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Items: 1 to 20 of 47


Modulefinder: a tool for computational discovery of cis regulatory modules.

Philippakis AA, He FS, Bulyk ML.

Pac Symp Biocomput. 2005:519-30.


Transcriptional regulatory code of a eukaryotic genome.

Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA.

Nature. 2004 Sep 2;431(7004):99-104.


Predicting gene expression from sequence.

Beer MA, Tavazoie S.

Cell. 2004 Apr 16;117(2):185-98.


Anlaysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol/fatty acid synthetic pathways as a possible major target of WT1.

Rae FK, Martinez G, Gillinder KR, Smith A, Shooter G, Forrest AR, Grimmond SM, Little MH.

Oncogene. 2004 Apr 15;23(17):3067-79.


Quantitative high-throughput analysis of transcription factor binding specificities.

Linnell J, Mott R, Field S, Kwiatkowski DP, Ragoussis J, Udalova IA.

Nucleic Acids Res. 2004 Feb 27;32(4):e44.


A gene-coexpression network for global discovery of conserved genetic modules.

Stuart JM, Segal E, Koller D, Kim SK.

Science. 2003 Oct 10;302(5643):249-55. Epub 2003 Aug 21.


Finding functional features in Saccharomyces genomes by phylogenetic footprinting.

Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M.

Science. 2003 Jul 4;301(5629):71-6. Epub 2003 May 29.


Sequencing and comparison of yeast species to identify genes and regulatory elements.

Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES.

Nature. 2003 May 15;423(6937):241-54.


FunSpec: a web-based cluster interpreter for yeast.

Robinson MD, Grigull J, Mohammad N, Hughes TR.

BMC Bioinformatics. 2002 Nov 13;3:35. Epub 2002 Nov 13.


Transcriptional regulatory networks in Saccharomyces cerevisiae.

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA.

Science. 2002 Oct 25;298(5594):799-804.


Depression of Saccharomyces cerevisiae invasive growth on non-glucose carbon sources requires the Snf1 kinase.

Palecek SP, Parikh AS, Huh JH, Kron SJ.

Mol Microbiol. 2002 Jul;45(2):453-69.


An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.

Liu XS, Brutlag DL, Liu JS.

Nat Biotechnol. 2002 Aug;20(8):835-9. Epub 2002 Jul 8.


Quantitative prediction of NF-kappa B DNA-protein interactions.

Udalova IA, Mott R, Field D, Kwiatkowski D.

Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8167-72. Epub 2002 Jun 4.


Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range.

Dudley AM, Aach J, Steffen MA, Church GM.

Proc Natl Acad Sci U S A. 2002 May 28;99(11):7554-9.


Combining location and expression data for principled discovery of genetic regulatory network models.

Hartemink AJ, Gifford DK, Jaakkola TS, Young RA.

Pac Symp Biocomput. 2002:437-49.


Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions.

Doi N, Takashima H, Kinjo M, Sakata K, Kawahashi Y, Oishi Y, Oyama R, Miyamoto-Sato E, Sawasaki T, Endo Y, Yanagawa H.

Genome Res. 2002 Mar;12(3):487-92.


Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.

Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sørensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M.

Nature. 2002 Jan 10;415(6868):180-3.


A protein interaction map for cell polarity development.

Drees BL, Sundin B, Brazeau E, Caviston JP, Chen GC, Guo W, Kozminski KG, Lau MW, Moskow JJ, Tong A, Schenkman LR, McKenzie A 3rd, Brennwald P, Longtine M, Bi E, Chan C, Novick P, Boone C, Pringle JR, Davis TN, Fields S, Drubin DG.

J Cell Biol. 2001 Aug 6;154(3):549-71.

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