{"id":"https://openalex.org/W2109275727","doi":"https://doi.org/10.1093/bib/bbq068","title":"Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts","display_name":"Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts","publication_year":2010,"publication_date":"2010-11-08","ids":{"openalex":"https://openalex.org/W2109275727","doi":"https://doi.org/10.1093/bib/bbq068","mag":"2109275727","pmid":"https://pubmed.ncbi.nlm.nih.gov/21059603"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbq068","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbq068","pdf_url":"https://academic.oup.com/bib/article-pdf/12/6/626/589051/bbq068.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/12/6/626/589051/bbq068.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062078558","display_name":"Adam M. Szalkowski","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"A. M. Szalkowski","raw_affiliation_strings":["ETH Zurich, Universit\u00e4tstrasse 6, 8092 Z\u00fcrich, Switzerland. adam.szalkowski@inf.ethz.ch"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ETH Zurich, Universit\u00e4tstrasse 6, 8092 Z\u00fcrich, Switzerland. adam.szalkowski@inf.ethz.ch","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105777249","display_name":"Christof Schmid","orcid":null},"institutions":[{"id":"https://openalex.org/I158937107","display_name":"Swiss Tropical and Public Health Institute","ror":"https://ror.org/03adhka07","country_code":"CH","type":"facility","lineage":["https://openalex.org/I158937107"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210119349","display_name":"Karlsruhe University of Education","ror":"https://ror.org/01t1kq612","country_code":"DE","type":"education","lineage":["https://openalex.org/I4210119349"]}],"countries":["CH","DE"],"is_corresponding":false,"raw_author_name":"C. D. Schmid","raw_affiliation_strings":["Christoph Schmid is a Project Leader in Bioinformatics at the Swiss Tropical and Public Health Institute. His research interests focus on the analysis of massively parallel sequencing data","ETH Zurich, Universita \u00a8tstrasse 6, 8092 Zu \u00a8rich, Switzerland","University of Karlsruhe, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Christoph Schmid is a Project Leader in Bioinformatics at the Swiss Tropical and Public Health Institute. His research interests focus on the analysis of massively parallel sequencing data","institution_ids":["https://openalex.org/I158937107"]},{"raw_affiliation_string":"ETH Zurich, Universita \u00a8tstrasse 6, 8092 Zu \u00a8rich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"University of Karlsruhe, Germany","institution_ids":["https://openalex.org/I4210119349"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":2.1191,"has_fulltext":true,"cited_by_count":54,"citation_normalized_percentile":{"value":0.87090548,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"12","issue":"6","first_page":"626","last_page":"633"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994999766349792,"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":0.9983000159263611,"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/benchmarking","display_name":"Benchmarking","score":0.9396811723709106},{"id":"https://openalex.org/keywords/chromatin-immunoprecipitation","display_name":"Chromatin immunoprecipitation","score":0.7498487830162048},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.6476430296897888},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6132781505584717},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.503323495388031},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47107163071632385},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.45716962218284607},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.42124977707862854},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4163815379142761},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3985470235347748},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3491341173648834},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3410411477088928},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.29395562410354614},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23222616314888},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2012336254119873},{"id":"https://openalex.org/keywords/business","display_name":"Business","score":0.08930310606956482},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.07982686161994934},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.06744429469108582}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.9396811723709106},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.7498487830162048},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.6476430296897888},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6132781505584717},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.503323495388031},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47107163071632385},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.45716962218284607},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.42124977707862854},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4163815379142761},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3985470235347748},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3491341173648834},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3410411477088928},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.29395562410354614},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23222616314888},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2012336254119873},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.08930310606956482},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.07982686161994934},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.06744429469108582},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbq068","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbq068","pdf_url":"https://academic.oup.com/bib/article-pdf/12/6/626/589051/bbq068.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21059603","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21059603","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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbq068","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbq068","pdf_url":"https://academic.oup.com/bib/article-pdf/12/6/626/589051/bbq068.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6200000047683716}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320321652","display_name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich","ror":"https://ror.org/05a28rw58"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109275727.pdf","grobid_xml":"https://content.openalex.org/works/W2109275727.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1859302788","https://openalex.org/W1967656072","https://openalex.org/W1968475238","https://openalex.org/W1996212302","https://openalex.org/W1998544165","https://openalex.org/W2013336813","https://openalex.org/W2015416439","https://openalex.org/W2034002639","https://openalex.org/W2041835455","https://openalex.org/W2042392223","https://openalex.org/W2044164623","https://openalex.org/W2044937161","https://openalex.org/W2049260878","https://openalex.org/W2092387193","https://openalex.org/W2097220641","https://openalex.org/W2104865962","https://openalex.org/W2108075537","https://openalex.org/W2115137176","https://openalex.org/W2115979107","https://openalex.org/W2116305918","https://openalex.org/W2117897510","https://openalex.org/W2124163981","https://openalex.org/W2125114453","https://openalex.org/W2129795133","https://openalex.org/W2133130714","https://openalex.org/W2138891173","https://openalex.org/W2141222038","https://openalex.org/W2141408320","https://openalex.org/W2142570576","https://openalex.org/W2142808828","https://openalex.org/W2143076232","https://openalex.org/W2150038257","https://openalex.org/W2151754128","https://openalex.org/W2157979030","https://openalex.org/W2171111703","https://openalex.org/W2171808845"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2341842940","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2059640416","https://openalex.org/W2329895846"],"abstract_inverted_index":{"The":[0,63],"current":[1],"understanding":[2],"of":[3,6,20,42,47,57,65,76,111],"the":[4,11,14,18,54,83],"regulation":[5,38],"transcription":[7,37],"does":[8],"not":[9],"keep":[10],"pace":[12],"with":[13],"spectacular":[15],"advances":[16],"in":[17,82],"determination":[19],"genomic":[21],"sequences.":[22],"Chromatin":[23],"immunoprecipitation":[24],"followed":[25],"by":[26,39,60],"massively":[27],"parallel":[28],"sequencing":[29],"(ChIP-seq)":[30],"promises":[31],"to":[32],"give":[33],"better":[34],"insight":[35],"into":[36],"locating":[40],"sites":[41],"protein-DNA":[43],"interactions.":[44],"Such":[45],"loci":[46],"putative":[48],"interactions":[49],"can":[50],"be":[51],"inferred":[52],"from":[53],"genome-wide":[55],"distributions":[56],"ChIP-seq":[58,66],"data":[59,67],"peak-calling":[61,93,96],"software.":[62],"analysis":[64],"critically":[68],"depends":[69],"on":[70],"this":[71],"step":[72],"and":[73,107],"a":[74],"multitude":[75],"these":[77],"peak-callers":[78],"have":[79],"been":[80],"deployed":[81],"recent":[84,87],"years.":[85],"A":[86],"study":[88],"reported":[89],"severe":[90],"variation":[91],"among":[92],"results.":[94],"Yet,":[95],"still":[97],"lacks":[98],"systematic":[99],"quantitative":[100],"benchmarking.":[101],"Here,":[102],"we":[103],"summarize":[104],"benchmarking":[105,113],"efforts":[106],"explain":[108],"potential":[109],"drawbacks":[110],"each":[112],"method.":[114]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":7}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}