{"id":"https://openalex.org/W4292723135","doi":"https://doi.org/10.1093/bioinformatics/btac569","title":"NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction","display_name":"NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction","publication_year":2022,"publication_date":"2022-08-23","ids":{"openalex":"https://openalex.org/W4292723135","doi":"https://doi.org/10.1093/bioinformatics/btac569","pmid":"https://pubmed.ncbi.nlm.nih.gov/35997560"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac569","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac569","pdf_url":null,"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":null,"license_id":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9563695","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101915554","display_name":"Ren Yi","orcid":"https://orcid.org/0000-0002-0238-3573"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ren Yi","raw_affiliation_strings":["Department of Computer Science, New York University , New York, NY 10011, USA","New York University Department of Computer Science, , New York, NY, 10011, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New York University , New York, NY 10011, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"New York University Department of Computer Science, , New York, NY, 10011, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091175785","display_name":"Kyunghyun Cho","orcid":"https://orcid.org/0000-0003-1669-3211"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyunghyun Cho","raw_affiliation_strings":["Center for Data Science, New York University , New York, NY 10011, USA","Department of Computer Science, New York University , New York, NY 10011, USA","Prescient Design, a Genentech accelerator , New York, NY 10010, USA","New York University Department of Computer Science, , New York, NY, 10011, USA; Prescient Design, a Genentech accelerator , New York, NY, 10010, USA"],"affiliations":[{"raw_affiliation_string":"Center for Data Science, New York University , New York, NY 10011, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Department of Computer Science, New York University , New York, NY 10011, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Prescient Design, a Genentech accelerator , New York, NY 10010, USA","institution_ids":[]},{"raw_affiliation_string":"New York University Department of Computer Science, , New York, NY, 10011, USA; Prescient Design, a Genentech accelerator , New York, NY, 10010, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055203249","display_name":"Richard Bonneau","orcid":"https://orcid.org/0000-0003-4354-7906"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard Bonneau","raw_affiliation_strings":["Center for Data Science, New York University , New York, NY 10011, USA","Department of Biology, New York University , New York, NY 10003, USA","Department of Computer Science, New York University , New York, NY 10011, USA","Prescient Design, a Genentech accelerator , New York, NY 10010, USA","New York University Department of Computer Science, , New York, NY, 10011, USA; Prescient Design, a Genentech accelerator , New York, NY, 10010, USA"],"affiliations":[{"raw_affiliation_string":"Center for Data Science, New York University , New York, NY 10011, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Department of Biology, New York University , New York, NY 10003, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Department of Computer Science, New York University , New York, NY 10011, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Prescient Design, a Genentech accelerator , New York, NY 10010, USA","institution_ids":[]},{"raw_affiliation_string":"New York University Department of Computer Science, , New York, NY, 10011, USA; Prescient Design, a Genentech accelerator , New York, NY, 10010, USA","institution_ids":["https://openalex.org/I57206974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101915554"],"corresponding_institution_ids":["https://openalex.org/I57206974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0858,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.42357682,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"38","issue":"20","first_page":"4762","last_page":"4770"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9901000261306763,"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":0.9865000247955322,"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":0.702978253364563},{"id":"https://openalex.org/keywords/multi-task-learning","display_name":"Multi-task learning","score":0.699256181716919},{"id":"https://openalex.org/keywords/transfer-of-learning","display_name":"Transfer of learning","score":0.6336613297462463},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6168485879898071},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5806028842926025},{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.5285619497299194},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3852628469467163},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.3834607005119324}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.702978253364563},{"id":"https://openalex.org/C28006648","wikidata":"https://www.wikidata.org/wiki/Q6934509","display_name":"Multi-task learning","level":3,"score":0.699256181716919},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.6336613297462463},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6168485879898071},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5806028842926025},{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.5285619497299194},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3852628469467163},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.3834607005119324},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac569","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac569","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35997560","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35997560","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:pubmedcentral.nih.gov:9563695","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9563695","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9563695","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9563695","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1086972642","display_name":null,"funder_award_id":"R01NS116350","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1327343320","display_name":null,"funder_award_id":"R35GM122515","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2726022791","display_name":null,"funder_award_id":"IOS-1546218","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4004435369","display_name":null,"funder_award_id":"R01HD096770","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320315121","display_name":"Samsung Advanced Institute of Technology","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1501531009","https://openalex.org/W1573323739","https://openalex.org/W1592870802","https://openalex.org/W1972792790","https://openalex.org/W1981030303","https://openalex.org/W1984173288","https://openalex.org/W1989419347","https://openalex.org/W1992436001","https://openalex.org/W2045362835","https://openalex.org/W2064675550","https://openalex.org/W2068379897","https://openalex.org/W2076513103","https://openalex.org/W2087592728","https://openalex.org/W2096863518","https://openalex.org/W2101231992","https://openalex.org/W2103777723","https://openalex.org/W2114709909","https://openalex.org/W2117757143","https://openalex.org/W2129795133","https://openalex.org/W2145091349","https://openalex.org/W2152941516","https://openalex.org/W2153561273","https://openalex.org/W2159324718","https://openalex.org/W2171111703","https://openalex.org/W2187089797","https://openalex.org/W2198606573","https://openalex.org/W2336509392","https://openalex.org/W2409532517","https://openalex.org/W2554247923","https://openalex.org/W2589838901","https://openalex.org/W2776802713","https://openalex.org/W2794084858","https://openalex.org/W2795927426","https://openalex.org/W2805619986","https://openalex.org/W2883594174","https://openalex.org/W2883945062","https://openalex.org/W2904110212","https://openalex.org/W2909781225","https://openalex.org/W2912321349","https://openalex.org/W2913340405","https://openalex.org/W2951410692","https://openalex.org/W2951529022","https://openalex.org/W2951644416","https://openalex.org/W2951890754","https://openalex.org/W2951934944","https://openalex.org/W2952239877","https://openalex.org/W2967923991","https://openalex.org/W2977079874","https://openalex.org/W2978541146","https://openalex.org/W2982420272","https://openalex.org/W2996140569","https://openalex.org/W3013690547","https://openalex.org/W3045910546","https://openalex.org/W3122486793","https://openalex.org/W3130819465","https://openalex.org/W3137533336","https://openalex.org/W3139265997","https://openalex.org/W3203588026","https://openalex.org/W3204042176","https://openalex.org/W4206192903","https://openalex.org/W4255421341","https://openalex.org/W6749706356"],"related_works":["https://openalex.org/W2821676139","https://openalex.org/W3043695725","https://openalex.org/W4382138864","https://openalex.org/W4387770285","https://openalex.org/W3022215768","https://openalex.org/W3135975972","https://openalex.org/W3016888008","https://openalex.org/W4385864216","https://openalex.org/W4387183713","https://openalex.org/W4403518771"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}