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Results: 1 to 20 of 83

1.

TFRank: network-based prioritization of regulatory associations underlying transcriptional responses.

Gonçalves JP, Francisco AP, Mira NP, Teixeira MC, Sá-Correia I, Oliveira AL, Madeira SC.

Bioinformatics. 2011 Nov 15;27(22):3149-57. doi: 10.1093/bioinformatics/btr546. Epub 2011 Sep 29.

PMID:
21965816
[PubMed - indexed for MEDLINE]
Free Article
2.

Robustness and evolvability in natural chemical resistance: identification of novel systems properties, biochemical mechanisms and regulatory interactions.

Venancio TM, Balaji S, Geetha S, Aravind L.

Mol Biosyst. 2010 Aug;6(8):1475-91. doi: 10.1039/c002567b. Epub 2010 Jun 2.

PMID:
20517567
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches.

Teixeira MC, Dias PJ, Monteiro PT, Sala A, Oliveira AL, Freitas AT, Sá-Correia I.

Mol Biosyst. 2010 Dec;6(12):2471-81. doi: 10.1039/c004881j. Epub 2010 Oct 11.

PMID:
20938527
[PubMed - indexed for MEDLINE]
4.

Transcriptional networks: reverse-engineering gene regulation on a global scale.

Chua G, Robinson MD, Morris Q, Hughes TR.

Curr Opin Microbiol. 2004 Dec;7(6):638-46. Review.

PMID:
15556037
[PubMed - indexed for MEDLINE]
5.

Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach.

Bailly-Bechet M, Braunstein A, Pagnani A, Weigt M, Zecchina R.

BMC Bioinformatics. 2010 Jun 29;11:355. doi: 10.1186/1471-2105-11-355.

PMID:
20587029
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae.

Teixeira MC, Monteiro PT, Guerreiro JF, Gonçalves JP, Mira NP, dos Santos SC, Cabrito TR, Palma M, Costa C, Francisco AP, Madeira SC, Oliveira AL, Freitas AT, Sá-Correia I.

Nucleic Acids Res. 2014 Jan;42(Database issue):D161-6. doi: 10.1093/nar/gkt1015. Epub 2013 Oct 28.

PMID:
24170807
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Genomic expression program involving the Haa1p-regulon in Saccharomyces cerevisiae response to acetic acid.

Mira NP, Becker JD, Sá-Correia I.

OMICS. 2010 Oct;14(5):587-601. doi: 10.1089/omi.2010.0048.

PMID:
20955010
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
18211684
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A stress regulatory network for co-ordinated activation of proteasome expression mediated by yeast heat shock transcription factor.

Hahn JS, Neef DW, Thiele DJ.

Mol Microbiol. 2006 Apr;60(1):240-51.

PMID:
16556235
[PubMed - indexed for MEDLINE]
10.

Regulatory Snapshots: integrative mining of regulatory modules from expression time series and regulatory networks.

Gonçalves JP, Aires RS, Francisco AP, Madeira SC.

PLoS One. 2012;7(5):e35977. doi: 10.1371/journal.pone.0035977. Epub 2012 May 1.

PMID:
22563474
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p.

Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G.

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6477-82. doi: 10.1073/pnas.0811091106. Epub 2009 Apr 3.

PMID:
19346491
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis.

Chen SF, Juang YL, Chou WK, Lai JM, Huang CY, Kao CY, Wang FS.

BMC Syst Biol. 2009 Nov 27;3:110. doi: 10.1186/1752-0509-3-110.

PMID:
19943917
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Evolutionary rates and centrality in the yeast gene regulatory network.

Jovelin R, Phillips PC.

Genome Biol. 2009;10(4):R35. doi: 10.1186/gb-2009-10-4-r35. Epub 2009 Apr 9.

PMID:
19358738
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
12399584
[PubMed - indexed for MEDLINE]
Free Article
15.

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.

PMID:
14555958
[PubMed - indexed for MEDLINE]
Free Article
16.

Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata.

Lelandais G, Tanty V, Geneix C, Etchebest C, Jacq C, Devaux F.

Genome Biol. 2008;9(11):R164. doi: 10.1186/gb-2008-9-11-r164. Epub 2008 Nov 24.

PMID:
19025642
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle.

Chen HC, Lee HC, Lin TY, Li WH, Chen BS.

Bioinformatics. 2004 Aug 12;20(12):1914-27. Epub 2004 Mar 25.

PMID:
15044243
[PubMed - indexed for MEDLINE]
Free Article
18.

Characterization of complex regulatory networks and identification of promoter regulatory elements in yeast: "in silico" and "wet-lab" approaches.

Mira NP, Teixeira MC, Sá-Correia I.

Methods Mol Biol. 2012;809:27-48. doi: 10.1007/978-1-61779-376-9_2.

PMID:
22113266
[PubMed - indexed for MEDLINE]
19.

Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.

Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1998-2003. Epub 2005 Jan 31.

PMID:
15684073
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Identification of context-specific gene regulatory networks with GEMULA--gene expression modeling using LAsso.

Geeven G, van Kesteren RE, Smit AB, de Gunst MC.

Bioinformatics. 2012 Jan 15;28(2):214-21. doi: 10.1093/bioinformatics/btr641. Epub 2011 Nov 21.

PMID:
22106333
[PubMed - indexed for MEDLINE]
Free Article

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