{"id":"https://openalex.org/W2739636023","doi":"https://doi.org/10.1093/bioinformatics/btx480","title":"Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape","display_name":"Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape","publication_year":2017,"publication_date":"2017-07-26","ids":{"openalex":"https://openalex.org/W2739636023","doi":"https://doi.org/10.1093/bioinformatics/btx480","mag":"2739636023","pmid":"https://pubmed.ncbi.nlm.nih.gov/28961686"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx480","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx480","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/22/3575/25167488/btx480.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":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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/22/3575/25167488/btx480.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040269658","display_name":"Hanjun Dai","orcid":null},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanjun Dai","raw_affiliation_strings":["College of Computing, Georgia Institute of Technology, Atlanta, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computing, Georgia Institute of Technology, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033647731","display_name":"Ramzan Umarov","orcid":"https://orcid.org/0000-0003-3477-7101"},"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":"Ramzan Umarov","raw_affiliation_strings":["King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005997934","display_name":"Hiroyuki Kuwahara","orcid":"https://orcid.org/0000-0001-5333-6729"},"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":"Hiroyuki Kuwahara","raw_affiliation_strings":["King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100345753","display_name":"Yu Li","orcid":"https://orcid.org/0000-0002-3664-6722"},"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":"Yu Li","raw_affiliation_strings":["King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030589527","display_name":"Le Song","orcid":"https://orcid.org/0000-0002-9655-2787"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Le Song","raw_affiliation_strings":["College of Computing, Georgia Institute of Technology, Atlanta, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computing, Georgia Institute of Technology, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100618900","display_name":"Xin Gao","orcid":"https://orcid.org/0000-0002-7108-3574"},"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":true,"raw_author_name":"Xin Gao","raw_affiliation_strings":["King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5030589527","https://openalex.org/A5100618900"],"corresponding_institution_ids":["https://openalex.org/I130701444","https://openalex.org/I71920554"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2433,"has_fulltext":false,"cited_by_count":54,"citation_normalized_percentile":{"value":0.88533572,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"33","issue":"22","first_page":"3575","last_page":"3583"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8575999736785889,"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":0.8575999736785889,"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":0.05260000005364418,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.021199999377131462,"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/embedding","display_name":"Embedding","score":0.6533569693565369},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5994544625282288},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5526132583618164},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.530657172203064},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5012304782867432},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4680114984512329},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.4602370262145996},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.45775899291038513},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4409443438053131},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4272116422653198},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4220316410064697},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.41119423508644104},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20389509201049805},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18008458614349365},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1200147271156311},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.0983177125453949}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6533569693565369},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5994544625282288},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5526132583618164},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.530657172203064},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5012304782867432},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4680114984512329},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.4602370262145996},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.45775899291038513},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4409443438053131},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4272116422653198},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4220316410064697},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.41119423508644104},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20389509201049805},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18008458614349365},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1200147271156311},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0983177125453949},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx480","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx480","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/22/3575/25167488/btx480.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28961686","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28961686","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:5870668","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5870668","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:repository.kaust.edu.sa:10754/625301","is_oa":true,"landing_page_url":"http://hdl.handle.net/10754/625301","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/bioinformatics/btx480","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx480","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/22/3575/25167488/btx480.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1120352242","display_name":null,"funder_award_id":"URF/1/3007-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G1309293717","display_name":null,"funder_award_id":"BIGDATA 1R01GM108341","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1843612087","display_name":null,"funder_award_id":"N00014-15-1-2340","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"},{"id":"https://openalex.org/G2863414432","display_name":null,"funder_award_id":"R01 GM108341","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3077527884","display_name":null,"funder_award_id":"CAREER IIS-1350983","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4858881665","display_name":null,"funder_award_id":"URF/1/1976-04","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G5847358043","display_name":null,"funder_award_id":"IIS-1639792 EAGER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6607072827","display_name":null,"funder_award_id":"IIS-1218749","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337345","display_name":"Office of Naval Research","ror":"https://ror.org/00rk2pe57"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2739636023.pdf"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W94861071","https://openalex.org/W284239745","https://openalex.org/W614012683","https://openalex.org/W1019830208","https://openalex.org/W1542652324","https://openalex.org/W1601795611","https://openalex.org/W1663973292","https://openalex.org/W1723510838","https://openalex.org/W1946137962","https://openalex.org/W1968631710","https://openalex.org/W2012354488","https://openalex.org/W2020816856","https://openalex.org/W2025611970","https://openalex.org/W2030446454","https://openalex.org/W2032609519","https://openalex.org/W2034145535","https://openalex.org/W2041557380","https://openalex.org/W2046842005","https://openalex.org/W2061834804","https://openalex.org/W2062237921","https://openalex.org/W2063257849","https://openalex.org/W2069985409","https://openalex.org/W2072128103","https://openalex.org/W2076063813","https://openalex.org/W2087085187","https://openalex.org/W2097467142","https://openalex.org/W2100305057","https://openalex.org/W2103598655","https://openalex.org/W2109535551","https://openalex.org/W2111765516","https://openalex.org/W2121356022","https://openalex.org/W2122429294","https://openalex.org/W2125810118","https://openalex.org/W2134224359","https://openalex.org/W2137334613","https://openalex.org/W2143855992","https://openalex.org/W2144015117","https://openalex.org/W2145429131","https://openalex.org/W2146393977","https://openalex.org/W2147946837","https://openalex.org/W2149769193","https://openalex.org/W2150475519","https://openalex.org/W2159324718","https://openalex.org/W2161012477","https://openalex.org/W2164943005","https://openalex.org/W2166116275","https://openalex.org/W2170960297","https://openalex.org/W2216669303","https://openalex.org/W2304402346","https://openalex.org/W2413160504","https://openalex.org/W2481378334","https://openalex.org/W2492794003","https://openalex.org/W2554247923","https://openalex.org/W3021577848","https://openalex.org/W3133236490","https://openalex.org/W4231109964","https://openalex.org/W6637581210","https://openalex.org/W6675565572"],"related_works":["https://openalex.org/W2364370872","https://openalex.org/W2053269318","https://openalex.org/W2025614924","https://openalex.org/W2294335174","https://openalex.org/W2097963413","https://openalex.org/W2001275470","https://openalex.org/W2073996508","https://openalex.org/W1591475660","https://openalex.org/W3145575561","https://openalex.org/W2164162849"],"abstract_inverted_index":{"MOTIVATION:":[0],"An":[1],"accurate":[2,40],"characterization":[3,41],"of":[4,16,42,94,134,137],"transcription":[5,64],"factor":[6,65],"(TF)-DNA":[7],"affinity":[8,36,45,67,177],"landscape":[9,46],"is":[10,97,130,185],"crucial":[11],"to":[12,123],"a":[13,49,56,76,98,113,125,131],"quantitative":[14],"understanding":[15],"the":[17,31,39,63,90,135,174],"molecular":[18],"mechanisms":[19],"underpinning":[20],"endogenous":[21],"gene":[22],"regulation.":[23],"While":[24],"recent":[25],"advances":[26],"in":[27,89],"biotechnology":[28],"have":[29],"brought":[30],"opportunity":[32],"for":[33,61],"building":[34],"binding":[35,44,66,73,176],"prediction":[37,178],"methods,":[38],"TF-DNA":[43,155],"still":[47],"remains":[48],"challenging":[50],"problem.":[51],"RESULTS:":[52],"Here":[53],"we":[54],"propose":[55],"novel":[57,99,132],"sequence":[58],"embedding":[59,102,143],"approach":[60],"modeling":[62],"landscape.":[68],"Our":[69,128,183],"method":[70,96,129],"represents":[71],"DNA":[72],"sequences":[74],"as":[75,171,173],"hidden":[77,109],"Markov":[78,110],"model":[79],"which":[80,106,157],"captures":[81],"both":[82],"position":[83],"specific":[84],"information":[85],"and":[86,118,144],"long-range":[87],"dependency":[88],"sequence.":[91],"A":[92],"cornerstone":[93],"our":[95],"message":[100],"passing-like":[101],"algorithm,":[103],"called":[104],"Sequence2Vec,":[105],"maps":[107],"these":[108,120],"models":[111],"into":[112],"common":[114],"nonlinear":[115],"feature":[116,141],"space":[117,142],"uses":[119],"embedded":[121],"features":[122],"build":[124],"predictive":[126],"model.":[127],"combination":[133],"strength":[136],"probabilistic":[138],"graphical":[139],"models,":[140],"deep":[145],"learning.":[146],"We":[147],"conducted":[148],"comprehensive":[149],"experiments":[150],"on":[151],"over":[152],"90":[153],"large-scale":[154],"datasets":[156],"were":[158],"measured":[159],"by":[160],"different":[161],"high-throughput":[162],"experimental":[163],"technologies.":[164],"Sequence2Vec":[165],"outperforms":[166],"alternative":[167],"machine":[168],"learning":[169],"methods":[170],"well":[172],"state-of-the-art":[175],"methods.":[179],"AVAILABILITY":[180],"AND":[181],"IMPLEMENTATION:":[182],"program":[184],"freely":[186],"available":[187,199],"at":[188,200],"https://github.com/ramzan1990/sequence2vec.":[189],"CONTACT:":[190],"xin.gao@kaust.edu.sa":[191],"or":[192],"lsong@cc.gatech.edu.":[193],"SUPPLEMENTARY":[194],"INFORMATION:":[195],"Supplementary":[196],"data":[197],"are":[198],"Bioinformatics":[201],"online.":[202]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}