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Results: 1 to 20 of 120

1.

Prediction of synergistic transcription factors by function conservation.

Hu Z, Hu B, Collins JF.

Genome Biol. 2007;8(12):R257.

PMID:
18053230
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Evaluating phylogenetic footprinting for human-rodent comparisons.

Sauer T, Shelest E, Wingender E.

Bioinformatics. 2006 Feb 15;22(4):430-7. Epub 2005 Dec 6.

PMID:
16332706
[PubMed - indexed for MEDLINE]
Free Article
3.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.

PMID:
16362910
[PubMed - indexed for MEDLINE]
4.

Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets.

Roy S, Heinrich K, Phan V, Berry MW, Homayouni R.

BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S19. doi: 10.1186/1471-2105-12-S10-S19.

PMID:
22165960
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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
6.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

PMID:
19956545
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Identification of conserved regulatory elements by comparative genome analysis.

Lenhard B, Sandelin A, Mendoza L, Engström P, Jareborg N, Wasserman WW.

J Biol. 2003;2(2):13. Epub 2003 May 22.

PMID:
12760745
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Discovering approximate-associated sequence patterns for protein-DNA interactions.

Chan TM, Wong KC, Lee KH, Wong MH, Lau CK, Tsui SK, Leung KS.

Bioinformatics. 2011 Feb 15;27(4):471-8. doi: 10.1093/bioinformatics/btq682. Epub 2010 Dec 30.

PMID:
21193520
[PubMed - indexed for MEDLINE]
Free Article
9.

Enrichment of regulatory signals in conserved non-coding genomic sequence.

Levy S, Hannenhalli S, Workman C.

Bioinformatics. 2001 Oct;17(10):871-7.

PMID:
11673231
[PubMed - indexed for MEDLINE]
Free Article
10.

TF-finder: a software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base.

Cui X, Wang T, Chen HS, Busov V, Wei H.

BMC Bioinformatics. 2010 Aug 12;11:425. doi: 10.1186/1471-2105-11-425.

PMID:
20704747
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.

Ward LD, Bussemaker HJ.

Bioinformatics. 2008 Jul 1;24(13):i165-71. doi: 10.1093/bioinformatics/btn154.

PMID:
18586710
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer.

Eisermann K, Tandon S, Bazarov A, Brett A, Fraizer G, Piontkivska H.

BMC Genomics. 2008 Jul 16;9:337. doi: 10.1186/1471-2164-9-337.

PMID:
18631392
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.

Huber BR, Bulyk ML.

BMC Bioinformatics. 2006 Apr 27;7:229.

PMID:
16643658
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs.

Croft L, Szklarczyk D, Jensen LJ, Gorodkin J.

BMC Syst Biol. 2012 Jul 23;6:90. doi: 10.1186/1752-0509-6-90.

PMID:
22824421
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome.

Mahony S, Corcoran DL, Feingold E, Benos PV.

Genome Biol. 2007;8(5):R84.

PMID:
17506886
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Systematic identification of yeast cell cycle transcription factors using multiple data sources.

Wu WS, Li WH.

BMC Bioinformatics. 2008 Dec 5;9:522. doi: 10.1186/1471-2105-9-522.

PMID:
19061501
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.

Berezikov E, Guryev V, Plasterk RH, Cuppen E.

Genome Res. 2004 Jan;14(1):170-8. Epub 2003 Dec 12.

PMID:
14672977
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1.

Francke C, Kerkhoven R, Wels M, Siezen RJ.

BMC Genomics. 2008 Mar 27;9:145. doi: 10.1186/1471-2164-9-145.

PMID:
18371204
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

TF-Cluster: a pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM).

Nie J, Stewart R, Zhang H, Thomson JA, Ruan F, Cui X, Wei H.

BMC Syst Biol. 2011 Apr 15;5:53. doi: 10.1186/1752-0509-5-53.

PMID:
21496241
[PubMed - indexed for MEDLINE]
Free PMC Article

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