{"id":"https://openalex.org/W2183523328","doi":"https://doi.org/10.1093/bib/bbv101","title":"Progress and challenges in bioinformatics approaches for enhancer identification","display_name":"Progress and challenges in bioinformatics approaches for enhancer identification","publication_year":2015,"publication_date":"2015-12-03","ids":{"openalex":"https://openalex.org/W2183523328","doi":"https://doi.org/10.1093/bib/bbv101","mag":"2183523328","pmid":"https://pubmed.ncbi.nlm.nih.gov/26634919"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv101","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv101","pdf_url":"https://academic.oup.com/bib/article-pdf/17/6/967/8280356/bbv101.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/17/6/967/8280356/bbv101.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064001499","display_name":"Dimitrios Kleftogiannis","orcid":"https://orcid.org/0000-0003-1086-821X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Dimitrios Kleftogiannis","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014399734","display_name":"Panos Kalnis","orcid":"https://orcid.org/0000-0002-5060-1360"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Panos Kalnis","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5055569646","display_name":"Vladimir B. Baji\u0107","orcid":"https://orcid.org/0000-0001-5435-4750"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Vladimir B. Bajic","raw_affiliation_strings":["KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY"],"affiliations":[{"raw_affiliation_string":"KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5064001499"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.615,"has_fulltext":false,"cited_by_count":111,"citation_normalized_percentile":{"value":0.93631076,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"17","issue":"6","first_page":"967","last_page":"979"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"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":0.9994000196456909,"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/T12254","display_name":"Machine Learning in Bioinformatics","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987000226974487,"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/enhancer","display_name":"Enhancer","score":0.8876075744628906},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.7654320597648621},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7318251132965088},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5807963013648987},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.4740716516971588},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37722116708755493},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22344207763671875},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17898264527320862},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15513062477111816},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13688835501670837}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.8876075744628906},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7654320597648621},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7318251132965088},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5807963013648987},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.4740716516971588},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37722116708755493},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22344207763671875},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17898264527320862},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15513062477111816},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13688835501670837},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bbv101","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv101","pdf_url":"https://academic.oup.com/bib/article-pdf/17/6/967/8280356/bbv101.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26634919","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26634919","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":null},{"id":"pmh:oai:europepmc.org:4088881","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5142011","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bib:17/6/967","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/6/967","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"},{"id":"pmh:oai:repository.kaust.edu.sa:10754/622949","is_oa":true,"landing_page_url":"http://hdl.handle.net/10754/622949","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv101","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv101","pdf_url":"https://academic.oup.com/bib/article-pdf/17/6/967/8280356/bbv101.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2183523328.pdf","grobid_xml":"https://content.openalex.org/works/W2183523328.grobid-xml"},"referenced_works_count":107,"referenced_works":["https://openalex.org/W571682839","https://openalex.org/W1506066766","https://openalex.org/W1964963969","https://openalex.org/W1968083284","https://openalex.org/W1973518241","https://openalex.org/W1976209715","https://openalex.org/W1978240236","https://openalex.org/W1985621639","https://openalex.org/W1986586739","https://openalex.org/W1986865417","https://openalex.org/W1987523347","https://openalex.org/W1988581590","https://openalex.org/W1989004527","https://openalex.org/W1991740019","https://openalex.org/W1997590968","https://openalex.org/W1998306196","https://openalex.org/W2000515602","https://openalex.org/W2002832354","https://openalex.org/W2006918465","https://openalex.org/W2007694108","https://openalex.org/W2008226163","https://openalex.org/W2010789111","https://openalex.org/W2014787267","https://openalex.org/W2015845481","https://openalex.org/W2016015848","https://openalex.org/W2018363492","https://openalex.org/W2019251848","https://openalex.org/W2020046094","https://openalex.org/W2022993325","https://openalex.org/W2023386301","https://openalex.org/W2026690931","https://openalex.org/W2029949273","https://openalex.org/W2030545812","https://openalex.org/W2033201031","https://openalex.org/W2034502656","https://openalex.org/W2043485161","https://openalex.org/W2044164623","https://openalex.org/W2046842005","https://openalex.org/W2048263136","https://openalex.org/W2060484997","https://openalex.org/W2063815548","https://openalex.org/W2067956561","https://openalex.org/W2068607091","https://openalex.org/W2071206791","https://openalex.org/W2073700708","https://openalex.org/W2075016035","https://openalex.org/W2077874719","https://openalex.org/W2078034709","https://openalex.org/W2080466240","https://openalex.org/W2084160423","https://openalex.org/W2091533196","https://openalex.org/W2094468530","https://openalex.org/W2098071274","https://openalex.org/W2098740506","https://openalex.org/W2100847260","https://openalex.org/W2104698381","https://openalex.org/W2105081948","https://openalex.org/W2107916366","https://openalex.org/W2112500061","https://openalex.org/W2113974339","https://openalex.org/W2115272837","https://openalex.org/W2117247812","https://openalex.org/W2117792884","https://openalex.org/W2118646732","https://openalex.org/W2119000216","https://openalex.org/W2119419044","https://openalex.org/W2122692578","https://openalex.org/W2123564569","https://openalex.org/W2124025352","https://openalex.org/W2127230663","https://openalex.org/W2127835459","https://openalex.org/W2128817132","https://openalex.org/W2134854530","https://openalex.org/W2135993011","https://openalex.org/W2137255856","https://openalex.org/W2137704220","https://openalex.org/W2140240158","https://openalex.org/W2142410561","https://openalex.org/W2145674897","https://openalex.org/W2146648681","https://openalex.org/W2147144635","https://openalex.org/W2150009446","https://openalex.org/W2151754128","https://openalex.org/W2152257990","https://openalex.org/W2154706222","https://openalex.org/W2154746182","https://openalex.org/W2154855927","https://openalex.org/W2155484811","https://openalex.org/W2155717510","https://openalex.org/W2157750191","https://openalex.org/W2158670138","https://openalex.org/W2159164310","https://openalex.org/W2159664283","https://openalex.org/W2160655220","https://openalex.org/W2164354446","https://openalex.org/W2165102934","https://openalex.org/W2165460636","https://openalex.org/W2168191908","https://openalex.org/W2168602111","https://openalex.org/W2168909179","https://openalex.org/W2169056802","https://openalex.org/W2169819154","https://openalex.org/W2171808845","https://openalex.org/W2952358992","https://openalex.org/W4230875896","https://openalex.org/W4233310067","https://openalex.org/W4252183347"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W1641042124","https://openalex.org/W2152841149","https://openalex.org/W2586783543","https://openalex.org/W4387598842","https://openalex.org/W2973036402","https://openalex.org/W2745970610"],"abstract_inverted_index":{"Enhancers":[0],"are":[1],"cis-acting":[2],"DNA":[3],"elements":[4],"that":[5,27,83,194],"play":[6],"critical":[7],"roles":[8],"in":[9,47,68,109,146],"distal":[10],"regulation":[11],"of":[12,37,44,90,101,121,140,159,173,212,226],"gene":[13,24],"expression.":[14],"Identifying":[15],"enhancers":[16,38,92,103,122,160],"is":[17,39],"an":[18,138],"important":[19],"step":[20],"for":[21,79,87,117,132,170,210],"understanding":[22],"distinct":[23],"expression":[25],"programs":[26],"may":[28],"reflect":[29],"normal":[30],"and":[31,99,107,143,157,179,204,223],"pathogenic":[32],"cellular":[33,64,73],"conditions.":[34],"Experimental":[35],"identification":[36,89,156,172,192],"constrained":[40],"by":[41,161],"the":[42,48,114,118,133,141,155],"set":[43],"conditions":[45,65],"used":[46,86],"experiment.":[49],"This":[50,75],"requires":[51],"multiple":[52],"experiments":[53],"to":[54,93,136],"identify":[55],"enhancers,":[56,174],"as":[57],"they":[58],"can":[59,84],"be":[60,85,130],"active":[61],"under":[62],"specific":[63],"but":[66],"not":[67],"different":[69,125],"cell":[70],"types/tissues":[71],"or":[72],"states.":[74],"has":[76],"opened":[77],"prospects":[78],"computational":[80,119,171,182,190,215],"prediction":[81,120,217],"methods":[82,116,193],"high-throughput":[88],"putative":[91],"complement":[94],"experimental":[95],"approaches.":[96,163],"Potential":[97],"functions":[98],"properties":[100],"predicted":[102],"have":[104,137],"been":[105],"catalogued":[106],"summarized":[108],"several":[110],"enhancer-oriented":[111],"databases.":[112],"Because":[113],"current":[115],"produce":[123],"significantly":[124],"enhancer":[126,191,216],"predictions,":[127],"it":[128],"will":[129],"beneficial":[131],"research":[134],"community":[135],"overview":[139],"strategies":[142],"solutions":[144],"developed":[145,196],"this":[147,150,227],"field.":[148],"In":[149],"review,":[151],"we":[152,165,185,220],"focus":[153],"on":[154],"analysis":[158],"bioinformatics":[162],"First,":[164],"describe":[166],"a":[167],"general":[168],"framework":[169],"present":[175],"relevant":[176],"data":[177],"types":[178],"discuss":[180,221],"possible":[181],"solutions.":[183],"Next,":[184],"cover":[186],"over":[187],"30":[188],"existing":[189],"were":[195],"since":[197],"2000.":[198],"Our":[199],"review":[200],"highlights":[201],"advantages,":[202],"limitations":[203],"potentials,":[205],"while":[206],"suggesting":[207],"pragmatic":[208],"guidelines":[209],"development":[211],"more":[213],"efficient":[214],"methods.":[218],"Finally,":[219],"challenges":[222],"open":[224],"problems":[225],"topic,":[228],"which":[229],"require":[230],"further":[231],"consideration.":[232]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":19},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":6}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
