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Items 1 - 20 of 120
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1:

Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.

Gibbons FD, Proft M, Struhl K, Roth FP.

Genome Biol. 2005;6(11):R96. Epub 2005 Nov 1.

PMID: 16277751 [PubMed - indexed for MEDLINE]

2:

A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.

Li W, Meyer CA, Liu XS.

Bioinformatics. 2005 Jun;21 Suppl 1:i274-82.

PMID: 15961467 [PubMed - indexed for MEDLINE]

3:

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.

Liu XS, Brutlag DL, Liu JS.

Nat Biotechnol. 2002 Aug;20(8):835-9. Epub 2002 Jul 8.

PMID: 12101404 [PubMed - indexed for MEDLINE]

4:

Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis.

Jolly ER, Chin CS, Herskowitz I, Li H.

BMC Bioinformatics. 2005 Nov 18;6:275.

PMID: 16297241 [PubMed - indexed for MEDLINE]

5:

TileMap: create chromosomal map of tiling array hybridizations.

Ji H, Wong WH.

Bioinformatics. 2005 Sep 15;21(18):3629-36. Epub 2005 Jul 26.

PMID: 16046496 [PubMed - indexed for MEDLINE]

6:

A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1.

Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ.

Genome Res. 2006 Dec;16(12):1585-95. Epub 2006 Oct 19.

PMID: 17053090 [PubMed - indexed for MEDLINE]

7:

Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment.

Kim J, Bhinge AA, Morgan XC, Iyer VR.

Nat Methods. 2005 Jan;2(1):47-53. Epub 2004 Dec 21.

PMID: 15782160 [PubMed - indexed for MEDLINE]

8:

Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities.

Sanguinetti G, Lawrence ND, Rattray M.

Bioinformatics. 2006 Nov 15;22(22):2775-81. Epub 2006 Sep 11.

PMID: 16966362 [PubMed - indexed for MEDLINE]

9:

Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray.

Jin VX, Leu YW, Liyanarachchi S, Sun H, Fan M, Nephew KP, Huang TH, Davuluri RV.

Nucleic Acids Res. 2004 Dec 17;32(22):6627-35. Print 2004.

PMID: 15608294 [PubMed - indexed for MEDLINE]

10:

Explicit equilibrium modeling of transcription-factor binding and gene regulation.

Granek JA, Clarke ND.

Genome Biol. 2005;6(10):R87. Epub 2005 Sep 30.

PMID: 16207358 [PubMed - indexed for MEDLINE]

11:

Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays.

Hanlon SE, Lieb JD.

Curr Opin Genet Dev. 2004 Dec;14(6):697-705. Review.

PMID: 15531167 [PubMed - indexed for MEDLINE]

12:

Genomic studies of transcription factor-DNA interactions.

Sikder D, Kodadek T.

Curr Opin Chem Biol. 2005 Feb;9(1):38-45. Review.

PMID: 15701451 [PubMed - indexed for MEDLINE]

13:

Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments.

Kuznetsov VA, Orlov YL, Wei CL, Ruan Y.

Genome Inform. 2007;19:83-94.

PMID: 18546507 [PubMed - indexed for MEDLINE]

14:

Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques.

Elnitski L, Jin VX, Farnham PJ, Jones SJ.

Genome Res. 2006 Dec;16(12):1455-64. Epub 2006 Oct 19. Review.

PMID: 17053094 [PubMed - indexed for MEDLINE]

15:

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

Sun H, Palaniswamy SK, Pohar TT, Jin VX, Huang TH, Davuluri RV.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D98-103.

PMID: 16381984 [PubMed - indexed for MEDLINE]

16:

Multiple testing methods for ChIP-Chip high density oligonucleotide array data.

Keleş S, van der Laan MJ, Dudoit S, Cawley SE.

J Comput Biol. 2006 Apr;13(3):579-613.

PMID: 16706714 [PubMed - indexed for MEDLINE]

17:

Clustering of genes into regulons using integrated modeling-COGRIM.

Chen G, Jensen ST, Stoeckert CJ Jr.

Genome Biol. 2007;8(1):R4.

PMID: 17204163 [PubMed - indexed for MEDLINE]

18:

High-resolution computational models of genome binding events.

Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Nat Biotechnol. 2006 Aug;24(8):963-70. Erratum in: Nat Biotechnol. 2006 Oct;24(10):1293.

PMID: 16900145 [PubMed - indexed for MEDLINE]

19:

BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments.

Wang LY, Snyder M, Gerstein M.

Genome Biol. 2006;7(11):R102.

PMID: 17078876 [PubMed - indexed for MEDLINE]

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