{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T03:10:10Z","timestamp":1776395410141,"version":"3.51.2"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1817,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein\u2013DNA and protein\u2013RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing.<\/jats:p>\n               <jats:p>Results: We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics.<\/jats:p>\n               <jats:p>Availability: Open-source software, with tutorials and protocol files, is available at http:\/\/regulatorygenomics.upf.edu\/pyicos or as a Galaxy server at http:\/\/regulatorygenomics.upf.edu\/galaxy<\/jats:p>\n               <jats:p>Contact: \u00a0eduardo.eyras@upf.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr570","type":"journal-article","created":{"date-parts":[[2011,10,13]],"date-time":"2011-10-13T00:14:29Z","timestamp":1318464869000},"page":"3333-3340","source":"Crossref","is-referenced-by-count":85,"title":["Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data"],"prefix":"10.1093","volume":"27","author":[{"given":"Sonja","family":"Althammer","sequence":"first","affiliation":[{"name":"1 Universitat Pompeu Fabra, 2Centre for Genomic Regulation (CRG), Dr Aiguader 88, E08003 Barcelona and 3Catalan Institution for Research and Advanced Studies (ICREA), Passeig Llu\u00eds Companys 23, E08010 Barcelona, Spain"}]},{"given":"Juan","family":"Gonz\u00e1lez-Vallinas","sequence":"additional","affiliation":[{"name":"1 Universitat Pompeu Fabra, 2Centre for Genomic Regulation (CRG), Dr Aiguader 88, E08003 Barcelona and 3Catalan Institution for Research and Advanced Studies (ICREA), Passeig Llu\u00eds Companys 23, E08010 Barcelona, Spain"}]},{"given":"Cecilia","family":"Ballar\u00e9","sequence":"additional","affiliation":[{"name":"1 Universitat Pompeu Fabra, 2Centre for Genomic Regulation (CRG), Dr Aiguader 88, E08003 Barcelona and 3Catalan Institution for Research and Advanced Studies (ICREA), Passeig Llu\u00eds Companys 23, E08010 Barcelona, Spain"}]},{"given":"Miguel","family":"Beato","sequence":"additional","affiliation":[{"name":"1 Universitat Pompeu Fabra, 2Centre for Genomic Regulation (CRG), Dr Aiguader 88, E08003 Barcelona and 3Catalan Institution for Research and Advanced Studies (ICREA), Passeig Llu\u00eds Companys 23, E08010 Barcelona, Spain"},{"name":"1 Universitat Pompeu Fabra, 2Centre for Genomic Regulation (CRG), Dr Aiguader 88, E08003 Barcelona and 3Catalan Institution for Research and Advanced Studies (ICREA), Passeig Llu\u00eds Companys 23, E08010 Barcelona, Spain"}]},{"given":"Eduardo","family":"Eyras","sequence":"additional","affiliation":[{"name":"1 Universitat Pompeu Fabra, 2Centre for Genomic Regulation (CRG), Dr Aiguader 88, E08003 Barcelona and 3Catalan Institution for Research and Advanced Studies (ICREA), Passeig Llu\u00eds Companys 23, E08010 Barcelona, Spain"},{"name":"1 Universitat Pompeu Fabra, 2Centre for Genomic Regulation (CRG), Dr Aiguader 88, E08003 Barcelona and 3Catalan Institution for Research and Advanced Studies (ICREA), Passeig Llu\u00eds Companys 23, E08010 Barcelona, Spain"}]}],"member":"286","published-online":{"date-parts":[[2011,10,12]]},"reference":[{"key":"2023012511302984900_B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"2023012511302984900_B2","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/1471-2105-11-94","article-title":"Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments","volume":"11","author":"Bullard","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012511302984900_B3","doi-asserted-by":"crossref","first-page":"e1001046","DOI":"10.1371\/journal.pbio.1001046","article-title":"A User's Guide to the Encyclopedia of DNA Elements (ENCODE)","volume":"9","author":"ENCODE Consortium","year":"2011","journal-title":"PLoS Biol."},{"key":"2023012511302984900_B4","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":"Fejes","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012511302984900_B5","doi-asserted-by":"crossref","first-page":"D800","DOI":"10.1093\/nar\/gkq1064","article-title":"Ensembl 2011","volume":"39","author":"Flicek","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012511302984900_B6","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":"Ji","year":"2008","journal-title":"Nat. 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