{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:20:38Z","timestamp":1764688838759},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Increasing number of ChIP-seq experiments are investigating transcription factor binding under multiple experimental conditions, for example, various treatment conditions, several distinct time points and different treatment dosage levels. Hence, identifying differential binding sites across multiple conditions is of practical importance in biological and medical research. To this end, we have developed a powerful and flexible program, called DBChIP, to detect differentially bound sharp binding sites across multiple conditions, with or without matching control samples. By assigning uncertainty measure to the putative differential binding sites, DBChIP facilitates downstream analysis. DBChIP is implemented in R programming language and can work with a wide range of sequencing file formats.<\/jats:p>\n               <jats:p>Availability: R package DBChIP is available at http:\/\/pages.cs.wisc.edu\/~kliang\/DBChIP\/<\/jats:p>\n               <jats:p>Contact: \u00a0kliang@stat.wisc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr605","type":"journal-article","created":{"date-parts":[[2011,11,5]],"date-time":"2011-11-05T04:36:36Z","timestamp":1320467796000},"page":"121-122","source":"Crossref","is-referenced-by-count":79,"title":["Detecting differential binding of transcription factors with ChIP-seq"],"prefix":"10.1093","volume":"28","author":[{"given":"Kun","family":"Liang","sequence":"first","affiliation":[{"name":"1 Department of Statistics and 2Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA"},{"name":"1 Department of Statistics and 2Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA"}]},{"given":"S\u00fcnd\u00fcz","family":"Kele\u015f","sequence":"additional","affiliation":[{"name":"1 Department of Statistics and 2Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA"},{"name":"1 Department of Statistics and 2Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,11,3]]},"reference":[{"key":"2023061011441419100_B1","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1126\/science.1183621","article-title":"Variation in transcription factor binding among humans","volume":"328","author":"Kasowski","year":"2010","journal-title":"Science"},{"key":"2023061011441419100_B2","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1101\/gr.114587.110","article-title":"Diverse transcription factor binding features revealed by genomewide ChIP-seq in C. elegans","volume":"21","author":"Niu","year":"2011","journal-title":"Genome Res."},{"key":"2023061011441419100_B3","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023061011441419100_B4","doi-asserted-by":"crossref","first-page":"e11471","DOI":"10.1371\/journal.pone.0011471","article-title":"Evaluation of algorithm performance in ChIP-seq peak detection","volume":"5","author":"Wilbanks","year":"2010","journal-title":"PloS One"},{"key":"2023061011441419100_B5","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1093\/bioinformatics\/btq128","article-title":"A signal-noise model for significance analysis of ChIP-seq with negative control","volume":"26","author":"Xu","year":"2010","journal-title":"Bioinformatics"},{"key":"2023061011441419100_B6","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1038\/nature08934","article-title":"Genetic analysis of variation in transcription factor binding in yeast","volume":"464","author":"Zheng","year":"2010","journal-title":"Nature"},{"key":"2023061011441419100_B7","doi-asserted-by":"crossref","first-page":"e1000848","DOI":"10.1371\/journal.pgen.1000848","article-title":"Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4\/FOXA in development and environmental response","volume":"6","author":"Zhong","year":"2010","journal-title":"PLoS Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/1\/121\/50568390\/bioinformatics_28_1_121.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/1\/121\/50568390\/bioinformatics_28_1_121.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T11:45:16Z","timestamp":1686397516000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/1\/121\/219907"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11,3]]},"references-count":7,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr605","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,1,1]]},"published":{"date-parts":[[2011,11,3]]}}}