{"id":"https://openalex.org/W2475924856","doi":"https://doi.org/10.1186/s12918-016-0302-3","title":"Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions","display_name":"Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions","publication_year":2016,"publication_date":"2016-08-01","ids":{"openalex":"https://openalex.org/W2475924856","doi":"https://doi.org/10.1186/s12918-016-0302-3","mag":"2475924856","pmid":"https://pubmed.ncbi.nlm.nih.gov/27490187"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-016-0302-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0302-3","pdf_url":null,"source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.1186/s12918-016-0302-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080573103","display_name":"Seong\u2010Gon Kim","orcid":"https://orcid.org/0000-0001-5088-2732"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Seong Gon Kim","raw_affiliation_strings":["Department of Computer Science, Purdue University, West Lafayette, IN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070708809","display_name":"Nawanol Theera-Ampornpunt","orcid":"https://orcid.org/0000-0002-7594-8061"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nawanol Theera-Ampornpunt","raw_affiliation_strings":["Department of Computer Science, Purdue University, West Lafayette, IN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055672710","display_name":"Chih-Hao Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chih-Hao Fang","raw_affiliation_strings":["Department of Computer Science, Purdue University, West Lafayette, IN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004916726","display_name":"Mrudul Harwani","orcid":null},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mrudul Harwani","raw_affiliation_strings":["Department of Computer Science, Purdue University, West Lafayette, IN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019202832","display_name":"Ananth Grama","orcid":"https://orcid.org/0000-0002-9378-9244"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ananth Grama","raw_affiliation_strings":["Department of Computer Science, Purdue University, West Lafayette, IN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055585728","display_name":"Somali Chaterji","orcid":"https://orcid.org/0000-0002-3651-6362"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Somali Chaterji","raw_affiliation_strings":["Department of Computer Science, Purdue University, West Lafayette, IN, USA. schaterj@purdue.edu","Department of Computer Science, Purdue University, West Lafayette, IN, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, IN, USA. schaterj@purdue.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5080573103"],"corresponding_institution_ids":["https://openalex.org/I219193219"],"apc_list":null,"apc_paid":null,"fwci":2.2662,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.88166451,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"10","issue":"S2","first_page":"54","last_page":"54"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9915000200271606,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10604","display_name":"RNA Research and Splicing","score":0.9772999882698059,"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":0.7076870799064636},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6429550051689148},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6382066011428833},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6317172050476074},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.6190164089202881},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5047005414962769},{"id":"https://openalex.org/keywords/deep-neural-networks","display_name":"Deep neural networks","score":0.45019155740737915},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.44319865107536316},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.41986629366874695},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3708920478820801},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3294064998626709},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2685128450393677},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.11975550651550293},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06890633702278137}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.7076870799064636},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6429550051689148},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6382066011428833},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6317172050476074},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.6190164089202881},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5047005414962769},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.45019155740737915},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.44319865107536316},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.41986629366874695},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3708920478820801},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3294064998626709},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2685128450393677},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.11975550651550293},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06890633702278137},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12918-016-0302-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0302-3","pdf_url":null,"source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:27490187","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27490187","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4977478","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4977478","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-016-0302-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0302-3","pdf_url":null,"source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W189091806","https://openalex.org/W1543604048","https://openalex.org/W1900657670","https://openalex.org/W1963553964","https://openalex.org/W1965425724","https://openalex.org/W1968083284","https://openalex.org/W1976140288","https://openalex.org/W1977855308","https://openalex.org/W1979521131","https://openalex.org/W1979821700","https://openalex.org/W1986223165","https://openalex.org/W1986586739","https://openalex.org/W1986865417","https://openalex.org/W1996060670","https://openalex.org/W2006252838","https://openalex.org/W2016015848","https://openalex.org/W2022993325","https://openalex.org/W2029236612","https://openalex.org/W2036619779","https://openalex.org/W2039309132","https://openalex.org/W2045362835","https://openalex.org/W2067956561","https://openalex.org/W2073700708","https://openalex.org/W2084160423","https://openalex.org/W2091432990","https://openalex.org/W2094678200","https://openalex.org/W2095705004","https://openalex.org/W2102017903","https://openalex.org/W2102619694","https://openalex.org/W2115272837","https://openalex.org/W2116584178","https://openalex.org/W2117723622","https://openalex.org/W2118646732","https://openalex.org/W2128817132","https://openalex.org/W2134854530","https://openalex.org/W2140240158","https://openalex.org/W2142946358","https://openalex.org/W2145144631","https://openalex.org/W2151754128","https://openalex.org/W2152635629","https://openalex.org/W2157444450","https://openalex.org/W2160815625","https://openalex.org/W2164240145","https://openalex.org/W2168602111","https://openalex.org/W2187089797","https://openalex.org/W2259938310","https://openalex.org/W4299828299","https://openalex.org/W6675112735","https://openalex.org/W6683161245"],"related_works":["https://openalex.org/W2113330652","https://openalex.org/W2061914098","https://openalex.org/W4309683845","https://openalex.org/W2118646732","https://openalex.org/W4387565139","https://openalex.org/W4389440207","https://openalex.org/W4377865163","https://openalex.org/W3193857078","https://openalex.org/W2888956734","https://openalex.org/W3208304128"],"abstract_inverted_index":{"In":[0],"this":[1],"paper,":[2],"we":[3,31,38],"developed":[4,39],"EP-DNN,":[5],"which":[6,49,57],"has":[7],"high":[8],"accuracy":[9],"of":[10,22],"prediction,":[11],"with":[12],"validation":[13],"rates":[14],"above":[15],"90":[16],"%":[17],"for":[18,25],"the":[19,63],"operational":[20],"region":[21],"enhancer":[23,64],"prediction":[24],"all":[26],"four":[27],"cell":[28],"lines":[29],"that":[30],"studied,":[32],"outperforming":[33],"DEEP-ENCODE":[34],"and":[35,47,54],"RFECS.":[36],"Then,":[37],"a":[40,44],"method":[41],"to":[42,62],"analyze":[43],"trained":[45],"DNN":[46],"determine":[48],"histone":[50],"modifications":[51],"are":[52,66],"important,":[53],"within":[55],"that,":[56],"features":[58],"proximal":[59],"or":[60],"distal":[61],"site,":[65],"important.":[67]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}