ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.

[1]  Raymond K. Auerbach,et al.  PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls , 2009, Nature Biotechnology.

[2]  David A. Nix,et al.  Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks , 2008, BMC Bioinformatics.

[3]  Richard Durbin,et al.  A large genome center's improvements to the Illumina sequencing system , 2008, Nature Methods.

[4]  Rory Stark,et al.  Genome-Scale Validation of Deep-Sequencing Libraries , 2008, PloS one.

[5]  Victor X Jin,et al.  E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. , 2008, Genome research.

[6]  E. Liu,et al.  Evolution of the mammalian transcription factor binding repertoire via transposable elements. , 2008, Genome research.

[7]  P. Park,et al.  Design and analysis of ChIP-seq experiments for DNA-binding proteins , 2008, Nature Biotechnology.

[8]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[9]  Michael D. Wilson,et al.  Species-Specific Transcription in Mice Carrying Human Chromosome 21 , 2008, Science.

[10]  Ioannis Xenarios,et al.  BMC Bioinformatics BioMed Central Methodology article Probabilistic base calling of Solexa sequencing data , 2022 .

[11]  Gabor T. Marth,et al.  Rapid whole-genome mutational profiling using next-generation sequencing technologies. , 2008, Genome research.

[12]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[13]  S. Batzoglou,et al.  Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data , 2008, Nature Methods.

[14]  M. Marra,et al.  Applications of next-generation sequencing technologies in functional genomics. , 2008, Genomics.

[15]  Raja Jothi,et al.  Genome-wide identification of in vivo protein–DNA binding sites from ChIP-Seq data , 2008, Nucleic acids research.

[16]  P. Mitra,et al.  Alta-Cyclic: a self-optimizing base caller for next-generation sequencing , 2008, Nature Methods.

[17]  Steven J. M. Jones,et al.  FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology , 2008, Bioinform..

[18]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[19]  Matthias Meyer,et al.  From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing , 2007, Nucleic acids research.

[20]  B. Wold,et al.  Sequence census methods for functional genomics , 2008, Nature Methods.

[21]  Roland Green,et al.  Genome-scale ChIP-chip analysis using 10,000 human cells. , 2007, BioTechniques.

[22]  Mark Gerstein,et al.  Divergence of transcription factor binding sites across related yeast species. , 2007, Science.

[23]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[24]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[25]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[26]  D. Gifford,et al.  Tissue-specific transcriptional regulation has diverged significantly between human and mouse , 2007, Nature Genetics.

[27]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[28]  Michael Q. Zhang,et al.  Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome , 2007, Cell.

[29]  Steven J. M. Jones,et al.  Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. , 2006, Genome research.

[30]  Tae Hoon Kim,et al.  Genome-wide analysis of protein-DNA interactions. , 2006, Annual review of genomics and human genetics.

[31]  Richard A Young,et al.  Chromatin immunoprecipitation and microarray-based analysis of protein location , 2006, Nature Protocols.

[32]  B. Turner,et al.  Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations , 2006, Nature Genetics.

[33]  Clifford A. Meyer,et al.  Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1 , 2005, Cell.

[34]  S. Cawley,et al.  Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs , 2004, Cell.

[35]  B. Turner,et al.  Immunoprecipitation of native chromatin: NChIP. , 2003, Methods.

[36]  V. Orlando,et al.  Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. , 2000, Trends in biochemical sciences.

[37]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[38]  B. Wold,et al.  In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. , 1990, Science.

[39]  Alexander Varshavsky,et al.  Mapping proteinDNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene , 1988, Cell.