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Results: 1 to 20 of 117

1.

Combining multiple ChIP-seq peak detection systems using combinatorial fusion.

Schweikert C, Brown S, Tang Z, Smith PR, Hsu DF.

BMC Genomics. 2012;13 Suppl 8:S12. doi: 10.1186/1471-2164-13-S8-S12. Epub 2012 Dec 17.

PMID:
23282014
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Evaluation of algorithm performance in ChIP-seq peak detection.

Wilbanks EG, Facciotti MT.

PLoS One. 2010 Jul 8;5(7):e11471. doi: 10.1371/journal.pone.0011471.

PMID:
20628599
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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]
4.

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
5.

An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.

Cheng CY, Chu CH, Hsu HW, Hsu FR, Tang CY, Wang WC, Kung HJ, Chang PC.

BMC Genomics. 2014;15 Suppl 1:S1. doi: 10.1186/1471-2164-15-S1-S1. Epub 2014 Jan 24.

PMID:
24564277
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.

Kornacker K, Rye MB, Håndstad T, Drabløs F.

BMC Bioinformatics. 2012 Jul 24;13:176. doi: 10.1186/1471-2105-13-176.

PMID:
22827163
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data.

Han Z, Tian L, Pécot T, Huang T, Machiraju R, Huang K.

BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S2. doi: 10.1186/1471-2105-13-S2-S2.

PMID:
22536865
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
9.

Characterising ChIP-seq binding patterns by model-based peak shape deconvolution.

Mendoza-Parra MA, Nowicka M, Van Gool W, Gronemeyer H.

BMC Genomics. 2013 Nov 26;14:834. doi: 10.1186/1471-2164-14-834.

PMID:
24279297
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A fully Bayesian hidden Ising model for ChIP-seq data analysis.

Mo Q.

Biostatistics. 2012 Jan;13(1):113-28. doi: 10.1093/biostatistics/kxr029. Epub 2011 Sep 13.

PMID:
21914728
[PubMed - indexed for MEDLINE]
Free Article
11.

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data.

Qin ZS, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM.

BMC Bioinformatics. 2010 Jul 2;11:369. doi: 10.1186/1471-2105-11-369.

PMID:
20598134
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Mapping protein-DNA interactions using ChIP-sequencing.

Massie CE, Mills IG.

Methods Mol Biol. 2012;809:157-73. doi: 10.1007/978-1-61779-376-9_11.

PMID:
22113275
[PubMed - indexed for MEDLINE]
13.

Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information.

Osmanbeyoglu HU, Hartmaier RJ, Oesterreich S, Lu X.

BMC Genomics. 2012;13 Suppl 1:S1. doi: 10.1186/1471-2164-13-S1-S1. Epub 2012 Jan 17.

PMID:
22369349
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.

Nix DA, Courdy SJ, Boucher KM.

BMC Bioinformatics. 2008 Dec 5;9:523. doi: 10.1186/1471-2105-9-523.

PMID:
19061503
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Identifying ChIP-seq enrichment using MACS.

Feng J, Liu T, Qin B, Zhang Y, Liu XS.

Nat Protoc. 2012 Sep;7(9):1728-40. doi: 10.1038/nprot.2012.101. Epub 2012 Aug 30.

PMID:
22936215
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data.

Malone BM, Tan F, Bridges SM, Peng Z.

PLoS One. 2011;6(9):e25260. doi: 10.1371/journal.pone.0025260. Epub 2011 Sep 30.

PMID:
21984925
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.

Kuznetsov VA, Singh O, Jenjaroenpun P.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S12. doi: 10.1186/1471-2164-11-S1-S12.

PMID:
20158869
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

[Genomic analysis of DNA-protein interaction by chromatin immunoprecipitation].

Li ML, Wang W, Lu ZH.

Yi Chuan. 2010 Mar;32(3):219-28. Review. Chinese.

PMID:
20233698
[PubMed - indexed for MEDLINE]
19.

ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data.

Wu S, Wang J, Zhao W, Pounds S, Cheng C.

Theor Biol Med Model. 2010 Jun 3;7:18. doi: 10.1186/1742-4682-7-18.

PMID:
20525272
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Shape-based peak identification for ChIP-Seq.

Hower V, Evans SN, Pachter L.

BMC Bioinformatics. 2011 Jan 12;12:15. doi: 10.1186/1471-2105-12-15.

PMID:
21226895
[PubMed - indexed for MEDLINE]
Free PMC Article

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