{"id":"https://openalex.org/W2277285385","doi":"https://doi.org/10.1093/bib/bbv110","title":"A comprehensive comparison of tools for differential ChIP-seq analysis","display_name":"A comprehensive comparison of tools for differential ChIP-seq analysis","publication_year":2016,"publication_date":"2016-01-13","ids":{"openalex":"https://openalex.org/W2277285385","doi":"https://doi.org/10.1093/bib/bbv110","mag":"2277285385","pmid":"https://pubmed.ncbi.nlm.nih.gov/26764273"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv110","pdf_url":"https://academic.oup.com/bib/article-pdf/17/6/953/8280399/bbv110.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/17/6/953/8280399/bbv110.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000491037","display_name":"Sebastian Steinhauser","orcid":"https://orcid.org/0000-0002-5940-3870"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sebastian Steinhauser","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089774776","display_name":"Nils Kurzawa","orcid":"https://orcid.org/0000-0002-7846-2817"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nils Kurzawa","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044191947","display_name":"Roland Eils","orcid":"https://orcid.org/0000-0002-0034-4036"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Roland Eils","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5045118783","display_name":"Carl Herrmann","orcid":"https://orcid.org/0000-0003-4989-4722"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Carl Herrmann","raw_affiliation_strings":["Corresponding author: Carl Herrmann, IPMB Universit Heidelberg and Department of Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 364, D-69120 Heidelberg, Tel.: (+49) 6221 423612"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Corresponding author: Carl Herrmann, IPMB Universit Heidelberg and Department of Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 364, D-69120 Heidelberg, Tel.: (+49) 6221 423612","institution_ids":["https://openalex.org/I223822909"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5045118783"],"corresponding_institution_ids":["https://openalex.org/I223822909"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":8.8702,"has_fulltext":false,"cited_by_count":126,"citation_normalized_percentile":{"value":0.98269733,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"17","issue":"6","first_page":"bbv110","last_page":"bbv110"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7176811099052429},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.5198907852172852},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.517519474029541},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.4811905026435852},{"id":"https://openalex.org/keywords/chip","display_name":"Chip","score":0.45418137311935425},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4523719549179077},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.45137327909469604},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24833545088768005},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21813738346099854},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20247739553451538},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15396153926849365},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07654839754104614}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7176811099052429},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.5198907852172852},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.517519474029541},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.4811905026435852},{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.45418137311935425},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4523719549179077},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.45137327909469604},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24833545088768005},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21813738346099854},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20247739553451538},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15396153926849365},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07654839754104614},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbv110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv110","pdf_url":"https://academic.oup.com/bib/article-pdf/17/6/953/8280399/bbv110.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26764273","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26764273","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":"Comparative Study"},{"id":"pmh:oai:europepmc.org:4088883","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5142015","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bib:17/6/953","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/6/953","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv110","pdf_url":"https://academic.oup.com/bib/article-pdf/17/6/953/8280399/bbv110.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2277285385.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1873501834","https://openalex.org/W1964963969","https://openalex.org/W1977109152","https://openalex.org/W1979594866","https://openalex.org/W2010461536","https://openalex.org/W2011463791","https://openalex.org/W2013287009","https://openalex.org/W2014677321","https://openalex.org/W2023342647","https://openalex.org/W2024800350","https://openalex.org/W2029994182","https://openalex.org/W2035769168","https://openalex.org/W2037562190","https://openalex.org/W2067658227","https://openalex.org/W2070021921","https://openalex.org/W2081942683","https://openalex.org/W2085184586","https://openalex.org/W2088091102","https://openalex.org/W2091244202","https://openalex.org/W2099199578","https://openalex.org/W2101384205","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2114104545","https://openalex.org/W2118532317","https://openalex.org/W2124163981","https://openalex.org/W2124514674","https://openalex.org/W2131478115","https://openalex.org/W2131610374","https://openalex.org/W2141408320","https://openalex.org/W2146303939","https://openalex.org/W2146648681","https://openalex.org/W2155826575","https://openalex.org/W2156143491","https://openalex.org/W2157232603","https://openalex.org/W2158789637","https://openalex.org/W2159288784","https://openalex.org/W2162557359","https://openalex.org/W2166244392","https://openalex.org/W2167967077","https://openalex.org/W2168191908","https://openalex.org/W2170117519","https://openalex.org/W2170830174","https://openalex.org/W2171808845","https://openalex.org/W3104066961","https://openalex.org/W4231356616","https://openalex.org/W4248204441"],"related_works":["https://openalex.org/W2032233321","https://openalex.org/W3121970507","https://openalex.org/W2110028391","https://openalex.org/W54497855","https://openalex.org/W217960748","https://openalex.org/W3125814499","https://openalex.org/W2090827041","https://openalex.org/W2565703248","https://openalex.org/W187246281","https://openalex.org/W2143548620"],"abstract_inverted_index":{"ChIP-seq":[0,64,73],"has":[1],"become":[2],"a":[3,43,51,93,165,178],"widely":[4],"adopted":[5],"genomic":[6],"assay":[7],"in":[8,75,89,123,129,168],"recent":[9,90],"years":[10],"to":[11,35,69,114,157],"determine":[12,36,115],"binding":[13],"sites":[14],"for":[15,20,46,49,63,144],"transcription":[16,145],"factors":[17,146],"or":[18,28],"enrichments":[19],"specific":[21],"histone":[22,148],"modifications.":[23],"Beside":[24],"detection":[25],"of":[26,54,72,77,98,132,171,182,188,193],"enriched":[27],"bound":[29],"regions,":[30],"an":[31],"important":[32],"question":[33,62],"is":[34,42,65,101,164],"differences":[37],"between":[38,118],"conditions.":[39,120],"While":[40],"this":[41],"common":[44],"analysis":[45,189],"gene":[47],"expression,":[48],"which":[50,110],"large":[52],"number":[53],"computational":[55],"approaches":[56],"have":[57,84,106,111,136],"been":[58,85,112],"validated,":[59],"the":[60,70,130,169,186,191,198],"same":[61],"particularly":[66],"challenging":[67],"owing":[68],"complexity":[71],"data":[74,142,155],"terms":[76],"noisiness":[78],"and":[79,87,96,127,147],"variability.":[80],"Many":[81],"different":[82],"tools":[83,100,139,176],"developed":[86,113],"published":[88],"years.":[91],"However,":[92],"comprehensive":[94],"comparison":[95],"review":[97],"these":[99,138,175],"still":[102],"missing.":[103],"Here,":[104],"we":[105,135],"reviewed":[107],"14":[108],"tools,":[109],"differential":[116],"enrichment":[117],"two":[119],"They":[121],"differ":[122],"their":[124,160],"algorithmic":[125],"setups,":[126],"also":[128],"range":[131],"applicability.":[133],"Hence,":[134],"benchmarked":[137],"on":[140,153,185],"real":[141],"sets":[143,156],"modifications,":[149],"as":[150,152],"well":[151],"simulated":[154],"quantitatively":[158],"evaluate":[159],"performance.":[161],"Overall,":[162],"there":[163],"great":[166],"variety":[167],"type":[170,187],"signal":[172],"detected":[173],"by":[174],"with":[177],"surprisingly":[179],"low":[180],"level":[181],"agreement.":[183],"Depending":[184],"performed,":[190],"choice":[192],"method":[194],"will":[195],"crucially":[196],"impact":[197],"outcome.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":22},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":18},{"year":2017,"cited_by_count":17},{"year":2016,"cited_by_count":7}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
