{"id":"https://openalex.org/W2060387155","doi":"https://doi.org/10.1093/bib/bbq060","title":"Evolution of gene regulation--on the road towards computational inferences","display_name":"Evolution of gene regulation--on the road towards computational inferences","publication_year":2010,"publication_date":"2010-08-11","ids":{"openalex":"https://openalex.org/W2060387155","doi":"https://doi.org/10.1093/bib/bbq060","mag":"2060387155","pmid":"https://pubmed.ncbi.nlm.nih.gov/20702596"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbq060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbq060","pdf_url":"https://academic.oup.com/bib/article-pdf/12/2/122/726069/bbq060.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/12/2/122/726069/bbq060.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089023752","display_name":"Georg Fuellen","orcid":"https://orcid.org/0000-0002-4994-9829"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"G. Fuellen","raw_affiliation_strings":["Institute for Biostatistics and Informatics in Medicine and Ageing Research-IBIMA, University of Rostock, Medical Faculty, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany. fuellen@uni-rostock.de","Institute for Biostatistics and Informatics in Medicine and Ageing Research - IBIMA, University of Rostock, Medical Faculty, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Biostatistics and Informatics in Medicine and Ageing Research-IBIMA, University of Rostock, Medical Faculty, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany. fuellen@uni-rostock.de","institution_ids":["https://openalex.org/I4665924"]},{"raw_affiliation_string":"Institute for Biostatistics and Informatics in Medicine and Ageing Research - IBIMA, University of Rostock, Medical Faculty, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5089023752"],"corresponding_institution_ids":["https://openalex.org/I4665924"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":0.7479,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.69234159,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"12","issue":"2","first_page":"122","last_page":"131"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9990000128746033,"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":0.9990000128746033,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12929","display_name":"Animal Genetics and Reproduction","score":0.9943000078201294,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/gene","display_name":"Gene","score":0.6544029116630554},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6088811755180359},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5899002552032471},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5766516327857971},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5115616917610168},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5069018006324768},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.4795477092266083},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.47697529196739197},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4753023087978363},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.4549611806869507},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"Transcriptional regulation","score":0.44614213705062866},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.428718239068985},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4183924198150635},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.41280174255371094},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.22916874289512634},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.21783417463302612}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6544029116630554},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6088811755180359},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5899002552032471},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5766516327857971},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5115616917610168},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5069018006324768},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4795477092266083},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.47697529196739197},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4753023087978363},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4549611806869507},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.44614213705062866},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.428718239068985},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4183924198150635},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.41280174255371094},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.22916874289512634},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.21783417463302612},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbq060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbq060","pdf_url":"https://academic.oup.com/bib/article-pdf/12/2/122/726069/bbq060.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:20702596","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20702596","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/bbq060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbq060","pdf_url":"https://academic.oup.com/bib/article-pdf/12/2/122/726069/bbq060.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":[],"awards":[{"id":"https://openalex.org/G2304404308","display_name":null,"funder_award_id":"SPP 1356","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6752722531","display_name":"Verbundprojekt: Podozyten aus adulten multipotenten Progenitorzellen; Teilprojekt 3 (Bioinformatik/Netzwerkanalysen)","funder_award_id":"01GN0901","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2060387155.pdf","grobid_xml":"https://content.openalex.org/works/W2060387155.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W1970212790","https://openalex.org/W1976150153","https://openalex.org/W1978240236","https://openalex.org/W1981723163","https://openalex.org/W1986548033","https://openalex.org/W1989608726","https://openalex.org/W1993252465","https://openalex.org/W1994158184","https://openalex.org/W2006711870","https://openalex.org/W2010204279","https://openalex.org/W2015900846","https://openalex.org/W2017668215","https://openalex.org/W2023508819","https://openalex.org/W2023635398","https://openalex.org/W2026074998","https://openalex.org/W2029375121","https://openalex.org/W2032293502","https://openalex.org/W2036511906","https://openalex.org/W2047001743","https://openalex.org/W2049311981","https://openalex.org/W2052590262","https://openalex.org/W2057885377","https://openalex.org/W2058288932","https://openalex.org/W2060399360","https://openalex.org/W2063566427","https://openalex.org/W2066624398","https://openalex.org/W2071241326","https://openalex.org/W2072972020","https://openalex.org/W2092638438","https://openalex.org/W2095573498","https://openalex.org/W2095595375","https://openalex.org/W2105134201","https://openalex.org/W2105291162","https://openalex.org/W2105796031","https://openalex.org/W2107575419","https://openalex.org/W2109314645","https://openalex.org/W2110015307","https://openalex.org/W2110451680","https://openalex.org/W2118533197","https://openalex.org/W2118596665","https://openalex.org/W2121271640","https://openalex.org/W2125164550","https://openalex.org/W2128016314","https://openalex.org/W2128035760","https://openalex.org/W2128713736","https://openalex.org/W2129061533","https://openalex.org/W2135859486","https://openalex.org/W2140741853","https://openalex.org/W2142067151","https://openalex.org/W2147710217","https://openalex.org/W2150681269","https://openalex.org/W2156885385","https://openalex.org/W2159164310","https://openalex.org/W2159433765","https://openalex.org/W2159861974","https://openalex.org/W2163141464","https://openalex.org/W2166425625","https://openalex.org/W2166894044","https://openalex.org/W2167934696","https://openalex.org/W2168571706","https://openalex.org/W2171193618","https://openalex.org/W2171689933","https://openalex.org/W4252706339"],"related_works":["https://openalex.org/W2010571965","https://openalex.org/W2912720016","https://openalex.org/W2002709996","https://openalex.org/W3128451840","https://openalex.org/W4387092964","https://openalex.org/W2103471012","https://openalex.org/W2277277196","https://openalex.org/W2043274041","https://openalex.org/W2620422757","https://openalex.org/W2056161765"],"abstract_inverted_index":{"If":[0],"fragments":[1],"of":[2,34,41,68,76,106,127,137,143,147,157,173,181,192,205],"DNA":[3,44],"are":[4,100,161],"transcribed":[5],"(expressed),":[6],"they":[7],"deserve":[8],"to":[9,201],"be":[10,185],"called":[11],"(parts":[12],"of)":[13],"a":[14,63,109],"gene.":[15],"Whether":[16],"transcription":[17,129],"takes":[18],"place":[19],"depends":[20],"on":[21,85,178],"the":[22,31,35,42,46,55,74,77,86,95,120,124,135,141,144,158,170,179,193,203],"'gene":[23],"regulatory":[24,47,60],"network'.":[25],"This":[26],"network":[27],"is":[28,91],"defined":[29],"as":[30,70,72,150],"complex":[32],"interplay":[33],"sequence,":[36],"biochemical":[37],"modifications":[38],"and":[39,54,97,165],"structure":[40],"chromosomal":[43],"with":[45],"proteins/RNA":[48],"(transcription":[49],"factors,":[50],"co-factors,":[51],"regulating":[52],"RNA":[53],"transcriptional":[56],"apparatus":[57],"itself).":[58],"Gene":[59],"networks":[61],"play":[62],"role":[64],"in":[65,73,79,101,119,140],"various":[66],"stages":[67],"development":[69],"well":[71],"maintenance":[75],"organism;":[78],"this":[80],"review":[81],"we":[82,188],"will":[83],"concentrate":[84],"former.":[87],"Their":[88],"evolutionary":[89,114],"reconstruction":[90],"daunting":[92],"(to":[93],"say":[94],"least),":[96],"bioinformatics":[98,175],"tools":[99],"their":[102,166],"infancy.":[103],"However,":[104],"gain":[105],"understanding":[107],"offers":[108],"reward":[110],"beyond":[111],"itself,":[112],"since":[113],"considerations":[115],"can":[116],"enable":[117],"discoveries":[118],"first":[121],"place,":[122],"e.g.":[123],"computational":[125],"identification":[126],"conserved":[128],"factor":[130],"binding":[131],"sites.":[132],"We":[133,168],"discuss":[134,169],"evolution":[136,180,204],"gene":[138,182,206],"regulation":[139,183],"context":[142],"'Genetic":[145],"Theory":[146],"Morphological":[148],"Evolution'":[149],"described":[151],"by":[152],"Carroll,":[153],"identifying":[154],"those":[155],"parts":[156],"theory":[159],"that":[160],"relevant":[162],"for":[163],"bioinformatics,":[164],"implications.":[167],"important":[171],"question":[172],"how":[174],"analysis":[176],"results":[177],"may":[184],"validated.":[186],"Finally,":[187],"briefly":[189],"exemplify":[190],"use":[191],"UCSC":[194],"genome":[195],"browser,":[196],"exploiting":[197],"its":[198],"pre-computed":[199],"alignments":[200],"describe":[202],"regulation.":[207]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
