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Items: 1 to 20 of 39


ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.

Miller CA, Hampton O, Coarfa C, Milosavljevic A.

PLoS One. 2011 Jan 31;6(1):e16327. doi: 10.1371/journal.pone.0016327.


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.


Next-generation genomics: an integrative approach.

Hawkins RD, Hon GC, Ren B.

Nat Rev Genet. 2010 Jul;11(7):476-86. doi: 10.1038/nrg2795. Review.


Q&A: ChIP-seq technologies and the study of gene regulation.

Liu ET, Pott S, Huss M.

BMC Biol. 2010 May 14;8:56. doi: 10.1186/1741-7007-8-56. No abstract available.


A signal-noise model for significance analysis of ChIP-seq with negative control.

Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK.

Bioinformatics. 2010 May 1;26(9):1199-204. doi: 10.1093/bioinformatics/btq128. Epub 2010 Apr 5.


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.


BEDTools: a flexible suite of utilities for comparing genomic features.

Quinlan AR, Hall IM.

Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.


On the detection and refinement of transcription factor binding sites using ChIP-Seq data.

Hu M, Yu J, Taylor JM, Chinnaiyan AM, Qin ZS.

Nucleic Acids Res. 2010 Apr;38(7):2154-67. doi: 10.1093/nar/gkp1180. Epub 2010 Jan 6.


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.


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.


The UCSC Genome Browser database: update 2010.

Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ.

Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9. doi: 10.1093/nar/gkp939. Epub 2009 Nov 11.


Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.

Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ.

Nucleic Acids Res. 2010 Jan;38(3):e13. doi: 10.1093/nar/gkp1012. Epub 2009 Nov 11.


Computation for ChIP-seq and RNA-seq studies.

Pepke S, Wold B, Mortazavi A.

Nat Methods. 2009 Nov;6(11 Suppl):S22-32. doi: 10.1038/nmeth.1371. Review.


ChIP-seq: advantages and challenges of a maturing technology.

Park PJ.

Nat Rev Genet. 2009 Oct;10(10):669-80. doi: 10.1038/nrg2641. Epub 2009 Sep 8. Review.


Mapping accessible chromatin regions using Sono-Seq.

Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M.

Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14926-31. doi: 10.1073/pnas.0905443106. Epub 2009 Aug 18.


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.


A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.

Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W.

Bioinformatics. 2009 Aug 1;25(15):1952-8. doi: 10.1093/bioinformatics/btp340. Epub 2009 Jun 8.


MEME SUITE: tools for motif discovery and searching.

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8. doi: 10.1093/nar/gkp335. Epub 2009 May 20.


Genome-wide views of chromatin structure.

Rando OJ, Chang HY.

Annu Rev Biochem. 2009;78:245-71. doi: 10.1146/annurev.biochem.78.071107.134639. Review.


Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).

Giresi PG, Lieb JD.

Methods. 2009 Jul;48(3):233-9. doi: 10.1016/j.ymeth.2009.03.003. Epub 2009 Mar 18.

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