Pepke S, Wold B, Mortazavi A: Computation for ChIP- seq and RNA-seq studies. Nat Methods. 2009, 6 (11 Suppl): S22-S32.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, et al: PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009, 27: 66-75. 10.1038/nbt.1518.
Article
PubMed Central
CAS
PubMed
Google Scholar
Baugh LR, Demodena J, Sternberg PW: RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science. 2009, 324: 92-94. 10.1126/science.1169628.
Article
CAS
PubMed
Google Scholar
Kharchenko PV, Tolstorukov MY, Park PJ: Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008, 26: 1351-1359. 10.1038/nbt.1508.
Article
PubMed Central
CAS
PubMed
Google Scholar
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, et al: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007, 4: 651-657. 10.1038/nmeth1068.
Article
CAS
PubMed
Google Scholar
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol. 2008, 26: 1293-1300. 10.1038/nbt.1505.
Article
PubMed Central
CAS
PubMed
Google Scholar
Benjamini Y, Hochberg Y: Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995, 57: 289-300.
Google Scholar
Dohm JC, Lottaz C, Borodina T, Himmelbauer H: Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008, 36: e105-10.1093/nar/gkn425.
Article
PubMed Central
PubMed
Google Scholar
Vega VB, Cheung E, Palanisamy N, Sung WK: Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries. PLoS One. 2009, 4: e5241-10.1371/journal.pone.0005241.
Article
PubMed Central
PubMed
Google Scholar
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al: Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008, 9: R137-10.1186/gb-2008-9-9-r137.
Article
PubMed Central
PubMed
Google Scholar
Boyle AP, Guinney J, Crawford GE, Furey TS: F-Seq: A feature density estimator for high-throughput sequence tags. Bioinformatics. 2008, 24: 2537-2538. 10.1093/bioinformatics/btn480.
Article
PubMed Central
CAS
PubMed
Google Scholar
Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, et al: Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods. 2008, 5: 829-834. 10.1038/nmeth.1246.
Article
PubMed Central
CAS
PubMed
Google Scholar
Xu H, Handoko L, Wei X, Ye C, Sheng J, et al: A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010, 26: 1199-1204. 10.1093/bioinformatics/btq128.
Article
CAS
PubMed
Google Scholar
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K: Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 2008, 36: 5221-5231. 10.1093/nar/gkn488.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics. 2009, 25: 1952-1958. 10.1093/bioinformatics/btp340.
Article
PubMed Central
CAS
PubMed
Google Scholar
Johnson DS, Mortazavi A, Myers RM, Wold B: Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007, 316: 1497-1502. 10.1126/science.1141319.
Article
CAS
PubMed
Google Scholar
Nix DA, Courdy SJ, Boucher KM: Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics. 2008, 9: 523-10.1186/1471-2105-9-523.
Article
PubMed Central
PubMed
Google Scholar
Xu H, Wei CL, Lin F, Sung WK: An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics. 2008, 24: 2344-2349. 10.1093/bioinformatics/btn402.
Article
CAS
PubMed
Google Scholar
Hon G, Ren B, Wang W: ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol. 2008, 4: e1000201-10.1371/journal.pcbi.1000201.
Article
PubMed Central
PubMed
Google Scholar
Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD: Evidence for nucleosome depletion at active regulatory regions genomewide. Nat Genet. 2004, 36: 900-905. 10.1038/ng1400.
Article
CAS
PubMed
Google Scholar