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Items: 1 to 20 of 110

1.

Quantitative analysis of genome-wide chromatin remodeling.

Baek S, Sung MH, Hager GL.

Methods Mol Biol. 2012;833:433-41. doi: 10.1007/978-1-61779-477-3_26.

PMID:
22183609
2.

Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes.

Baek S, Sung MH.

Methods Mol Biol. 2016;1418:225-40. doi: 10.1007/978-1-4939-3578-9_12.

3.

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.

4.

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data.

Alawi M, Kurtz S, Beckstette M.

J Integr Bioinform. 2011 Jun 21;8(2):155. doi: 10.2390/biecoll-jib-2011-155.

PMID:
21690655
5.

BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data.

Kähärä J, Lähdesmäki H.

Bioinformatics. 2015 Sep 1;31(17):2852-9. doi: 10.1093/bioinformatics/btv294. Epub 2015 May 7.

PMID:
25957350
6.

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.

7.

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
8.

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.

Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen RC.

Bioinformatics. 2010 Apr 15;26(8):1000-6. doi: 10.1093/bioinformatics/btq087. Epub 2010 Mar 5.

PMID:
20208068
9.

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
10.

Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.

Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR.

PLoS Biol. 2008 Mar 18;6(3):e65. doi: 10.1371/journal.pbio.0060065.

11.

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.

12.

The analysis of ChIP-Seq data.

Ma W, Wong WH.

Methods Enzymol. 2011;497:51-73. doi: 10.1016/B978-0-12-385075-1.00003-2.

PMID:
21601082
13.

Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains.

Shu W, Chen H, Bo X, Wang S.

Nucleic Acids Res. 2011 Sep 1;39(17):7428-43. doi: 10.1093/nar/gkr443. Epub 2011 Jun 17.

14.

Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries.

Sabo PJ, Humbert R, Hawrylycz M, Wallace JC, Dorschner MO, McArthur M, Stamatoyannopoulos JA.

Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4537-42. Epub 2004 Mar 19.

15.

MochiView: versatile software for genome browsing and DNA motif analysis.

Homann OR, Johnson AD.

BMC Biol. 2010 Apr 21;8:49. doi: 10.1186/1741-7007-8-49.

16.

Visualizing and characterizing in vivo DNA-binding events and direct target genes of plant transcription factors.

Muiño JM, Angenent GC, Kaufmann K.

Methods Mol Biol. 2011;754:293-305. doi: 10.1007/978-1-61779-154-3_17. Review.

PMID:
21720960
17.

DNaseI hypersensitivity analysis of chromatin structure.

Lu Q, Richardson B.

Methods Mol Biol. 2004;287:77-86.

PMID:
15273405
18.

seqMINER: an integrated ChIP-seq data interpretation platform.

Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L.

Nucleic Acids Res. 2011 Mar;39(6):e35. doi: 10.1093/nar/gkq1287. Epub 2010 Dec 21.

19.

GenomicTools: a computational platform for developing high-throughput analytics in genomics.

Tsirigos A, Haiminen N, Bilal E, Utro F.

Bioinformatics. 2012 Jan 15;28(2):282-3. doi: 10.1093/bioinformatics/btr646. Epub 2011 Nov 22.

PMID:
22113082
20.

Genome-wide in vivo cross-linking of sequence-specific transcription factors.

Li XY, Biggin MD.

Methods Mol Biol. 2012;809:3-26. doi: 10.1007/978-1-61779-376-9_1.

PMID:
22113265

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