{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T20:39:13Z","timestamp":1767904753937,"version":"3.49.0"},"reference-count":62,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2011,7,14]],"date-time":"2011-07-14T00:00:00Z","timestamp":1310601600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002111","type":"journal-article","created":{"date-parts":[[2011,7,14]],"date-time":"2011-07-14T16:33:22Z","timestamp":1310661202000},"page":"e1002111","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":81,"title":["Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data"],"prefix":"10.1371","volume":"7","author":[{"given":"Dongjun","family":"Chung","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pei Fen","family":"Kuan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajendran","family":"Sanalkumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kun","family":"Liang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emery H.","family":"Bresnick","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Colin","family":"Dewey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S\u00fcnd\u00fcz","family":"Kele\u015f","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2011,7,14]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1038\/nature06008","article-title":"Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.","volume":"448","author":"T Mikkelsen","year":"2007","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome.","volume":"129","author":"A Barski","year":"2007","journal-title":"Cell"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","article-title":"Genome-wide mapping of in vivo protein-DNA interactions.","volume":"316","author":"D Johnson","year":"2007","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"13765","DOI":"10.1073\/pnas.0904246106","article-title":"Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif.","volume":"106","author":"Y Seo","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1016\/j.molcel.2009.11.001","article-title":"Discovering hematopoietic mechanisms through genomewide analysis of GATA factor chromatin occupancy.","volume":"36","author":"T Fujiwara","year":"2009","journal-title":"Mol Cell"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"2306","DOI":"10.1126\/science.290.5500.2306","article-title":"Genome-wide location and function of DNA binding proteins.","volume":"290","author":"B Ren","year":"2000","journal-title":"Science"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/S0092-8674(04)00127-8","article-title":"Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of non-coding RNAs.","volume":"116","author":"S Cawley","year":"2004","journal-title":"Cell"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/j.cell.2004.05.023","article-title":"Mapping global histone acetylation patterns to gene expression.","volume":"117","author":"S Kurdistani","year":"2004","journal-title":"Cell"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1126\/science.1112178","article-title":"Genome-scale identification of nucleosome positions in S. cerevisiae.","volume":"309","author":"G Yuan","year":"2005","journal-title":"Science"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1038\/nbt.1518","article-title":"PeakSeq enables systematic scoring of ChIP-Seq experiments relative to controls.","volume":"27","author":"J Rozowsky","year":"2009","journal-title":"Nat Biotechnol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1038\/nbt.1505","article-title":"An integrated software system for analyzing ChIP-chip and ChIP-seq data.","volume":"26","author":"H Ji","year":"2008","journal-title":"Nat Biotechnol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e13","DOI":"10.1093\/nar\/gkp1012","article-title":"Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.","volume":"38","author":"K Blahnik","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.ygeno.2007.11.003","article-title":"A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.","volume":"91","author":"GJ Faulkner","year":"2008","journal-title":"Genomics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/bioinformatics\/btp692","article-title":"RNA-Seq gene expression estimation with read mapping uncertainty.","volume":"26","author":"B Li","year":"2010","journal-title":"Bioinformatics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq.","volume":"5","author":"A Mortazavi","year":"2008","journal-title":"Nat Methods"},{"key":"ref16","first-page":"69","article-title":"Methods for allocating ambiguous short-reads.","volume":"Sys10","author":"M Taub","year":"2010","journal-title":"Commun Inf"},{"key":"ref17","first-page":"202","article-title":"Estimation of alternative splicing isoform frequencies from RNA-Seq data.","author":"M Nicolae","year":"2010"},{"key":"ref18","first-page":"397","article-title":"Accurate estimation of expression levels of homologous genes in RNA-seq experiments.","author":"B Pasaniuc","year":"2010"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nrg1895","article-title":"Primate segmental duplications: crucibles of evolution, diversity and disease.","volume":"7","author":"J Bailey","year":"2006","journal-title":"Nat Rev Genet"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.tig.2009.08.002","article-title":"The origins and impact of primate segmental duplications.","volume":"25","author":"T Marques-Bonet","year":"2009","journal-title":"Trends Genet"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1712","DOI":"10.1093\/molbev\/msi166","article-title":"Interchromosomal segmental duplications explain the unusual structure of PRSS3, the gene for an inhibitor-resistant trypsinogen.","volume":"22","author":"L Rowen","year":"2005","journal-title":"Mol Biol Evol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"e206","DOI":"10.1371\/journal.pbio.0020206","article-title":"Gene duplication: the genomic trade in spare parts.","volume":"2","author":"M Hurles","year":"2004","journal-title":"PLoS Biol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1434","DOI":"10.1126\/science.1101160","article-title":"The influence of CCL3L1 gene-containing segmental duplications on HIV-1\/AIDS susceptibility.","volume":"307","author":"E Gonzalez","year":"2005","journal-title":"Science"},{"key":"ref24","first-page":"10053","article-title":"Recent segmental duplications in the human genome.","volume":"297","author":"JBZ Gu","year":"2002","journal-title":"Science"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1186\/1471-2164-7-133","article-title":"Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes.","volume":"7","author":"P Polak","year":"2006","journal-title":"BMC Genomics"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1073\/pnas.0708366105","article-title":"Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo.","volume":"105","author":"AC Roman","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"18613","DOI":"10.1073\/pnas.0703637104","article-title":"Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53.","volume":"47","author":"T Wang","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"R69","DOI":"10.1186\/gb-2010-11-6-r69","article-title":"Estimating enrichment of repetitive elements from high-throughput sequence data.","volume":"11","author":"D Day","year":"2010","journal-title":"Genome Biol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1159\/000084979","article-title":"Repbase Update, a database of eukaryotic repetitive elements.","volume":"110","author":"J Jurka","year":"2005","journal-title":"Cytogenet Genome Res"},{"key":"ref30","author":"AFA Smit","year":"2010"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2501","DOI":"10.1093\/bioinformatics\/btq460","article-title":"A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags.","volume":"26","author":"J Wang","year":"2010","journal-title":"Bioinformatics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS).","volume":"9","author":"Y Zhang","year":"2008","journal-title":"Genome Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1093\/bioinformatics\/btn119","article-title":"GeneTrack-a genomic data processing and visualization framework.","volume":"24","author":"I Albert","year":"2008","journal-title":"Bioinformatics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1093\/bioinformatics\/btn480","article-title":"F-Seq: a feature density estimator for highthroughput sequence tags.","volume":"24","author":"A Boyle","year":"2008","journal-title":"Bioinformatics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1729","DOI":"10.1093\/bioinformatics\/btn305","article-title":"FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology.","volume":"24","author":"A Fejes","year":"2008","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"5221","DOI":"10.1093\/nar\/gkn488","article-title":"Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.","volume":"36","author":"R Jothi","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1038\/nbt.1508","article-title":"Design and analysis of ChIP-seq experiments for DNA-binding proteins.","volume":"6","author":"PV Kharchenko","year":"2008","journal-title":"Nat Biotechnol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1186\/1471-2105-11-369","article-title":"HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data.","volume":"11","author":"Z Qin","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1186\/1471-2105-9-523","article-title":"Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.","volume":"9","author":"D Nix","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e113","DOI":"10.1093\/nar\/gkp536","article-title":"Extracting transcription factor targets from ChIPSeq data.","volume":"37","author":"G Tuteja","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1186\/1471-2105-10-299","article-title":"BayesPeak: Bayesian analysis of ChIP-seq data.","volume":"10","author":"C Spyrou","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1038\/nmeth.1246","article-title":"Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.","volume":"5","author":"A Valouev","year":"2008","journal-title":"Nature Methods"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1101\/gr.098921.109","article-title":"Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression.","volume":"19","author":"Y Cheng","year":"2009","journal-title":"Genome Res"},{"key":"ref44","article-title":"A statistical framework for the analysis of ChIP-Seq data.","author":"P Kuan","year":"2009"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"e105","DOI":"10.1093\/nar\/gkn425","article-title":"Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.","volume":"36","author":"J Dohm","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME Suite: tools for motif discovery and searching.","volume":"37","author":"TL Bailey","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"D105","DOI":"10.1093\/nar\/gkp950","article-title":"JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.","volume":"38","author":"E Portales-Casamar","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"5976","DOI":"10.1073\/pnas.85.16.5976","article-title":"An erythrocyte-specific DNA-binding factor recognizes a regulatory sequence common to all chicken globin genes.","volume":"85","author":"T Evans","year":"1988","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1101\/gr.084715.108","article-title":"The genomic architecture of segmental duplications and associated copy number variants in dogs.","volume":"19","author":"T Nicholas","year":"2009","journal-title":"Genome Res"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"D613","DOI":"10.1093\/nar\/gkp939","article-title":"The UCSC Genome Browser database: update 2010.","volume":"38","author":"B Rhead","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"14926","DOI":"10.1073\/pnas.0905443106","article-title":"Mapping accessible chromatin regions using Sono-Seq.","volume":"106","author":"RK Auerbach","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"P3","DOI":"10.1186\/gb-2003-4-5-p3","article-title":"DAVID: Database for Annotation, Visualization, and Integrated Discovery.","volume":"4","author":"G Dennis","year":"2003","journal-title":"Genome Biol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.","volume":"4","author":"D Huang","year":"2009","journal-title":"Nat Protoc"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"R130","DOI":"10.1186\/gb-2009-10-11-r130","article-title":"BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.","volume":"10","author":"C Wu","year":"2009","journal-title":"Genome Biol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1038\/nrg2337","article-title":"Transposable elements and the evolution of regulatory networks.","volume":"9","author":"C Feschotte","year":"2008","journal-title":"Nature Rev Genet"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1101\/gr.080663.108","article-title":"Evolution of the mammalian transcription factor binding repertoire via transposable elements.","volume":"18","author":"G Bourque","year":"2008","journal-title":"Genome Res"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.","volume":"10","author":"B Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1002\/spe.4380240306","article-title":"A new data structure for cumulative frequency tables.","volume":"24","author":"PM Fenwick","year":"1994","journal-title":"Software Pract Exper"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics.","volume":"5","author":"R Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1101\/gr.GR-1871R","article-title":"Segmental duplications: organization and impact within the current human genome project assembly.","volume":"11","author":"J Bailey","year":"2001","journal-title":"Genome Res"},{"key":"ref61","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology.","volume":"28-36","author":"T Bailey","year":"1994","journal-title":"Menlo Park, California: AAAI Press,"},{"key":"ref62","first-page":"129","article-title":"Measurement of protein-DNA interactions in vivo by chromatin immunoprecipitation.","volume":"284","author":"H Im","year":"2004","journal-title":"Methods Mol Biol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002111","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T16:51:51Z","timestamp":1540313511000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002111"}},"subtitle":[],"editor":[{"given":"Wyeth W.","family":"Wasserman","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2011,7,14]]},"references-count":62,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2011,7,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002111","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,7,14]]}}}