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Main.YeastGenomicsResources History
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October 02, 2012, at 09:56 AM
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* http://www.yeastnet.org/ , predicted network
* pixie at Princeton, predicted network
May 19, 2012, at 12:23 PM
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*Sherlock lab
*Siegal lab
*Fay lab
May 17, 2012, at 10:47 AM
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* Chemogenomics
http://chemogenomics.stanford.edu:16080/supplements/global/download.html
March 31, 2012, at 04:02 PM
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*genetic interactions:
* By double-deletion assay, Costanzo 2010 Science
March 27, 2012, at 04:02 PM
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Stanford fitness measures. to:
* Yeast deletion project, fitness data
http://www-deletion.stanford.edu/YDPM/YDPM_index.html
* Yeast fitness database
http://fitdb.stanford.edu/
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* Yeast morphology database to:
* Yeast morphology database (SCMD) March 23, 2012, at 10:28 PM
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* http://genome.wustl.edu/genomes/saccharomyces_cerevisiae_strain_project_genomes
February 06, 2012, at 12:45 PM
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* [[http://mips.helmholtz-muenchen.de/genre/proj/mpact/ | MPact @ MIPS\\ to:
* [[http://mips.helmholtz-muenchen.de/genre/proj/mpact/ | MPact @ MIPS ]] and [[ftp://ftpmips.gsf.de/yeast/PPI/ | FTP site]] February 06, 2012, at 12:44 PM
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'''For protein interaction data, see:\\''' to:
February 06, 2012, at 12:43 PM
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*For protein interaction data, see:\\
DIP [[http://dip.doe-mbi.ucla.edu/]] (Registration is required. Pairwise data is provided)\\
[[http://mips.helmholtz-muenchen.de/genre/proj/mpact/ | MPact @ MIPS
BIND \\
to:
'''For protein interaction data, see:\\'''
* DIP [[http://dip.doe-mbi.ucla.edu/]] (Registration is required. Pairwise data is provided)\\
* [[http://mips.helmholtz-muenchen.de/genre/proj/mpact/ | MPact @ MIPS\\
* BIND \\
February 06, 2012, at 12:42 PM
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[[http://mips.helmholtz-muenchen.de/genre/proj/mpact/ | MPact @ MIPS February 06, 2012, at 10:53 AM
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* Strains \\
* [[ http://www.openbiosystems.com/GeneExpression/Yeast/YKO/ | Deletion collection, Open Biosystem]] to:
* Strains
* [[ http://www.openbiosystems.com/GeneExpression/Yeast/YKO/ | Deletion collection, Open Biosystem, now at Invitrogen]] February 06, 2012, at 10:52 AM
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[[ http://www.openbiosystems.com/GeneExpression/Yeast/YKO/ | Deletion collection, Open Biosystem]]
* Deletion collection at Invitrogen to:
* [[ http://www.openbiosystems.com/GeneExpression/Yeast/YKO/ | Deletion collection, Open Biosystem]]
* Deletion collection, GFP colleciton at Invitrogen February 06, 2012, at 10:37 AM
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February 06, 2012, at 10:37 AM
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February 06, 2012, at 10:36 AM
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Positive selection for elevated gene expression noise in yeast
Labs to follow to:
Positive selection for elevated gene expression noise in yeast, George Zhang's lab
'''Reviews'''
[[http://www.ncbi.nlm.nih.gov/pubmed/19743424 | Proteomics. 2009 Oct;9(20):4731-43.
Recent advances in yeast organelle and membrane proteomics. Premsler T, Zahedi RP, Lewandrowski U, Sickmann A.]]
'''Labs to follow''' February 06, 2012, at 10:32 AM
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* protein localization
[[http://www.ncbi.nlm.nih.gov/pubmed/14562095 | Nature. 2003 Oct 16;425(6959):686-91. Global analysis of protein localization in budding yeast. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK.]]
February 06, 2012, at 10:29 AM
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*[[http://www.utoronto.ca/boonelab/publications/index.shtml | Boone lab]] February 06, 2012, at 10:27 AM
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February 06, 2012, at 10:26 AM
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February 06, 2012, at 10:26 AM
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Botstein lab
Oshea lab
Weismann lab
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*Botstein lab
*Oshea lab
*Weismann lab
February 06, 2012, at 10:26 AM
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Positive selection for elevated gene expression noise in yeast
Botstein lab
Oshea lab
Weismann lab
February 06, 2012, at 10:15 AM
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* protein expression noise\\
[[http://www.ncbi.nlm.nih.gov/pubmed/16699522?dopt=Abstract&holding=npg | Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840–846 ]]
February 06, 2012, at 10:03 AM
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* protein abundance
[[http://www.ncbi.nlm.nih.gov/pubmed/14562106 |
S. Ghaemmaghami, W. K. Huh, K. Bower, R. W. Howson,
A. Belle, N. Dephoure, E. K. O’Shea and J. S. Weissman, Nature,
2003, 425, 737–741.]]
to:
* protein abundance \\
[[http://www.ncbi.nlm.nih.gov/pubmed/14562106 | S. Ghaemmaghami, W. K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O’Shea and J. S. Weissman, Nature, 2003, 425, 737–741.]]
February 06, 2012, at 10:02 AM
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[[http://www.ncbi.nlm.nih.gov/pubmed/14562106 | Changed lines 39-41 from:
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February 06, 2012, at 10:01 AM
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* protein abundance
S. Ghaemmaghami, W. K. Huh, K. Bower, R. W. Howson,
A. Belle, N. Dephoure, E. K. O’Shea and J. S. Weissman, Nature,
2003, 425, 737–741.
February 06, 2012, at 09:44 AM
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Complex data
Nature 440, 637-643 (30 March 2006)
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
http://www.nature.com/nature/journal/v440/n7084/full/nature04670.html
December 21, 2011, at 04:54 PM
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Molecular Systems Biology 4; Article number 179; doi:10.1038/msb.2008.16
The role of disorder in interaction networks: a structural analysis
Philip M Kim1,5,*, Andrea Sboner1,5, Yu Xia2 and Mark Gerstein1,3,4,*
December 21, 2011, at 10:26 AM
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Molecular Biology of the Cell Vol. 16, 5410–5417, November 2005
Role of Essential Genes in Mitochondrial Morphogenesis in Saccharomyces cerevisiae□D
Katrin Altmann* and Benedikt Westermann
December 19, 2011, at 06:46 PM
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Hunter B. Frasera,1, Alan M. Mosesb, and Eric E. Schadtc
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Hunter B. Frasera,1, Alan M. Mosesb, and Eric E. Schadtc, PNAS
Comparative analysis of gene expression and regulation of replicative aging associated genes in S. cerevisiaew
Sukhraj Pal Singh Dhami,a Nitish Mittal,ab Sarath Chandra Jangab and Nilanjan Roy
December 19, 2011, at 05:51 PM
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Evidence for widespread adaptive evolution of gene expression in budding yeast
Hunter B. Frasera,1, Alan M. Mosesb, and Eric E. Schadtc
December 18, 2011, at 07:08 PM
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Mol Biol Cell. 2011 Apr;22(7):988-98. Epub 2011 Feb 2.
The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures.
Davidson GS, Joe RM, Roy S, Meirelles O, Allen CP, Wilson MR, Tapia PH, Manzanilla EE, Dodson AE, Chakraborty S, Carter M, Young S, Edwards B, Sklar L, Werner-Washburne M.
http://www.ncbi.nlm.nih.gov/pubmed/21289090
December 16, 2011, at 10:39 AM
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Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis
David C Hess, Chad L Myers, Curtis Huttenhower, Matthew A Hibbs, Alicia P Hayes, Jadine Paw, John J Clore, Rosa M Mendoza, Bryan San Luis, Corey Nislow, Guri Giaever, Michael Costanzo, Olga G Troyanskaya, Amy A Caudy (2009), PLoS Genetics 5 (3) p. 16
August 22, 2011, at 11:54 AM
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* http://www.cbs.knaw.nl/
August 15, 2011, at 04:59 PM
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Supplementary information From the following article Quantification of the yeast transcriptome by single-molecule sequencing Doron Lipson, Tal Raz, Alix Kieu, Daniel R Jones, Eldar Giladi, Edward Thayer, John F Thompson, Stan Letovsky, Patrice Milos & M
July 16, 2011, at 11:18 PM
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[[ftp://gen-ftp.princeton.edu/yfgdb/ | Princeton ftp site ]]
July 16, 2011, at 11:15 PM
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* Natural variation
* [[http://gmgm.u-strasbg.fr/~js/js_Data.html | Joseph Schacherer]] July 12, 2011, at 12:04 PM
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*mRNA FISH data
Botstein lab.
June 17, 2011, at 01:09 PM
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* Positive selection markers to:
* Positive selection markers\\ June 17, 2011, at 01:09 PM
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[[URA3]] [[LYS2]] LEU2(?)
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[[URA3]] [[LYS2]] LEU2(?)
June 17, 2011, at 01:07 PM
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[[URA3]] [[LYS2]] LEU2(?)
June 17, 2011, at 01:07 PM
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* Deletion colleciton at Invitrogen
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* Deletion collection at Invitrogen
* Positive selection markers
URA3 LYS2 LEU2(?)
June 13, 2011, at 02:18 PM
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Stanford fitness measures.
multiple sources. Austria.
* Yeast morphology database
http://yeast.gi.k.u-tokyo.ac.jp/datamine/
June 13, 2011, at 02:16 PM
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* Yeast metabolic cycle
http://www.genomics.princeton.edu/~nslavov/ymc/metabolites.html
* cell cycle
http://genomics.princeton.edu/~nslavov/grr_html/transcripts.html
* growth curves
June 09, 2011, at 09:41 AM
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* Deletion colleciton at Invitrogen
June 04, 2011, at 03:15 PM
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* Strains
[[ http://www.openbiosystems.com/GeneExpression/Yeast/YKO/ | Deletion collection, Open Biosystem]]
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* Strains \\
[[ http://www.openbiosystems.com/GeneExpression/Yeast/YKO/ | Deletion collection, Open Biosystem]]
June 04, 2011, at 03:15 PM
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* Strains
[[ http://www.openbiosystems.com/GeneExpression/Yeast/YKO/ | Deletion collection, Open Biosystem]]
March 06, 2009, at 01:51 PM
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*Expression and aging \\
[[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13420 | CLS, Longo]]
March 06, 2009, at 01:11 PM
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[[http://cbi.labri.fr/Genolevures/index.php# | Genolevures, Sce relatives ]]
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[[http://cbi.labri.fr/Genolevures/index.php# | Genolevures, Sce relatives ]]\\
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March 06, 2009, at 01:09 PM
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[[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4932&lvl=3&keep=1&srchmode=1&unlock | NCBI, Sce sequences ]]
to:
[[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4932&lvl=3&keep=1&srchmode=1&unlock | NCBI, Sce sequences ]]\\
[[http://www.sanger.ac.uk/Projects/S_cerevisiae/ | Sanger Sce project]]\\
March 06, 2009, at 12:55 PM
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*UCSC genome browser on yeast to:
*UCSC genome browser on yeast \\ Changed line 21 from:
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March 06, 2009, at 12:54 PM
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Genomes:
[[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4932&lvl=3&keep=1&srchmode=1&unlock | NCBI Sce sequences ]]
[[http://cbi.labri.fr/Genolevures/index.php# | Genolevures ]]
UCSC genome browser on yeast to:
*Genomes of Sce:
[[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4932&lvl=3&keep=1&srchmode=1&unlock | NCBI, Sce sequences ]]
*Genomes of Sce relatives: \\
[[http://cbi.labri.fr/Genolevures/index.php# | Genolevures, Sce relatives ]]
*UCSC genome browser on yeast Changed line 13 from:
For protein interaction data, see:\\ to:
*For protein interaction data, see:\\ Changed lines 18-21 from:
genetic interaction:
protein half lives: to:
*genetic interaction:
*protein half lives: Changed line 24 from:
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March 06, 2009, at 12:52 PM
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Genomes:
[[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4932&lvl=3&keep=1&srchmode=1&unlock | NCBI Sce sequences ]]
November 28, 2008, at 07:30 PM
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Cell cycle
[[http://yeast.swmed.edu/cgi-bin/cc_dload.cgi | expression and cell cycle]] November 17, 2008, at 12:41 PM
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UCSC genome browser on yeast
http://hgdownload.cse.ucsc.edu/downloads.html#yeast
November 17, 2008, at 12:38 PM
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SGD
CGD
[[http://cbi.labri.fr/Genolevures/index.php# | Genolevures ]]
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[[http://cbi.labri.fr/Genolevures/index.php# | Genolevures ]] November 17, 2008, at 12:37 PM
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[[http://mbe.oxfordjournals.org/cgi/reprint/22/6/1403]] to:
[[http://mbe.oxfordjournals.org/cgi/reprint/22/6/1403]]
[[http://cbi.labri.fr/Genolevures/index.php# | Genolevures ]] October 22, 2008, at 09:20 AM
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[[http://www.pnas.org/content/103/35/13004.abstract| Archana Belle etal PNAS 2006]] to:
[[http://www.pnas.org/content/103/35/13004.abstract| Archana Belle etal PNAS 2006]]
mRNA half lives:
[[http://mbe.oxfordjournals.org/cgi/reprint/22/6/1403]] October 20, 2008, at 04:43 PM
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protein half lives:
[[http://www.pnas.org/content/103/35/13004.abstract| Archana Belle etal PNAS 2006]] March 23, 2006, at 05:16 PM
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[[DIP]http://dip.doe-mbi.ucla.edu/] (Registration is required. Pairwise data is provided)\\ to:
DIP [[http://dip.doe-mbi.ucla.edu/]] (Registration is required. Pairwise data is provided)\\ March 23, 2006, at 05:15 PM
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DIP (Registration is required. Pairwise data is provided)\\
MIPS
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[[DIP]http://dip.doe-mbi.ucla.edu/] (Registration is required. Pairwise data is provided)\\
MIPS \\
BIND \\
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The budding yeast Saccharomyces ceresivisiae has been a model of choice for genomic studies. So far, the yeast genome is the best annotated eukaryotic genome, its protein interaction network has the best coverage and quality, its gene profiling data is one of the largest ones, its collections of mutants is unmatched. \\ to:
The budding yeast Saccharomyces ceresivisiae has been a model of choice for genomic studies. So far, the yeast genome is the best annotated eukaryotic genome, its protein interaction network has the best coverage and quality, its gene profiling data is one of the largest ones, its collections of mutants is unmatched.
For protein interaction data, see:\\
DIP (Registration is required. Pairwise data is provided)\\
MIPS
BIND
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The budding yeast Saccharomyces ceresivisiae has been a model of choice for genomic studies. So far, the yeast genome is the best annotated eukaryotic genome, its protein interaction network has the best coverage and quality, its gene profiling data is one of the largest ones, its collections of mutants is unmatched. \\
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