing most of the published yeast microarray expression datasets as described in [http://nar.oxfordjournals.org/cgi/content/abstract/29/13/e63 Marc et al. (2001) Nucleic Acids Res 29(13):e63]

*[http://www-stat.stanford.edu/~tibs/PAM/ PAM: Prediction Analysis for Microarrays] a software tool for interpretation of microarray expression datasets

*[http://www.genmapp.org/ GenMAPP] a Visual Basic application that displays expression data on biochemical and cellular pathways as well as groups of genes.  MAPPFinder is a related tool that integrates GO annotations with GenMAPP to create a global expression profile (see [http://genomebiology.com/2003/4/1/R7 Doniger et al. (2003) Genome Biology 4:R7])

*[http://www.sagenet.org/index.htm Yeast SAGE] homepage for Serial Analysis of Gene Expression project at Johns Hopkins University

= Localization Data Resources=

*[http://images.yeastrc.org/ Yeast Resource Center Public Image Repository (YRC PIR)] Very large repository of images and metadata from fluorescence microscopy experiments, including localization, colocalization and FRET experiments. Mostly contains data from S. cerevisiae, but also currently includes some S. pombe. Submission of data is welcome and encouraged. Please see [http://www.ncbi.nlm.nih.gov/pubmed/20482811 Riffle et al (2010)] for more information.

*[http://ypl.uni-graz.at/pages/home.html YeastProtein Localization database (YPL.db)] S. cerevisiae protein localization data from University Graz. Users may also [http://wwwoas.kfunigraz.ac.at:8010/pls/al12/submit.logon submit] images.

*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES- a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu Yale Genome Analysis Center.]

*[http://www.cbs.umn.edu/yeast/ Yeast Membrane Protein Library] A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from S. cerevisiae

*[http://yeastgfp.yeastgenome.org/ Yeast GFP Fusion Localization Database] S. cerevisiae protein localization data from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD.

=Phenotype Data Resources=

*[http://syllabus.syr.edu/bio/seerdman/TTG/ Agria Triterpene Glycoside (TTG) Phenotype Query Page] A chemical genomics phenotype database to query for phenotypes of href="#deletions yeast deletion strains] grown in the presence of triterpene glycosides (TTG's) from the cactus Stenocereus gummosus (common name agria). Pre-publication access provided by Scott Erdman at Syracuse University.

*[http://yeast.gi.k.u-tokyo.ac.jp/ The Saccharomyces Cerevisiae Morphological Database (SCMD)] A collection of micrographs of budding yeast mutants. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000075221 Saito et al. (2004) Nucleic Acids Res 32:D319-22.]

*[http://prophecy.lundberg.gu.se/ PROPHECY] A database that provides quantitative information regarding growth rate, growth efficiency, and adaptation time for haploid deletion strains. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000119344 Warringer et al. (2003) Proc Natl Acad Sci USA 100:15724-9.]

*[http://genomics.senescence.info/genes/models.html GenAge] GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.

=Genetic Interactions Resources=

*[http://drygin.ccbr.utoronto.ca/ DRYGIN] A database of quantitative genetic interactions of ''S. cerevisiae'' derived from the SGA double-mutant arrays conducted in Boone lab at Terrence Donnelly Centre for Cellular and Biochemical Research, University of Toronto.

=Literature Resources=

*[http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

*[http://www.ncbi.nlm.nih.gov/pmc/ PMC] is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM).

*[http://scholar.google.com/ Google Scholar] Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.

=Additional Yeast Research Resources=

*[http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Yeast Deletion Strains] Deletion strains created by the Saccharomyces Genome Deletion project] are available via [http://www.atcc.org ATCC] ([http://www.atcc.org/catalog/all/allIndex.cfm online catalog] available), [http://www.openbiosystems.com/ Open Biosystems], and [http://mp.invitrogen.com/ Invitrogen] (Research Genetics). The [http://www-sequence.stanford.edu/group/yeast_deletion_project/gb/ykocp.html Community Posting Page] provided by the [http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Saccharomyces Genome Deletion Project] enables users of the mutant collection to share information about the collection. [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/ EUROSCARF] makes deletion strains available from the EUROFAN projects.

*[http://depts.washington.edu/~yeastrc/index.html NCRR Yeast Resource Center] Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]

*[http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ The Saccharomyces Genome Resequencing Project (SGRP)] A colloboration between the [http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ Sanger Institute] and [http://www.nottingham.ac.uk/genetics/people/louis/index.php?from=genContact&ID=205&S=Yeast%20Genomic%20Resources Prof. Ed Louis' group] at the Institute of Genetics, University of Nottingham to analyze sequences from multiple strains of S. cerevisiae and S. paradoxus.

*[http://www.ysbn.org/ Yeast Systems Biology Network] Promotes the study of S. cerevisiae systems biology by facilitating cooperation between experimental scientists and theoreticians, generating quantitative data, and developing new resources. Download YSBN's [http:www.yeastgenome.org/community/ysbn.pdf brochure] for more information and contacts.

*[http://www.addgene.org Addgene] Repository and distributor of plasmid constructs described in published literature. [http://www.addgene.org:8080/pgvec1?f=c&cmd=showfile&file=colinfo Search] for a plasmid or [http://www.addgene.org/pgvec1?f=d&cmd=showfile&file=submit deposit] your plasmid to the repository.

=Other Resources=
*[http://www.openhelix.com/sgd SGD Tutorial] Developed by [http://www.openhelix.com/index.shtml OpenHelix], this online tutorial describes navigation of SGD and many features of the database.

*[http://www.geneontology.org Gene Ontology] Gene Ontology (GO) Consortium home page

*[http://www.genome.ad.jp/kegg/ KEGG] metabolic reactions and pathways from Kyoto University, Kyoto, Japan

*[http://restools.sdsc.edu/ Molecular Biology] resources from CMS. An impressive set of hyperlinks with a great presentation on all aspects of molecular biology, biotechnology, molecular evolution, biochemistry, and biomolecular modeling.

*[http://mcb.harvard.edu/BioLinks.html WWW Virtual Library: Biosciences] provided by the Harvard Biolabs

*[http://www.microbes.info/ Microbes.info] The Microbiology Information Portal. This site contains resources, news, and information about many different aspects of microbiology. Its [http://www.microbes.info/resources/General_Microbiology/ General Microbiology] section contains links to various databases, culture collections, genetic analysis sites, and method sites.

*[http://www.els.net/ Encyclopedia of Life Sciences] a collection of articles on a wide variety of biological topics, from the Nature Publishing Group

*[http://dir.yahoo.com/Science/biology/ Yahoo] list of WWW biological information resources

*[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.

=Nucleic Acids Research Database Issues=
Articles about genomic and biological databases.
Go to NAR Database Issue for: 
[http://nar.oxfordjournals.org/content/38/suppl_1 2010]|
[http://nar.oxfordjournals.org/content/37/suppl_1 2009] |
[http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl 2008] |
[http://nar.oxfordjournals.org/content/vol35/suppl_1/ 2007] |
[http://nar.oxfordjournals.org/content/vol34/suppl_1/ 2006] |
[http://nar.oxfordjournals.org/content/vol33/suppl_1/ 2005] |
[http://nar.oxfordjournals.org/content/vol32/suppl_1/ 2004] |
[http://nar.oxfordjournals.org/content/vol31/issue1/ 2003] |
[http://nar.oxfordjournals.org/content/vol30/issue1/ 2002] |
[http://nar.oxfordjournals.org/content/vol29/issue1/ 2001] |
[http://nar.oxfordjournals.org/content/vol28/issue1/ 2000] |
[http://nar.oxfordjournals.org/content/vol27/issue1/ 1999] |
[http://nar.oxfordjournals.org/content/vol26/issue1/ 1998] |

 
View SGD's article for: 
[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D577 2008] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D468 2007] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D442 2006] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D374 2005]|
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D311 2004] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/31/1/216 2003] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/30/1/69 2002] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/29/1/80 2001] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/28/1/77 2000] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/27/1/74 1999] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/26/1/73 1998]

External Links

2013-05-06T16:25:39Z

Fisk: /* Genome and Protein Resources */

=General Yeast Resources=
* Information about [[General_S._cerevisiae_Information|Saccharomyces cerevisiae ]] (budding, bakers', and sometimes brewers')
* Information about [[Other_Fungi|Schizosaccharomyces pombe (fission), Candida albicans and other fungi]]
* [[Educational_Resources| Educational resources]] contains information for non-specialists and teachers

*[http://www.bio.net/hypermail/yeast/ BioSci Yeast Archives] search the Yeast Biosci Newsgroup

=Nucleic Acid Data Resources=

*[http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html GenBank] sequence repository at the [http://www.ncbi.nlm.nih.gov/ NCBI], Bethesda, Maryland, USA

*[http://www.ebi.ac.uk/embl/index.html EMBL] sequence repository at the [http://www.ebi.ac.uk/ EBI], Hinxton Hall, Cambridge, UK

*[http://www.nig.ac.jp/index-e.html DDBJ] sequence repository at Mishima, Japan

*[http://www.genepalette.org/index.html GenePalette] software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences

*[http://www.oridb.org OriDB] catalog of confirmed and predicted DNA replication origin sites, currently limited to S. cerevisiae

*[http://seq.cbrc.jp/~wataru/PROSPECT/ PROSPECT: Promoter Inspection Tool] explore promoter regions by searching for genes or a sequence. Also contains a list of yeast transcription factor binding sites.

*[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools] search for regulatory signals in the non-coding sequences of S. cerevisiae, S. pombe, and other organisms

*[http://rulai.cshl.edu/SCPD/ SCPD: The Promoter Database of Saccharomyces cerevisiae] explore the promoter regions of all ORFs in the yeast genome. Note that this web site is not exhaustive, and some of the information is outdated.

*[http://www2.imtech.res.in/anand/sacch_prom_pat.html Search for conserved patterns in Saccharomyces spp.] search tool for identification and analysis of conserved patterns in Saccharomyces promoters. Formore information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079651 Kohli DK, et al (2004) In Silico Biol 4(3):0034]]

*[http://www.cse.ucsc.edu/research/compbio/yeast_introns.html Yeast Introns] yeast intron data from the Ares Lab, U.C. Santa Cruz

*[http://people.biochem.umass.edu/fournierlab/snornadb/main.php Yeast snoRNAs] yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts

*[http://lowelab.cse.ucsc.edu/GtRNAdb/Sacc_cere/ Yeast tRNAs] yeast tRNA information from Todd Lowe, UC-Santa Cruz

=Genome and Protein Resources=

*[http://www.uniprot.org/ UniProt] comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

*[http://www.ebi.ac.uk/interpro/ InterPro] functional analysis of proteins through classification into families and predicting domains and important sites.

*[http://www.ncbi.nlm.nih.gov/homologene HomoloGene] a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.

*[http://ygob.ucd.ie/ Yeast Gene Order Browser (YGOB)] an online tool for visualising the syntenic context of any gene from several yeast genomes.

*[http://www.yeastgenome.org/community/nature_genome_dir_pdf/ Yeast Genome Directory] A collection of papers describing the sequencing of each chromosome of the S. cerevisiae genome

*[http://supfam.org/SUPERFAMILY/index.html Structural assignments of proteins] This website provides structural assignments to protein sequences at the superfamily level. You can browse an [http://supfam.org/SUPERFAMILY/cgi-bin/gen_list.cgi?genome=sc overview] of all the superfamilies currently identified in S. cerevisiae; the site also provides several different ways to search this information. See [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11697912&dopt=Abstract Gough et al.] for more information.

*[http://genome.wustl.edu/tools/blast/ Genome Sequence Center: BLAST Server]at the Washington University GSC in St. Louis. BLAST searches may be performed against genomic sequences from five Saccharomyces species: S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri.

*[http://mips.gsf.de/proj/yeast/CYGD/db/index.html Yeast Project at MIPS] yeast information from the Munich Information Center for Protein Sequences ([http://mips.gsf.de/ MIPS])

*[http://www.incyte.com/control/tools/proteome Yeast Proteome Database (YPD)] yeast protein information from Incyte Genomics, Inc. Access to this resource requires a subscription.

*[http://www.doe-mbi.ucla.edu/Services/GPofYPF/index.html Genome-Wide Protein Function Prediction] Links between functionally related yeast proteins are used to predict functions for about two thirds of all predicted yeast proteins in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044838 Marcotte et al. (1999) Nature 402:83-86.]

*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES - a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu Yale Genome Analysis Center.]

*[http://depts.washington.edu/~sfields/yp_interactions/index.html Yeast Protein Linkage Map] The Fields lab's systematic Two-Hybrid project. Results are described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043128 Uetz et al. (2000) Nature 403:623-627.]

*[http://www.thebiogrid.org/ General Repository for Interaction Datasets (BioGRID)] a database of genetic and physical interactions. BioGRID, developed in Mike Tyers group, contains interaction data from many sources, including both small-scale and genome/proteome-wide studies, the [http://mips.gsf.de/proj/yeast/CYGD/db/index.html MIPS] database, and BIND.

*[http://biodata.mshri.on.ca/osprey/servlet/Index Osprey: A Network Visualization System] a powerful application for graphically representing physical and genetic biological interactions. It provides many features that are helpful in analysis of interaction data. Osprey is also coupled with the [http://www.thebiogrid.org/ General Repository of Interaction Datasets (BioGRID)] and as a result brings a large dataset of interactions to your fingertips.

*[http://www.yeastrc.org/pdr/ Yeast Resource Center Public Data Repository] provides protein searching from multiple yeast databases and provides experimental data from mass spectrometry, yeast two-hybrid, fluorescence microscopy, protein structure prediction and protein complex predictions for S. cerevisiae proteins. Please see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15608220 Riffle et al. (2005) Nucleic Acids Res 33(Database issue):D378-82] for more information.

*[http://gpmdb.thegpm.org/gpmdb_help.html The Global Proteome Machine Database (GPMDB)] a database of mass spectrometry based proteomics information, populated by the general proteomics community.

*[http://wolfe.gen.tcd.ie/ygob/ Yeast Gene Order Browser] a tool used to visualize the syntenic context of any gene from S. cerevisiae, S. castellii, C. glabrata, A. gossypii, K. lactis, K. waltii, and S. kluyveri. This tool was developed by Kevin Byrne and Ken Wolfe (Trinity College, Dublin, Ireland), as described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000113653 Byrne and Wolfe].

*[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/index.shtml YOGY:eukarYotic OrtholoGY] a tool to view orthologous proteins from eukaryotic orgranisms (Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe, and Saccharomyces cerevisiae). This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL and manually curated orthologs between S. cerevisiae and S. pombe. This tool was developed by [http://www.sanger.ac.uk/PostGenomics/S_pombe/ Penkett CJ, Morris JA, Wood V, and Bahler J] (Wellcome Trust Sanger Institute, Cambridge, UK).

*[http://www.binofo.com/en/bioinformatics/iproto/ iProto Yeast] an iPhone application containing proteome information for several different Saccharomyces and Schizosaccharomyces strains

*[http://refnucl.atlas.bx.psu.edu/ Yeast Nucleosome Positions] a compiled and systematic reference map of nucleosome positions across the S. cerevisiae genome

*[http://interologfinder.org/simpleIfWS?operation=doStart InterologFinder] A database of conserved and predicted novel protein-protein interactions (interologs or interologues) in human, mouse, fly, worm, and yeast based on interaction of orthologous proteins found in the other organisms. For more information please see [http://www.ncbi.nlm.nih.gov/pubmed/20353594 Wiles et al., (2010) BMC Syst Biol. Mar 30;4:36.].

=Expression Data Resources=

*[http://www.yeastract.com/ YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking)] A curated database of regulatory associations between transcription factors and their target genes, and information on transcription factor binding sites (see [http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D132 Monteiro et al.</a], (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136).

*[http://sceptrans.org/ SCEPTRANS] A website for visualizing and studying periodic transcription in yeast (see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000122214 Kudlicki et al. (2007) Bioinformatics])

*[http://genome-www.stanford.edu/cellcycle/ Yeast Cell Cycle Analysis Projects] Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman et al. (1998) Mol Cell Biol 9:3273-3297.] These data were re-analyzed in: (1) [http://www.pnas.org/cgi/content/full/98/10/5631 Zhao LP, et al. (2001)] Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc Natl Acad Sci U S A 98(10):5631-6. [http://www.fhcrc.org/science/labs/breeden/spm/ View data], and (2) [http://www.yeasgenome.org/cgi-bin/reference/reference.pl?dbid=S000060075 Alter O, Brown PO, Botstein D (2000)] Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 97(18):10101-6. [http://genome-www.stanford.edu/SVD/ View data].

*[http://www.fhcrc.org/science/labs/breeden/cellcycle/ Periodic Genes of the Yeast Saccharomyces cerevisiae] A combined analysis of five cell cycle microarray data sets, has been published in G&D by Pramila et al. (in press). This includes access to three new expression data sets generated using spotted cDNA arrays after sampling alpha factor synchronized cells across a time-course. Two of these data sets and three additional data sets from the public domain have been analyzed using a permutation based method published by [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15513999&dopt=Abstract de Lichtenberg et al. (2005) Bioinformatics 21:1164-71] to calculate a weighted average peak time base. This interactive resource allows users to sort and filter data, as well as access expression plots and heat maps.

*[http://www.transcriptome.ens.fr/ymgv/ Yeast Microarray Global Viewer] a database containing most of the published yeast microarray expression datasets as described in [http://nar.oxfordjournals.org/cgi/content/abstract/29/13/e63 Marc et al. (2001) Nucleic Acids Res 29(13):e63]

*[http://www-stat.stanford.edu/~tibs/PAM/ PAM: Prediction Analysis for Microarrays] a software tool for interpretation of microarray expression datasets

*[http://www.genmapp.org/ GenMAPP] a Visual Basic application that displays expression data on biochemical and cellular pathways as well as groups of genes.  MAPPFinder is a related tool that integrates GO annotations with GenMAPP to create a global expression profile (see [http://genomebiology.com/2003/4/1/R7 Doniger et al. (2003) Genome Biology 4:R7])

*[http://www.sagenet.org/index.htm Yeast SAGE] homepage for Serial Analysis of Gene Expression project at Johns Hopkins University

= Localization Data Resources=

*[http://images.yeastrc.org/ Yeast Resource Center Public Image Repository (YRC PIR)] Very large repository of images and metadata from fluorescence microscopy experiments, including localization, colocalization and FRET experiments. Mostly contains data from S. cerevisiae, but also currently includes some S. pombe. Submission of data is welcome and encouraged. Please see [http://www.ncbi.nlm.nih.gov/pubmed/20482811 Riffle et al (2010)] for more information.

*[http://ypl.uni-graz.at/pages/home.html YeastProtein Localization database (YPL.db)] S. cerevisiae protein localization data from University Graz. Users may also [http://wwwoas.kfunigraz.ac.at:8010/pls/al12/submit.logon submit] images.

*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES- a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu Yale Genome Analysis Center.]

*[http://www.cbs.umn.edu/yeast/ Yeast Membrane Protein Library] A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from S. cerevisiae

*[http://yeastgfp.yeastgenome.org/ Yeast GFP Fusion Localization Database] S. cerevisiae protein localization data from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD.

=Phenotype Data Resources=

*[http://syllabus.syr.edu/bio/seerdman/TTG/ Agria Triterpene Glycoside (TTG) Phenotype Query Page] A chemical genomics phenotype database to query for phenotypes of href="#deletions yeast deletion strains] grown in the presence of triterpene glycosides (TTG's) from the cactus Stenocereus gummosus (common name agria). Pre-publication access provided by Scott Erdman at Syracuse University.

*[http://yeast.gi.k.u-tokyo.ac.jp/ The Saccharomyces Cerevisiae Morphological Database (SCMD)] A collection of micrographs of budding yeast mutants. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000075221 Saito et al. (2004) Nucleic Acids Res 32:D319-22.]

*[http://prophecy.lundberg.gu.se/ PROPHECY] A database that provides quantitative information regarding growth rate, growth efficiency, and adaptation time for haploid deletion strains. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000119344 Warringer et al. (2003) Proc Natl Acad Sci USA 100:15724-9.]

*[http://genomics.senescence.info/genes/models.html GenAge] GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.

=Genetic Interactions Resources=

*[http://drygin.ccbr.utoronto.ca/ DRYGIN] A database of quantitative genetic interactions of ''S. cerevisiae'' derived from the SGA double-mutant arrays conducted in Boone lab at Terrence Donnelly Centre for Cellular and Biochemical Research, University of Toronto.

=Additional Yeast Research Resources=

*[http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Yeast Deletion Strains] Deletion strains created by the Saccharomyces Genome Deletion project] are available via [http://www.atcc.org ATCC] ([http://www.atcc.org/catalog/all/allIndex.cfm online catalog] available), [http://www.openbiosystems.com/ Open Biosystems], and [http://mp.invitrogen.com/ Invitrogen] (Research Genetics). The [http://www-sequence.stanford.edu/group/yeast_deletion_project/gb/ykocp.html Community Posting Page] provided by the [http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Saccharomyces Genome Deletion Project] enables users of the mutant collection to share information about the collection. [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/ EUROSCARF] makes deletion strains available from the EUROFAN projects.

*[http://depts.washington.edu/~yeastrc/index.html NCRR Yeast Resource Center] Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]

*[http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ The Saccharomyces Genome Resequencing Project (SGRP)] A colloboration between the [http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ Sanger Institute] and [http://www.nottingham.ac.uk/genetics/people/louis/index.php?from=genContact&ID=205&S=Yeast%20Genomic%20Resources Prof. Ed Louis' group] at the Institute of Genetics, University of Nottingham to analyze sequences from multiple strains of S. cerevisiae and S. paradoxus.

*[http://www.ysbn.org/ Yeast Systems Biology Network] Promotes the study of S. cerevisiae systems biology by facilitating cooperation between experimental scientists and theoreticians, generating quantitative data, and developing new resources. Download YSBN's [http:www.yeastgenome.org/community/ysbn.pdf brochure] for more information and contacts.

*[http://www.addgene.org Addgene] Repository and distributor of plasmid constructs described in published literature. [http://www.addgene.org:8080/pgvec1?f=c&cmd=showfile&file=colinfo Search] for a plasmid or [http://www.addgene.org/pgvec1?f=d&cmd=showfile&file=submit deposit] your plasmid to the repository.

=Other Resources=
*[http://www.openhelix.com/sgd SGD Tutorial] Developed by [http://www.openhelix.com/index.shtml OpenHelix], this online tutorial describes navigation of SGD and many features of the database.

*[http://www.geneontology.org Gene Ontology] Gene Ontology (GO) Consortium home page

*[http://www.genome.ad.jp/kegg/ KEGG] metabolic reactions and pathways from Kyoto University, Kyoto, Japan

*[http://restools.sdsc.edu/ Molecular Biology] resources from CMS. An impressive set of hyperlinks with a great presentation on all aspects of molecular biology, biotechnology, molecular evolution, biochemistry, and biomolecular modeling.

*[http://mcb.harvard.edu/BioLinks.html WWW Virtual Library: Biosciences] provided by the Harvard Biolabs

*[http://www.microbes.info/ Microbes.info] The Microbiology Information Portal. This site contains resources, news, and information about many different aspects of microbiology. Its [http://www.microbes.info/resources/General_Microbiology/ General Microbiology] section contains links to various databases, culture collections, genetic analysis sites, and method sites.

*[http://www.els.net/ Encyclopedia of Life Sciences] a collection of articles on a wide variety of biological topics, from the Nature Publishing Group

*[http://dir.yahoo.com/Science/biology/ Yahoo] list of WWW biological information resources

*[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.

=Nucleic Acids Research Database Issues=
Articles about genomic and biological databases.
Go to NAR Database Issue for: 
[http://nar.oxfordjournals.org/content/38/suppl_1 2010]|
[http://nar.oxfordjournals.org/content/37/suppl_1 2009] |
[http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl 2008] |
[http://nar.oxfordjournals.org/content/vol35/suppl_1/ 2007] |
[http://nar.oxfordjournals.org/content/vol34/suppl_1/ 2006] |
[http://nar.oxfordjournals.org/content/vol33/suppl_1/ 2005] |
[http://nar.oxfordjournals.org/content/vol32/suppl_1/ 2004] |
[http://nar.oxfordjournals.org/content/vol31/issue1/ 2003] |
[http://nar.oxfordjournals.org/content/vol30/issue1/ 2002] |
[http://nar.oxfordjournals.org/content/vol29/issue1/ 2001] |
[http://nar.oxfordjournals.org/content/vol28/issue1/ 2000] |
[http://nar.oxfordjournals.org/content/vol27/issue1/ 1999] |
[http://nar.oxfordjournals.org/content/vol26/issue1/ 1998] |

 
View SGD's article for: 
[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D577 2008] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D468 2007] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D442 2006] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D374 2005]|
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D311 2004] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/31/1/216 2003] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/30/1/69 2002] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/29/1/80 2001] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/28/1/77 2000] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/27/1/74 1999] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/26/1/73 1998]

Meetings

2012-08-16T18:30:27Z

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

[http://imya-2012.caspur.it/ 9th International Meeting on Yeast Apoptosis] 
Rome, Italy 
September 16 - 20, 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.bodl.bt.tudelft.nl/content/ac.html Advanced Course Metabolomics for Microbial Systems Biology] 
Delft University of Technology, The Netherlands 
October 29 – November 2, 2012

[http://www.britishyeastgroup.org British Yeast Group Meeting - BYG2013] 
Nottingham, UK 
March 20 - 22, 2013

[http://www.issy2013.org/index.php/Main_Page 30th International Specialised Symposium on Yeast (ISSY)] 
Stara Lesna, Slovakia 
June 18 - 22, 2013

[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/2012/ 2012] | [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

2012-08-16T18:24:05Z

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

[http://imya-2012.caspur.it/ 9th International Meeting on Yeast Apoptosis] 
Rome, Italy 
September 16 - 20, 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://http://www.bodl.bt.tudelft.nl/content/ac.html Advanced Course Metabolomics for Microbial Systems Biology] 
Delft University of Technology, The Netherlands 
October 29 – November 2, 2012

[http://www.britishyeastgroup.org British Yeast Group Meeting - BYG2013] 
Nottingham, UK 
March 20 - 22, 2013

[http://www.issy2013.org/index.php/Main_Page 30th International Specialised Symposium on Yeast (ISSY)] 
Stara Lesna, Slovakia 
June 18 - 22, 2013

[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/2012/ 2012] | [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]

Positions in yeast labs

2011-11-08T21:26:18Z

Fisk:

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

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

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

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

Please send resume or inquiries to:

David J. Garfinkel

Department of Biochemistry and Molecular Biology

A130 Life Sciences

120 Green St.

University of Georgia

Athens, GA 30622

tel: 706-542-9403

djgarf@bmb.uga.edu

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

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

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

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

==Postdoctoral grants at the Max Planck Institute for Evolutionary Biology, Plön, Germany==
Post-doctoral grants are available for ambitious, motivated scientists to join Experimental Evolution Research Group. We can provide excellent research funding and support for projects that build on or complement our existing program. Positions are funded by the Max Planck Society for 2 years initially.

We use Saccharomyces yeasts as model organisms for evolution and ecology. ''Saccharomyces cerevisiae'' is probably the best known and most tractable model organism used in biology, but its life outside the laboratory is poorly understood. We study the evolution of various interesting yeast traits using both laboratory experiments and observations of wild yeast. For a primer on yeast evolutionary biology, and to understand the motivation for our research please read Greig, D. & Leu, J-Y. (2009) “Natural history of budding yeast” Curr. Biol. 19:R886-890. For our current work, please see our [http://www.evolbio.mpg.de/expevolution/Greig/Welcome.html lab web page]

The Max Planck Institute for Evolutionary Biology offers outstanding infrastructure and facilities, and is attractively located in Northern Germany, in a lake district near the Baltic coast. It is well connected by train to the university towns of Lübeck and Kiel, and Hamburg is the nearest major airport.

Applicants must have a PhD and at least one peer-reviewed publication in the field of evolution, ecology, or yeast genetics. Applicants should prepare a short (<500 word) research proposal, a CV, and contact details for three academic referees. They should combine these into a single PDF file and send it by email to Duncan Greig (d.greig@evolbio.mpg.de). Informal enquiries can be made to any member of the Research Group. Applications will be considered until suitable candidates are found. September 2011

==Postdoctoral position==
SEPTEMBER 2011: A postdoctoral position is available in the laboratory of Claudio Joazeiro, Department of Cell Biology, The Scripps Research Institute (San Diego, California).

Research in the laboratory addresses the function of E3 ubiquitin ligases in biology and disease.

The position available is to elucidate the functions and mechanisms of the E3 ligase LISTERIN. We had previously reported on a new mouse model of neurodegeneration caused by mutation of Listerin/Ltn1, a novel E3 (Chu et al. 2009). Homozygous mutant mice exhibit profound early-onset and progressive neurological and motor dysfunction. The focus of our most recent work has been on elucidating this E3’s critical biological role(s) and determining how defects in its function lead to the disease. Listerin/Ltn1 is conserved in all eukaryotes, so we have taken advantage of budding yeast and found that the E3 is ribosome-associated and functions in the quality control of a specific subset of aberrant, nascent proteins (Bengtson & Joazeiro 2010). Currently, we undertake biochemistry, yeast genetics, mammalian tissue culture and genomic approaches to continue our characterization of Listerin/Ltn1, and are positioned to readily test the relevance of the discoveries we make for neurodegeneration using the mouse model. There are opportunities for studies along any of the above research lines, depending on the background and interests of the applicant.

Selected references:
*Bengtson MH & Joazeiro CA. 2010. Role of a ribosome-associated E3 ubiquitin ligase in protein quality control. Nature 467:470-3.
*Deshaies RJ & Joazeiro CA. 2009. RING domain E3 ubiquitin ligases. Annu Rev Biochem. 78:399-434.
*Chu J et al. 2009. A mouse forward genetics screen identifies LISTERIN as an E3 ubiquitin ligase involved in neurodegeneration. PNAS 106:2097-103.

The candidate should be independent, hard working, proactive and productive, and should have strong conceptual and experimental background in biochemistry and molecular biology.

Please send CV, a 1-page statement of current and future research interests, and the names and contact information of three references to: 
Claudio Joazeiro 
c/o Miriam Berba (Email: mirberba@scripps.edu) 
The Scripps Research Institute, CB-163 
10550 N Torrey Pines Rd 
La Jolla, CA 92037 USA

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

==Yeast quantitative genetics post-doctoral positions at Duke University Medical Center==
Positions are available for post-docs to work on a recently NIH funded grant “High throughput S. cerevisiae HAM, GWA & QT/QTL architecture resource”. Our understanding of quantitative traits, which includes pharmacogenetic variations in human drug efficacy and side effects, is poor. Improving our understanding of quantitative traits and of pharmacogenetics is aided by tractable model systems, such as Saccharomyces cerevisiae. In this study, we develop a novel S. cerevisiae genetic resource population for high throughput haploid association mapping (HAM) and genome wide association (GWA).

We will use the high quality genome sequences of 96 S. cerevisiae strains to generate a novel genetic resource population that we will use to perform high throughput determination of quantitative trait (QT) and quantitative trait loci (QTL) architecture. Start dates are open. Candidates should have recently received their Ph.D. (0 to – at most – 4 years) and should have expertise in yeast genetics/molecular biology and/or quantitative/population genetics. Candidates should email their curriculum vitae (pdf), including the names and contact information for three references, to John McCusker at mccus001@mc.duke.edu.

We are also looking a bioinformatician to join the outstanding team of fungal researchers at Duke University in a position in comparative yeast genomics on an NIH funded project. This project will involve working with the groups of Drs. John McCusker, Fred Dietrich, and Paul Magwene. We are looking for an individual with either a PhD or a MS degree with a strong background in computer science, bioinformatics, and genetics.

The project involves assembly and annotation of complete Saccharomyces cerevisiae genome sequences from next generation sequence data. This project is both computationally challenging, as well as requiring in-depth knowledge of the organism. Good programming skills and project management skills as well bioinformatics skills are necessary.

Candidates should send their CV, including the names and contact information for three references, to Fred Dietrich (fred.dietrich@duke.edu)

Positions in yeast labs

2011-11-08T21:24:21Z

Fisk:

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

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

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

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

Please send resume or inquiries to:

David J. Garfinkel

Department of Biochemistry and Molecular Biology

A130 Life Sciences

120 Green St.

University of Georgia

Athens, GA 30622

tel: 706-542-9403

djgarf@bmb.uga.edu

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

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

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

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

=='''Postdoctoral grants at the Max Planck Institute for Evolutionary Biology, Plön, Germany'''==
Post-doctoral grants are available for ambitious, motivated scientists to join Experimental Evolution Research Group. We can provide excellent research funding and support for projects that build on or complement our existing program. Positions are funded by the Max Planck Society for 2 years initially.

We use Saccharomyces yeasts as model organisms for evolution and ecology. ''Saccharomyces cerevisiae'' is probably the best known and most tractable model organism used in biology, but its life outside the laboratory is poorly understood. We study the evolution of various interesting yeast traits using both laboratory experiments and observations of wild yeast. For a primer on yeast evolutionary biology, and to understand the motivation for our research please read Greig, D. & Leu, J-Y. (2009) “Natural history of budding yeast” Curr. Biol. 19:R886-890. For our current work, please see our [http://www.evolbio.mpg.de/expevolution/Greig/Welcome.html lab web page]

The Max Planck Institute for Evolutionary Biology offers outstanding infrastructure and facilities, and is attractively located in Northern Germany, in a lake district near the Baltic coast. It is well connected by train to the university towns of Lübeck and Kiel, and Hamburg is the nearest major airport.

Applicants must have a PhD and at least one peer-reviewed publication in the field of evolution, ecology, or yeast genetics. Applicants should prepare a short (<500 word) research proposal, a CV, and contact details for three academic referees. They should combine these into a single PDF file and send it by email to Duncan Greig (d.greig@evolbio.mpg.de). Informal enquiries can be made to any member of the Research Group. Applications will be considered until suitable candidates are found. September 2011

=='''Postdoctoral position'''==
SEPTEMBER 2011: A postdoctoral position is available in the laboratory of Claudio Joazeiro, Department of Cell Biology, The Scripps Research Institute (San Diego, California).

Research in the laboratory addresses the function of E3 ubiquitin ligases in biology and disease.

The position available is to elucidate the functions and mechanisms of the E3 ligase LISTERIN. We had previously reported on a new mouse model of neurodegeneration caused by mutation of Listerin/Ltn1, a novel E3 (Chu et al. 2009). Homozygous mutant mice exhibit profound early-onset and progressive neurological and motor dysfunction. The focus of our most recent work has been on elucidating this E3’s critical biological role(s) and determining how defects in its function lead to the disease. Listerin/Ltn1 is conserved in all eukaryotes, so we have taken advantage of budding yeast and found that the E3 is ribosome-associated and functions in the quality control of a specific subset of aberrant, nascent proteins (Bengtson & Joazeiro 2010). Currently, we undertake biochemistry, yeast genetics, mammalian tissue culture and genomic approaches to continue our characterization of Listerin/Ltn1, and are positioned to readily test the relevance of the discoveries we make for neurodegeneration using the mouse model. There are opportunities for studies along any of the above research lines, depending on the background and interests of the applicant.

Selected references:
*Bengtson MH & Joazeiro CA. 2010. Role of a ribosome-associated E3 ubiquitin ligase in protein quality control. Nature 467:470-3.
*Deshaies RJ & Joazeiro CA. 2009. RING domain E3 ubiquitin ligases. Annu Rev Biochem. 78:399-434.
*Chu J et al. 2009. A mouse forward genetics screen identifies LISTERIN as an E3 ubiquitin ligase involved in neurodegeneration. PNAS 106:2097-103.

The candidate should be independent, hard working, proactive and productive, and should have strong conceptual and experimental background in biochemistry and molecular biology.

Please send CV, a 1-page statement of current and future research interests, and the names and contact information of three references to: 
Claudio Joazeiro 
c/o Miriam Berba (Email: mirberba@scripps.edu) 
The Scripps Research Institute, CB-163 
10550 N Torrey Pines Rd 
La Jolla, CA 92037 USA

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

=='''Yeast quantitative genetics post-doctoral positions at Duke University Medical Center'''==
Positions are available for post-docs to work on a recently NIH funded grant “High throughput S. cerevisiae HAM, GWA & QT/QTL architecture resource”. Our understanding of quantitative traits, which includes pharmacogenetic variations in human drug efficacy and side effects, is poor. Improving our understanding of quantitative traits and of pharmacogenetics is aided by tractable model systems, such as Saccharomyces cerevisiae. In this study, we develop a novel S. cerevisiae genetic resource population for high throughput haploid association mapping (HAM) and genome wide association (GWA).

We will use the high quality genome sequences of 96 S. cerevisiae strains to generate a novel genetic resource population that we will use to perform high throughput determination of quantitative trait (QT) and quantitative trait loci (QTL) architecture. Start dates are open. Candidates should have recently received their Ph.D. (0 to – at most – 4 years) and should have expertise in yeast genetics/molecular biology and/or quantitative/population genetics. Candidates should email their curriculum vitae (pdf), including the names and contact information for three references, to John McCusker at mccus001@mc.duke.edu.

We are also looking a bioinformatician to join the outstanding team of fungal researchers at Duke University in a position in comparative yeast genomics on an NIH funded project. This project will involve working with the groups of Drs. John McCusker, Fred Dietrich, and Paul Magwene. We are looking for an individual with either a PhD or a MS degree with a strong background in computer science, bioinformatics, and genetics.

The project involves assembly and annotation of complete Saccharomyces cerevisiae genome sequences from next generation sequence data. This project is both computationally challenging, as well as requiring in-depth knowledge of the organism. Good programming skills and project management skills as well bioinformatics skills are necessary.

Candidates should send their CV, including the names and contact information for three references, to Fred Dietrich (fred.dietrich@duke.edu)