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Results: 1 to 20 of 55

1.

Systematic determination of genetic network architecture.

Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM.

Nat Genet. 1999 Jul;22(3):281-5.

PMID:
10391217
[PubMed - indexed for MEDLINE]
2.
3.

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA.

BMC Genomics. 2008 Feb 7;9:70. doi: 10.1186/1471-2164-9-70.

PMID:
18257930
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae.

Hughes JD, Estep PW, Tavazoie S, Church GM.

J Mol Biol. 2000 Mar 10;296(5):1205-14.

PMID:
10698627
[PubMed - indexed for MEDLINE]
5.

Detecting biological associations between genes based on the theory of phase synchronization.

Kim CS, Riikonen P, Salakoski T.

Biosystems. 2008 May;92(2):99-113. doi: 10.1016/j.biosystems.2007.12.006. Epub 2008 Jan 11.

PMID:
18289772
[PubMed - indexed for MEDLINE]
6.

Dynamic measure of gene co-regulation.

Farina L, De Santis A, Morelli G, Ruberti I.

IET Syst Biol. 2007 Jan;1(1):10-7.

PMID:
17370425
[PubMed - indexed for MEDLINE]
7.

Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm.

Zhu Z, Pilpel Y, Church GM.

J Mol Biol. 2002 Apr 19;318(1):71-81.

PMID:
12054769
[PubMed - indexed for MEDLINE]
8.

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
9.

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.

Roth FP, Hughes JD, Estep PW, Church GM.

Nat Biotechnol. 1998 Oct;16(10):939-45.

PMID:
9788350
[PubMed - indexed for MEDLINE]
10.

Adaptively inferring human transcriptional subnetworks.

Das D, Nahlé Z, Zhang MQ.

Mol Syst Biol. 2006;2:2006.0029. Epub 2006 Jun 6.

PMID:
16760900
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Combining sequence and time series expression data to learn transcriptional modules.

Kundaje A, Middendorf M, Gao F, Wiggins C, Leslie C.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jul-Sep;2(3):194-202.

PMID:
17044183
[PubMed - indexed for MEDLINE]
12.

Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.

Qian J, Dolled-Filhart M, Lin J, Yu H, Gerstein M.

J Mol Biol. 2001 Dec 14;314(5):1053-66.

PMID:
11743722
[PubMed - indexed for MEDLINE]
13.

Knowledge-guided multi-scale independent component analysis for biomarker identification.

Chen L, Xuan J, Wang C, Shih IeM, Wang Y, Zhang Z, Hoffman E, Clarke R.

BMC Bioinformatics. 2008 Oct 6;9:416. doi: 10.1186/1471-2105-9-416.

PMID:
18837990
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A predictive model of the oxygen and heme regulatory network in yeast.

Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C.

PLoS Comput Biol. 2008 Nov;4(11):e1000224. doi: 10.1371/journal.pcbi.1000224. Epub 2008 Nov 14.

PMID:
19008939
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1. doi: 10.1186/1471-2105-10-S4-S1.

PMID:
19426448
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites.

Qin ZS, McCue LA, Thompson W, Mayerhofer L, Lawrence CE, Liu JS.

Nat Biotechnol. 2003 Apr;21(4):435-9. Epub 2003 Mar 10.

PMID:
12627170
[PubMed - indexed for MEDLINE]
17.

Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae.

Jacobs Anderson JS, Parker R.

Nucleic Acids Res. 2000 Apr 1;28(7):1604-17.

PMID:
10710427
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Conservation and evolution of cis-regulatory systems in ascomycete fungi.

Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB.

PLoS Biol. 2004 Dec;2(12):e398. Epub 2004 Nov 9.

PMID:
15534694
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation.

Jensen LJ, Knudsen S.

Bioinformatics. 2000 Apr;16(4):326-33.

PMID:
10869030
[PubMed - indexed for MEDLINE]
Free Article
20.

Regulatory element detection using a probabilistic segmentation model.

Bussemaker HJ, Li H, Siggia ED.

Proc Int Conf Intell Syst Mol Biol. 2000;8:67-74.

PMID:
10977067
[PubMed - indexed for MEDLINE]

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