{"id":"https://openalex.org/W2554247923","doi":"https://doi.org/10.1109/bibm.2016.7822515","title":"DeeperBind: Enhancing prediction of sequence specificities of DNA binding proteins","display_name":"DeeperBind: Enhancing prediction of sequence specificities of DNA binding proteins","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2554247923","doi":"https://doi.org/10.1109/bibm.2016.7822515","mag":"2554247923","pmid":"https://pubmed.ncbi.nlm.nih.gov/32551184"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2016.7822515","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822515","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7302108","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103095515","display_name":"Hamid Reza Hassanzadeh","orcid":"https://orcid.org/0000-0002-1096-2727"},"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":"Hamid Reza Hassanzadeh","raw_affiliation_strings":["Department of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332","Department of Computational Science and Engineering, Georgia Institute of Technology Atlanta, Georgia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"Department of Computational Science and Engineering, Georgia Institute of Technology Atlanta, Georgia","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030096887","display_name":"May D. Wang","orcid":"https://orcid.org/0000-0003-3961-3608"},"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"]},{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"May D. Wang","raw_affiliation_strings":["Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332","Department of Biomedical Engineering, Emory University Atlanta, Georgia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332","institution_ids":["https://openalex.org/I130701444","https://openalex.org/I150468666"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Emory University Atlanta, Georgia","institution_ids":["https://openalex.org/I150468666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":154,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"2016","issue":null,"first_page":"178","last_page":"183"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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":0.9986000061035156,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7054967880249023},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.6001110076904297},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5974326729774475},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5285664200782776},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4752245545387268},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.43243879079818726},{"id":"https://openalex.org/keywords/binding-selectivity","display_name":"Binding selectivity","score":0.4311322569847107},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.42591628432273865},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4251851737499237},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4144956171512604},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.41338324546813965},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3960341811180115},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28739091753959656},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2516708970069885},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1554553210735321},{"id":"https://openalex.org/keywords/molecular-biology","display_name":"Molecular biology","score":0.12020227313041687}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7054967880249023},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.6001110076904297},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5974326729774475},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5285664200782776},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4752245545387268},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.43243879079818726},{"id":"https://openalex.org/C96739231","wikidata":"https://www.wikidata.org/wiki/Q4914025","display_name":"Binding selectivity","level":2,"score":0.4311322569847107},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.42591628432273865},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4251851737499237},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4144956171512604},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.41338324546813965},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3960341811180115},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28739091753959656},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2516708970069885},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1554553210735321},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.12020227313041687},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibm.2016.7822515","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822515","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmid:32551184","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32551184","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":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7302108","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7302108","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":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7302108","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7302108","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":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6053241097","display_name":null,"funder_award_id":"U54 CA119338","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1600744878","https://openalex.org/W1947481528","https://openalex.org/W1994122295","https://openalex.org/W2013449615","https://openalex.org/W2061834804","https://openalex.org/W2064675550","https://openalex.org/W2069985409","https://openalex.org/W2080099205","https://openalex.org/W2125810118","https://openalex.org/W2129795133","https://openalex.org/W2130942839","https://openalex.org/W2145429131","https://openalex.org/W2152121035","https://openalex.org/W2161849959","https://openalex.org/W2171407623","https://openalex.org/W2194775991","https://openalex.org/W2257979135","https://openalex.org/W2508429489","https://openalex.org/W2613332842","https://openalex.org/W6679436768","https://openalex.org/W6687483927"],"related_works":["https://openalex.org/W1969771092","https://openalex.org/W2795723184","https://openalex.org/W2025529750","https://openalex.org/W2891858816","https://openalex.org/W184057646","https://openalex.org/W2146631670","https://openalex.org/W2122429294","https://openalex.org/W2037787140","https://openalex.org/W4389024560","https://openalex.org/W2949588195"],"abstract_inverted_index":{"Transcription":[0],"factors":[1],"(TFs)":[2],"are":[3,81],"macromolecules":[4],"that":[5,56,79,212],"bind":[6],"to":[7,58,68,104,132,177],"cis-regulatory":[8],"specific":[9],"sub-regions":[10,153],"of":[11,21,32,65,87,93,110,126,141,192,203,217,229,232],"DNA":[12,70,133,155,218],"promoters":[13],"and":[14,38,47,60,91,144,166,196,238],"initiate":[15],"transcription.":[16],"Finding":[17],"the":[18,62,88,94,106,138,148,178,201,208,221,230],"exact":[19],"location":[20],"these":[22,76],"binding":[23,63,89,128,183,194,215],"sites":[24],"(aka":[25],"motifs)":[26],"is":[27,78,102,207],"important":[28],"in":[29,45,48,85,154,157],"a":[30,66,98,117],"variety":[31],"domains":[33],"such":[34],"as":[35],"drug":[36],"design":[37],"development.":[39],"To":[40,200],"address":[41],"this":[42,206],"need,":[43],"several":[44],"vivo":[46],"vitro":[49],"techniques":[50,77],"have":[51],"been":[52],"developed":[53],"so":[54],"far":[55],"try":[57],"characterize":[59],"predict":[61,214],"specificity":[64],"protein":[67,127,182],"different":[69],"loci.":[71],"The":[72],"major":[73],"problem":[74],"with":[75,130,147],"they":[80],"not":[82],"accurate":[83,210],"enough":[84],"prediction":[86,125],"affinity":[90],"characterization":[92],"corresponding":[95],"motifs.":[96],"As":[97],"result,":[99],"downstream":[100],"analysis":[101],"required":[103],"uncover":[105],"locations":[107],"where":[108],"proteins":[109],"interest":[111],"bind.":[112],"Here,":[113],"we":[114],"propose":[115],"DeeperBind,":[116],"long":[118],"short":[119],"term":[120],"recurrent":[121],"convolutional":[122],"network":[123],"for":[124,190,235],"specificities":[129,216],"respect":[131],"probes.":[134],"DeeperBind":[135],"can":[136,163,213],"model":[137],"positional":[139,239],"dynamics":[140,240],"probe":[142],"sequences":[143,219],"hence":[145],"reckons":[146],"contributions":[149],"made":[150],"by":[151,224],"individual":[152],"sequences,":[156],"an":[158,186],"effective":[159],"way.":[160],"Moreover,":[161],"it":[162],"be":[164],"trained":[165],"tested":[167],"on":[168],"datasets":[169,179],"containing":[170],"varying-length":[171],"sequences.":[172],"We":[173],"apply":[174],"our":[175,204],"pipeline":[176,211],"derived":[180],"from":[181,220],"microarrays":[184],"(PBMs),":[185],"in-vitro":[187],"high-throughput":[188,225],"technology":[189],"quantification":[191],"protein-DNA":[193],"preferences,":[195],"present":[197],"promising":[198],"results.":[199],"best":[202],"knowledge,":[205],"most":[209],"data":[222],"produced":[223],"technologies":[226],"through":[227],"utilization":[228],"power":[231],"deep":[233],"learning":[234],"feature":[236],"generation":[237],"modeling.":[241]},"counts_by_year":[{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":23},{"year":2021,"cited_by_count":29},{"year":2020,"cited_by_count":22},{"year":2019,"cited_by_count":21},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":11}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}