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Items: 1 to 20 of 73

1.

Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data.

Bedo J, Kowalczyk A.

Bioinformatics. 2011 Jun 15;27(12):1610-7. doi: 10.1093/bioinformatics/btr263. Epub 2011 May 9.

PMID:
21558156
2.

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data.

Gupta R, Wikramasinghe P, Bhattacharyya A, Perez FA, Pal S, Davuluri RV.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S65. doi: 10.1186/1471-2105-11-S1-S65.

3.

GPAT: retrieval of genomic annotation from large genomic position datasets.

Krebs A, Frontini M, Tora L.

BMC Bioinformatics. 2008 Dec 15;9:533. doi: 10.1186/1471-2105-9-533.

4.

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S.

Nat Methods. 2007 Aug;4(8):651-7. Epub 2007 Jun 11.

PMID:
17558387
5.

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.

Salmon-Divon M, Dvinge H, Tammoja K, Bertone P.

BMC Bioinformatics. 2010 Aug 6;11:415. doi: 10.1186/1471-2105-11-415.

6.

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.

7.

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.

Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E.

Nucleic Acids Res. 2010 Jun;38(11):e126. doi: 10.1093/nar/gkq217. Epub 2010 Apr 7.

8.

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.

9.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

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

PMID:
16362910
10.

Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq.

Liu Y, Han D, Han Y, Yan Z, Xie B, Li J, Qiao N, Hu H, Khaitovich P, Gao Y, Han JD.

Nucleic Acids Res. 2011 Mar;39(4):1408-18. doi: 10.1093/nar/gkq956. Epub 2010 Oct 14.

11.

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

Wang X, Zhang X.

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

12.

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.

13.

Integration of cap analysis of gene expression and chromatin immunoprecipitation analysis on array reveals genome-wide androgen receptor signaling in prostate cancer cells.

Takayama K, Tsutsumi S, Katayama S, Okayama T, Horie-Inoue K, Ikeda K, Urano T, Kawazu C, Hasegawa A, Ikeo K, Gojyobori T, Ouchi Y, Hayashizaki Y, Aburatani H, Inoue S.

Oncogene. 2011 Feb 3;30(5):619-30. doi: 10.1038/onc.2010.436. Epub 2010 Oct 4.

PMID:
20890304
14.

ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.

Hon G, Ren B, Wang W.

PLoS Comput Biol. 2008 Oct;4(10):e1000201. doi: 10.1371/journal.pcbi.1000201. Epub 2008 Oct 17.

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.

16.

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

Lefran├žois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M.

BMC Genomics. 2009 Jan 21;10:37. doi: 10.1186/1471-2164-10-37.

17.

Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts.

Szalkowski AM, Schmid CD.

Brief Bioinform. 2011 Nov;12(6):626-33. doi: 10.1093/bib/bbq068. Epub 2010 Nov 8.

PMID:
21059603
18.

MER41 repeat sequences contain inducible STAT1 binding sites.

Schmid CD, Bucher P.

PLoS One. 2010 Jul 6;5(7):e11425. doi: 10.1371/journal.pone.0011425.

19.

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.

Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ.

Genome Res. 2008 Dec;18(12):1906-17. doi: 10.1101/gr.078519.108. Epub 2008 Sep 11.

20.

POLYPHEMUS: R package for comparative analysis of RNA polymerase II ChIP-seq profiles by non-linear normalization.

Mendoza-Parra MA, Sankar M, Walia M, Gronemeyer H.

Nucleic Acids Res. 2012 Feb;40(4):e30. doi: 10.1093/nar/gkr1205. Epub 2011 Dec 7.

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