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Items: 1 to 20 of 116

1.

A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae.

Petti AA, Church GM.

Genome Res. 2005 Sep;15(9):1298-306. Epub 2005 Aug 18.

2.

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.

3.

Computational discovery of gene modules and regulatory networks.

Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Nat Biotechnol. 2003 Nov;21(11):1337-42. Epub 2003 Oct 12.

4.

Prioritization of gene regulatory interactions from large-scale modules in yeast.

Lee HJ, Manke T, Bringas R, Vingron M.

BMC Bioinformatics. 2008 Jan 22;9:32. doi: 10.1186/1471-2105-9-32.

5.

Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data.

Tanay A, Sharan R, Kupiec M, Shamir R.

Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2981-6. Epub 2004 Feb 18.

6.

A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle.

Hsu JT, Peng CH, Hsieh WP, Lan CY, Tang CY.

BMC Bioinformatics. 2011 Jul 12;12:281. doi: 10.1186/1471-2105-12-281.

7.

Genomic analysis of regulatory network dynamics reveals large topological changes.

Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M.

Nature. 2004 Sep 16;431(7006):308-12.

8.

Specificity and stability in topology of protein networks.

Maslov S, Sneppen K.

Science. 2002 May 3;296(5569):910-3.

9.

A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.

Wang W, Cherry JM, Botstein D, Li H.

Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16893-8. Epub 2002 Dec 13.

10.

Phenotype analysis using network motifs derived from changes in regulatory network dynamics.

Cavelier G, Anastassiou D.

Proteins. 2005 Aug 15;60(3):525-46.

PMID:
15971229
11.

Study of coordinative gene expression at the biological process level.

Yu T, Sun W, Yuan S, Li KC.

Bioinformatics. 2005 Sep 15;21(18):3651-7. Epub 2005 Aug 2.

12.

A Gibbs sampler for the identification of gene expression and network connectivity consistency.

Brynildsen MP, Tran LM, Liao JC.

Bioinformatics. 2006 Dec 15;22(24):3040-6. Epub 2006 Oct 23.

13.

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3.

Cimini D, Patil KR, Schiraldi C, Nielsen J.

BMC Syst Biol. 2009 Feb 6;3:17. doi: 10.1186/1752-0509-3-17.

14.

Exploring the impact of osmoadaptation on glycolysis using time-varying response-coefficients.

Kühn C, Petelenz E, Nordlander B, Schaber J, Hohmann S, Klipp E.

Genome Inform. 2008;20:77-90.

PMID:
19425124
15.

Genome-wide oscillation of transcription in yeast.

Reinke H, Gatfield D.

Trends Biochem Sci. 2006 Apr;31(4):189-91. Epub 2006 Feb 24. Review.

PMID:
16500104
16.

An in silico method for detecting overlapping functional modules from composite biological networks.

Maraziotis IA, Dimitrakopoulou K, Bezerianos A.

BMC Syst Biol. 2008 Nov 1;2:93. doi: 10.1186/1752-0509-2-93.

17.

Modularity of the transcriptional response of protein complexes in yeast.

Simonis N, Gonze D, Orsi C, van Helden J, Wodak SJ.

J Mol Biol. 2006 Oct 20;363(2):589-610. Epub 2006 Jul 3.

PMID:
16973176
18.

Identification of functional modules in a PPI network by clique percolation clustering.

Zhang S, Ning X, Zhang XS.

Comput Biol Chem. 2006 Dec;30(6):445-51. Epub 2006 Nov 13.

PMID:
17098476
19.

Development of a novel oligonucleotide array-based transcription factor assay platform for genome-wide active transcription factor profiling in Saccharomyces cerevisiae.

Zhao Y, Shao W, Wei H, Qiao J, Lu Y, Sun Y, Mitchelson K, Cheng J, Zhou Y.

J Proteome Res. 2008 Mar;7(3):1315-25. doi: 10.1021/pr700642g. Epub 2008 Jan 26.

PMID:
18220337
20.

Global analysis of protein expression in yeast.

Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS.

Nature. 2003 Oct 16;425(6959):737-41.

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