{"id":"https://openalex.org/W2997016650","doi":"https://doi.org/10.1186/s12859-019-3180-z","title":"DEEPSEN: a convolutional neural network based method for super-enhancer prediction","display_name":"DEEPSEN: a convolutional neural network based method for super-enhancer prediction","publication_year":2019,"publication_date":"2019-12-01","ids":{"openalex":"https://openalex.org/W2997016650","doi":"https://doi.org/10.1186/s12859-019-3180-z","mag":"2997016650","pmid":"https://pubmed.ncbi.nlm.nih.gov/31874597"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3180-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3180-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3180-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3180-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051265952","display_name":"Hongda Bu","orcid":null},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hongda Bu","raw_affiliation_strings":["Department of Computer Science and Technology, Tongji University, 4800 Cao'an Road, Shanghai, 201804, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Tongji University, 4800 Cao'an Road, Shanghai, 201804, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082393758","display_name":"Jiaqi Hao","orcid":"https://orcid.org/0009-0007-0909-7389"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaqi Hao","raw_affiliation_strings":["Department of Computer Science and Technology, Tongji University, 4800 Cao'an Road, Shanghai, 201804, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Tongji University, 4800 Cao'an Road, Shanghai, 201804, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076453110","display_name":"Yanglan Gan","orcid":"https://orcid.org/0000-0001-5931-9006"},"institutions":[{"id":"https://openalex.org/I181326427","display_name":"Donghua University","ror":"https://ror.org/035psfh38","country_code":"CN","type":"education","lineage":["https://openalex.org/I181326427"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanglan Gan","raw_affiliation_strings":["School of Computer Science and Technology, Donghua University, 2999 North Renmin Road, Shanghai, 201620, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Donghua University, 2999 North Renmin Road, Shanghai, 201620, China","institution_ids":["https://openalex.org/I181326427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017862559","display_name":"Shuigeng Zhou","orcid":"https://orcid.org/0000-0002-1949-2768"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuigeng Zhou","raw_affiliation_strings":["Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 220 Handan Road, Shanghai, 200433, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 220 Handan Road, Shanghai, 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086316879","display_name":"Jihong Guan","orcid":"https://orcid.org/0000-0003-2313-7635"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jihong Guan","raw_affiliation_strings":["Department of Computer Science and Technology, Tongji University, 4800 Cao'an Road, Shanghai, 201804, China. jhguan@tongji.edu.cn","Department of Computer Science and Technology, Tongji University, 4800 Cao'an Road, Shanghai, 201804, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Tongji University, 4800 Cao'an Road, Shanghai, 201804, China. jhguan@tongji.edu.cn","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science and Technology, Tongji University, 4800 Cao'an Road, Shanghai, 201804, China","institution_ids":["https://openalex.org/I116953780"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5051265952"],"corresponding_institution_ids":["https://openalex.org/I116953780"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.9423,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.75259511,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"20","issue":"S15","first_page":"598","last_page":"598"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":1.0,"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":1.0,"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/T10604","display_name":"RNA Research and Splicing","score":0.9986000061035156,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9947999715805054,"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/convolutional-neural-network","display_name":"Convolutional neural network","score":0.7307496070861816},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6617668271064758},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.6232190132141113},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5867980122566223},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5279216766357422},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.44093868136405945},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4151817858219147},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33753570914268494},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3336295783519745},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2644997239112854},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14617088437080383},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13369914889335632},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09679439663887024}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7307496070861816},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6617668271064758},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.6232190132141113},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5867980122566223},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5279216766357422},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44093868136405945},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4151817858219147},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33753570914268494},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3336295783519745},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2644997239112854},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14617088437080383},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13369914889335632},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09679439663887024}],"mesh":[{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-3180-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3180-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3180-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31874597","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31874597","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 bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:792af01eb5254034bbfbf6c69f9defe8","is_oa":true,"landing_page_url":"https://doaj.org/article/792af01eb5254034bbfbf6c69f9defe8","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss S15, Pp 1-9 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6929276","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6929276","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3180-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3180-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3180-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G229208632","display_name":null,"funder_award_id":"No. 17ZR1400200","funder_id":"https://openalex.org/F4320309612","funder_display_name":"Natural Science Foundation of Shanghai"},{"id":"https://openalex.org/G2504302143","display_name":null,"funder_award_id":"61772367","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4924742943","display_name":null,"funder_award_id":"2016YFC0901704","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5167091242","display_name":null,"funder_award_id":"No. 1","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5930665148","display_name":null,"funder_award_id":"17ZR1400200","funder_id":"https://openalex.org/F4320309612","funder_display_name":"Natural Science Foundation of Shanghai"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6737139634","display_name":null,"funder_award_id":"No. 61772367","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8114646031","display_name":null,"funder_award_id":"2016Y","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G850960841","display_name":null,"funder_award_id":"2016YFC","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320309612","display_name":"Natural Science Foundation of Shanghai","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2997016650.pdf","grobid_xml":"https://content.openalex.org/works/W2997016650.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1498436455","https://openalex.org/W1964963969","https://openalex.org/W1970831058","https://openalex.org/W1971578941","https://openalex.org/W2004966039","https://openalex.org/W2015416439","https://openalex.org/W2016015848","https://openalex.org/W2060484997","https://openalex.org/W2067956561","https://openalex.org/W2089894746","https://openalex.org/W2095705004","https://openalex.org/W2103393606","https://openalex.org/W2124985265","https://openalex.org/W2128151873","https://openalex.org/W2129795133","https://openalex.org/W2151754128","https://openalex.org/W2157810029","https://openalex.org/W2198606573","https://openalex.org/W2259938310","https://openalex.org/W2586783543","https://openalex.org/W3098248235"],"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/W2972483091","https://openalex.org/W2164437319","https://openalex.org/W2917637208","https://openalex.org/W2054923215"],"abstract_inverted_index":{"Convolutional":[0],"neural":[1],"network":[2],"is":[3],"effective":[4],"in":[5],"boosting":[6],"the":[7],"performance":[8],"of":[9],"super-enhancer":[10],"prediction.":[11]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}