{"id":"https://openalex.org/W2433743436","doi":"https://doi.org/10.1093/bioinformatics/btw255","title":"Convolutional neural network architectures for predicting DNA\u2013protein binding","display_name":"Convolutional neural network architectures for predicting DNA\u2013protein binding","publication_year":2016,"publication_date":"2016-06-11","ids":{"openalex":"https://openalex.org/W2433743436","doi":"https://doi.org/10.1093/bioinformatics/btw255","mag":"2433743436","pmid":"https://pubmed.ncbi.nlm.nih.gov/27307608"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw255","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw255","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/12/i121/49020280/bioinformatics_32_12_i121.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/bioinformatics/article-pdf/32/12/i121/49020280/bioinformatics_32_12_i121.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015255518","display_name":"Haoyang Zeng","orcid":"https://orcid.org/0000-0003-1057-2865"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haoyang Zeng","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073999524","display_name":"Matthew D. Edwards","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew D. Edwards","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100731233","display_name":"Ge Liu","orcid":"https://orcid.org/0009-0008-5124-9929"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ge Liu","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082442738","display_name":"David K. Gifford","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David K. Gifford","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5082442738"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":32.5962,"has_fulltext":true,"cited_by_count":537,"citation_normalized_percentile":{"value":0.99811718,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"32","issue":"12","first_page":"i121","last_page":"i127"},"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":0.9994999766349792,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9983999729156494,"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/computer-science","display_name":"Computer science","score":0.75083327293396},{"id":"https://openalex.org/keywords/pooling","display_name":"Pooling","score":0.7367472052574158},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.726227879524231},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5623168349266052},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.544054388999939},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.538285493850708},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5373799800872803},{"id":"https://openalex.org/keywords/compendium","display_name":"Compendium","score":0.5040492415428162},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.47245219349861145},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.4534499943256378},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3354046642780304},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12248426675796509},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.11402082443237305}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.75083327293396},{"id":"https://openalex.org/C70437156","wikidata":"https://www.wikidata.org/wiki/Q7228652","display_name":"Pooling","level":2,"score":0.7367472052574158},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.726227879524231},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5623168349266052},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.544054388999939},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.538285493850708},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5373799800872803},{"id":"https://openalex.org/C2778473407","wikidata":"https://www.wikidata.org/wiki/Q1459574","display_name":"Compendium","level":2,"score":0.5040492415428162},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.47245219349861145},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4534499943256378},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3354046642780304},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12248426675796509},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.11402082443237305},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"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/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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:10.1093/bioinformatics/btw255","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw255","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/12/i121/49020280/bioinformatics_32_12_i121.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27307608","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27307608","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/12/i121","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/12/i121","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:pubmedcentral.nih.gov:4908339","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4908339","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw255","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw255","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/12/i121/49020280/bioinformatics_32_12_i121.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"No poverty","id":"https://metadata.un.org/sdg/1","score":0.5899999737739563}],"awards":[{"id":"https://openalex.org/G1801578602","display_name":null,"funder_award_id":"1U01HG007037","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3798249464","display_name":null,"funder_award_id":"5P01NS055923","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2433743436.pdf","grobid_xml":"https://content.openalex.org/works/W2433743436.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1936750108","https://openalex.org/W1988581590","https://openalex.org/W2095705004","https://openalex.org/W2112739286","https://openalex.org/W2120480077","https://openalex.org/W2134868027","https://openalex.org/W2155893237","https://openalex.org/W2157009395","https://openalex.org/W2164700406","https://openalex.org/W2198606573","https://openalex.org/W2259938310","https://openalex.org/W2519244818","https://openalex.org/W2604272474","https://openalex.org/W2919115771","https://openalex.org/W2950094539","https://openalex.org/W2952422028","https://openalex.org/W3147600416","https://openalex.org/W6640494244","https://openalex.org/W6674330103","https://openalex.org/W6764076272"],"related_works":["https://openalex.org/W2810679507","https://openalex.org/W2289742279","https://openalex.org/W2162836426","https://openalex.org/W2734802753","https://openalex.org/W2149312834","https://openalex.org/W3089376739","https://openalex.org/W3185263489","https://openalex.org/W2156159819","https://openalex.org/W2000233467","https://openalex.org/W2143172590"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":40},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":52},{"year":2022,"cited_by_count":47},{"year":2021,"cited_by_count":89},{"year":2020,"cited_by_count":87},{"year":2019,"cited_by_count":74},{"year":2018,"cited_by_count":70},{"year":2017,"cited_by_count":39},{"year":2016,"cited_by_count":4},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
