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Results: 1 to 20 of 86

1.

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data.

Lun DS, Sherrid A, Weiner B, Sherman DR, Galagan JE.

Genome Biol. 2009;10(12):R142. doi: 10.1186/gb-2009-10-12-r142. Epub 2009 Dec 22.

PMID:
20028542
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments.

Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL.

BMC Genomics. 2009 Dec 18;10:618. doi: 10.1186/1471-2164-10-618.

PMID:
20017957
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data.

Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keleş S.

PLoS Comput Biol. 2013;9(10):e1003246. doi: 10.1371/journal.pcbi.1003246. Epub 2013 Oct 17.

PMID:
24146601
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Modeling ChIP sequencing in silico with applications.

Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M.

PLoS Comput Biol. 2008 Aug 22;4(8):e1000158. doi: 10.1371/journal.pcbi.1000158.

PMID:
18725927
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

ChIPModule: systematic discovery of transcription factors and their cofactors from ChIP-seq data.

Ding J, Cai X, Wang Y, Hu H, Li X.

Pac Symp Biocomput. 2013:320-31.

PMID:
23424137
[PubMed - indexed for MEDLINE]
Free Article
6.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.

PMID:
18684996
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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]
8.

An integrated software system for analyzing ChIP-chip and ChIP-seq data.

Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH.

Nat Biotechnol. 2008 Nov;26(11):1293-300. doi: 10.1038/nbt.1505. Epub 2008 Nov 2.

PMID:
18978777
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Epigenetic analysis: ChIP-chip and ChIP-seq.

Pellegrini M, Ferrari R.

Methods Mol Biol. 2012;802:377-87. doi: 10.1007/978-1-61779-400-1_25.

PMID:
22130894
[PubMed - indexed for MEDLINE]
10.

Computational analysis of ChIP-seq data.

Ji H.

Methods Mol Biol. 2010;674:143-59. doi: 10.1007/978-1-60761-854-6_9.

PMID:
20827590
[PubMed - indexed for MEDLINE]
11.

Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite.

Wang X, Zhang X.

BMC Syst Biol. 2011 Dec 14;5 Suppl 2:S3. doi: 10.1186/1752-0509-5-S2-S3. Epub 2011 Dec 14.

PMID:
22784574
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder.

Narlikar L, Jothi R.

Methods Mol Biol. 2012;802:305-22. doi: 10.1007/978-1-61779-400-1_20.

PMID:
22130889
[PubMed - indexed for MEDLINE]
13.

Genome-wide prediction of transcription factor binding sites using an integrated model.

Won KJ, Ren B, Wang W.

Genome Biol. 2010 Jan 22;11(1):R7. doi: 10.1186/gb-2010-11-1-r7.

PMID:
20096096
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Extracting transcription factor targets from ChIP-Seq data.

Tuteja G, White P, Schug J, Kaestner KH.

Nucleic Acids Res. 2009 Sep;37(17):e113. doi: 10.1093/nar/gkp536. Epub 2009 Jun 24.

PMID:
19553195
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites.

Lefrançois P, Zheng W, Snyder M.

Methods Enzymol. 2010;470:77-104. doi: 10.1016/S0076-6879(10)70004-5. Epub 2010 Mar 1.

PMID:
20946807
[PubMed - indexed for MEDLINE]
16.

Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq.

Conley AB, Jordan IK.

Methods Mol Biol. 2010;674:225-40. doi: 10.1007/978-1-60761-854-6_14.

PMID:
20827595
[PubMed - indexed for MEDLINE]
17.

ChIP-Seq and the complexity of bacterial transcriptional regulation.

Galagan J, Lyubetskaya A, Gomes A.

Curr Top Microbiol Immunol. 2013;363:43-68. doi: 10.1007/82_2012_257. Review.

PMID:
22983621
[PubMed - indexed for MEDLINE]
18.

An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data.

Wang C, Xu J, Zhang D, Wilson ZA, Zhang D.

BMC Bioinformatics. 2010 Feb 9;11:81. doi: 10.1186/1471-2105-11-81.

PMID:
20144209
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.

Goh WS, Orlov Y, Li J, Clarke ND.

PLoS Comput Biol. 2010 Jan 22;6(1):e1000649. doi: 10.1371/journal.pcbi.1000649.

PMID:
20098497
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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]
Free PMC Article

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