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Results: 1 to 20 of 76

1.

A distance difference matrix approach to identifying transcription factors that regulate differential gene expression.

De Bleser P, Hooghe B, Vlieghe D, van Roy F.

Genome Biol. 2007;8(5):R83.

PMID:
17504544
[PubMed - indexed for MEDLINE]
Free PMC Article
2.
3.

Discovery of sequence motifs related to coexpression of genes using evolutionary computation.

Fogel GB, Weekes DG, Varga G, Dow ER, Harlow HB, Onyia JE, Su C.

Nucleic Acids Res. 2004 Jul 20;32(13):3826-35. Print 2004.

PMID:
15266008
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes.

Ho Sui SJ, Mortimer JR, Arenillas DJ, Brumm J, Walsh CJ, Kennedy BP, Wasserman WW.

Nucleic Acids Res. 2005 Jun 2;33(10):3154-64. Print 2005.

PMID:
15933209
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Selective constraints in experimentally defined primate regulatory regions.

Gaffney DJ, Blekhman R, Majewski J.

PLoS Genet. 2008 Aug 15;4(8):e1000157. doi: 10.1371/journal.pgen.1000157.

PMID:
18704158
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Bayesian variable selection for gene expression modeling with regulatory motif binding sites in neuroinflammatory events.

Liu KY, Zhou X, Kan K, Wong ST.

Neuroinformatics. 2006 Winter;4(1):95-117.

PMID:
16595861
[PubMed - indexed for MEDLINE]
7.

The population genetics of cooperative gene regulation.

Stewart AJ, Seymour RM, Pomiankowski A, Plotkin JB.

BMC Evol Biol. 2012 Sep 6;12:173. doi: 10.1186/1471-2148-12-173.

PMID:
22954408
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Transcription factor binding sites detection by using alignment-based approach.

Mahdevar G, Sadeghi M, Nowzari-Dalini A.

J Theor Biol. 2012 Jul 7;304:96-102. doi: 10.1016/j.jtbi.2012.03.039. Epub 2012 Apr 6.

PMID:
22504445
[PubMed - indexed for MEDLINE]
9.

Analyzing miRNA co-expression networks to explore TF-miRNA regulation.

Bandyopadhyay S, Bhattacharyya M.

BMC Bioinformatics. 2009 May 28;10:163. doi: 10.1186/1471-2105-10-163.

PMID:
19476620
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
11.

A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites.

Kulakovskiy IV, Belostotsky AA, Kasianov AS, Esipova NG, Medvedeva YA, Eliseeva IA, Makeev VJ.

Bioinformatics. 2011 Oct 1;27(19):2621-4. doi: 10.1093/bioinformatics/btr453. Epub 2011 Aug 18.

PMID:
21852305
[PubMed - indexed for MEDLINE]
Free Article
12.

Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites.

Kamalakaran S, Radhakrishnan SK, Beck WT.

J Biol Chem. 2005 Jun 3;280(22):21491-7. Epub 2005 Mar 24.

PMID:
15790569
[PubMed - indexed for MEDLINE]
Free Article
13.

Identifying transcription factor binding sites through Markov chain optimization.

Ellrott K, Yang C, Sladek FM, Jiang T.

Bioinformatics. 2002;18 Suppl 2:S100-9.

PMID:
12385991
[PubMed - indexed for MEDLINE]
Free Article
14.

Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny.

Rouault H, Mazouni K, Couturier L, Hakim V, Schweisguth F.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14615-20. doi: 10.1073/pnas.1002876107. Epub 2010 Jul 29.

PMID:
20671200
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Incorporating evolution of transcription factor binding sites into annotated alignments.

Bais AS, Grossmann S, Vingron M.

J Biosci. 2007 Aug;32(5):841-50.

PMID:
17914226
[PubMed - indexed for MEDLINE]
Free Article
16.

Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs.

Veerla S, Ringnér M, Höglund M.

BMC Genomics. 2010 Mar 1;11:145. doi: 10.1186/1471-2164-11-145.

PMID:
20193056
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Regulatory motif finding by logic regression.

Keles S, van der Laan MJ, Vulpe C.

Bioinformatics. 2004 Nov 1;20(16):2799-811. Epub 2004 May 27.

PMID:
15166027
[PubMed - indexed for MEDLINE]
Free Article
18.

A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha.

Li L, Cheng AS, Jin VX, Paik HH, Fan M, Li X, Zhang W, Robarge J, Balch C, Davuluri RV, Kim S, Huang TH, Nephew KP.

Bioinformatics. 2006 Sep 15;22(18):2210-6. Epub 2006 Jun 29.

PMID:
16809387
[PubMed - indexed for MEDLINE]
Free Article
19.

Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency.

Yeh HY, Cheng SW, Lin YC, Yeh CY, Lin SF, Soo VW.

BMC Med Genomics. 2009 Dec 21;2:70. doi: 10.1186/1755-8794-2-70.

PMID:
20025723
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Grid methodology for identifying co-regulated genes and transcription factor binding sites.

van der Wath E, Moutsianas L, van der Wath R, Visagie A, Milanesi L, Liò P.

IEEE Trans Nanobioscience. 2007 Jun;6(2):162-7.

PMID:
17695752
[PubMed - indexed for MEDLINE]

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