{"id":"https://openalex.org/W4399425685","doi":"https://doi.org/10.1109/tcbb.2024.3411024","title":"Transcription Factor Binding Site Prediction Using CnNet Approach","display_name":"Transcription Factor Binding Site Prediction Using CnNet Approach","publication_year":2024,"publication_date":"2024-06-07","ids":{"openalex":"https://openalex.org/W4399425685","doi":"https://doi.org/10.1109/tcbb.2024.3411024","pmid":"https://pubmed.ncbi.nlm.nih.gov/38848239"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3411024","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3411024","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060391144","display_name":"Mohamed Divan Masood","orcid":"https://orcid.org/0000-0002-9396-3740"},"institutions":[{"id":"https://openalex.org/I94948490","display_name":"B.S. Abdur Rahman Crescent Institute of Science & Technology","ror":"https://ror.org/01fqhas03","country_code":"IN","type":"education","lineage":["https://openalex.org/I94948490"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"M. Mohamed Divan Masood","raw_affiliation_strings":["Department of Computer Science and Engineering, B S Abdur Rahman Crescent Institute of Science and Technology, Chennai, India","Department of Computer Science and Engineering, B S Abdur Rahman Crescent Institute of Science and Technology, Chennai, MI, India"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, B S Abdur Rahman Crescent Institute of Science and Technology, Chennai, India","institution_ids":["https://openalex.org/I94948490"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, B S Abdur Rahman Crescent Institute of Science and Technology, Chennai, MI, India","institution_ids":["https://openalex.org/I94948490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099046129","display_name":"Manjula","orcid":null},"institutions":[{"id":"https://openalex.org/I876193797","display_name":"Vellore Institute of Technology University","ror":"https://ror.org/00qzypv28","country_code":"IN","type":"education","lineage":["https://openalex.org/I876193797"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"D. Manjula","raw_affiliation_strings":["Department of Computer Science and Engineering, Vellore Institute of Technology, Chennai, India"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Vellore Institute of Technology, Chennai, India","institution_ids":["https://openalex.org/I876193797"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080285200","display_name":"Vijayan Sugumaran","orcid":"https://orcid.org/0000-0003-2557-3182"},"institutions":[{"id":"https://openalex.org/I177721651","display_name":"Oakland University","ror":"https://ror.org/01ythxj32","country_code":"US","type":"education","lineage":["https://openalex.org/I177721651"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vijayan Sugumaran","raw_affiliation_strings":["Department of Decision and Information Sciences, Oakland University, Rochester, MI, USA","Department of Decision and Information Sciences, Oakland University, Rochester, USA"],"affiliations":[{"raw_affiliation_string":"Department of Decision and Information Sciences, Oakland University, Rochester, MI, USA","institution_ids":["https://openalex.org/I177721651"]},{"raw_affiliation_string":"Department of Decision and Information Sciences, Oakland University, Rochester, USA","institution_ids":["https://openalex.org/I177721651"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060391144"],"corresponding_institution_ids":["https://openalex.org/I94948490"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08280094,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"6","first_page":"1721","last_page":"1730"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.8233000040054321,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.8233000040054321,"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/T10885","display_name":"Gene expression and cancer classification","score":0.7973999977111816,"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/transcription-factor","display_name":"Transcription factor","score":0.6262007355690002},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.6003201603889465},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.472050279378891},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4633531868457794},{"id":"https://openalex.org/keywords/factor","display_name":"Factor (programming language)","score":0.4160374104976654},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3858484625816345},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3333781659603119},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.318398654460907},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.18793824315071106},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12292537093162537},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08008340001106262},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07454133033752441}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6262007355690002},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.6003201603889465},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.472050279378891},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4633531868457794},{"id":"https://openalex.org/C2781039887","wikidata":"https://www.wikidata.org/wiki/Q1391724","display_name":"Factor (programming language)","level":2,"score":0.4160374104976654},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3858484625816345},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3333781659603119},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.318398654460907},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.18793824315071106},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12292537093162537},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08008340001106262},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07454133033752441}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep 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":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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","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},{"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3411024","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3411024","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38848239","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38848239","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1756039870","https://openalex.org/W1963778673","https://openalex.org/W1964141703","https://openalex.org/W1968682237","https://openalex.org/W1976579857","https://openalex.org/W1983887488","https://openalex.org/W1987061468","https://openalex.org/W1987626967","https://openalex.org/W1989169142","https://openalex.org/W1992605649","https://openalex.org/W1994122295","https://openalex.org/W1998300401","https://openalex.org/W2000262953","https://openalex.org/W2005486255","https://openalex.org/W2012169714","https://openalex.org/W2034145535","https://openalex.org/W2042392223","https://openalex.org/W2056002855","https://openalex.org/W2074231493","https://openalex.org/W2082319785","https://openalex.org/W2085755265","https://openalex.org/W2097175728","https://openalex.org/W2113117122","https://openalex.org/W2114104545","https://openalex.org/W2115761267","https://openalex.org/W2116052408","https://openalex.org/W2125810118","https://openalex.org/W2126246843","https://openalex.org/W2138270253","https://openalex.org/W2140204971","https://openalex.org/W2145091349","https://openalex.org/W2149769193","https://openalex.org/W2159324718","https://openalex.org/W2163102318","https://openalex.org/W2166637863","https://openalex.org/W2198606573","https://openalex.org/W2919115771","https://openalex.org/W2951410692","https://openalex.org/W3088452016","https://openalex.org/W3118460357","https://openalex.org/W3160687760","https://openalex.org/W3180669414","https://openalex.org/W4200363822","https://openalex.org/W4245023496","https://openalex.org/W4281691239","https://openalex.org/W4284989069","https://openalex.org/W4319333022","https://openalex.org/W4360994740","https://openalex.org/W4378189158","https://openalex.org/W4381046871","https://openalex.org/W6672416239"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2152664145","https://openalex.org/W2153561273","https://openalex.org/W2079197459","https://openalex.org/W2379997263","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W2367493320","https://openalex.org/W2131580913","https://openalex.org/W2090848290"],"abstract_inverted_index":{"Controlling":[0],"the":[1,5,34,52,131,146,167,187],"gene":[2,35,49,136],"expression":[3],"is":[4,40,61],"most":[6],"important":[7,46],"development":[8],"in":[9,48,72],"a":[10,41,97,164,170,174],"living":[11],"organism,":[12],"which":[13,95],"makes":[14],"it":[15,60],"easier":[16],"to":[17,29,63,196],"find":[18],"different":[19],"kinds":[20],"of":[21,134,151,169],"diseases":[22],"and":[23,67,100,161],"their":[24],"causes.":[25],"It's":[26],"very":[27],"difficult":[28],"know":[30],"what":[31],"factors":[32],"control":[33],"expression.":[36,50],"Transcription":[37],"Factor":[38],"(TF)":[39],"protein":[42],"that":[43,84,148],"plays":[44],"an":[45],"role":[47],"Discovering":[51],"transcription":[53,106],"factor":[54,107],"has":[55,126],"immense":[56],"biological":[57,73],"significance,":[58],"however,":[59],"challenging":[62],"develop":[64],"novel":[65],"techniques":[66],"evaluation":[68],"for":[69,104,113,129],"regulatory":[70],"developments":[71],"structures.":[74],"In":[75],"this":[76],"research,":[77],"we":[78],"mainly":[79],"focus":[80],"on":[81],"'sequence":[82,132],"specificities'":[83,133],"can":[85],"be":[86],"ascertained":[87],"from":[88],"experimental":[89],"data":[90],"with":[91,118,191],"'deep":[92],"learning'":[93],"techniques,":[94],"offer":[96],"scalable,":[98],"flexible":[99],"unified":[101],"computational":[102],"approach":[103,185],"predicting":[105],"binding.":[108],"Specifically,":[109],"Multiple":[110],"Expression":[111],"motifs":[112,147],"Motif":[114],"Elicitation":[115],"(MEME)":[116],"technique":[117],"Convolution":[119],"Neural":[120],"Network":[121],"(CNN)":[122],"named":[123],"as":[124],"CnNet,":[125],"been":[127],"used":[128],"discovering":[130,145],"DNA":[135],"sequences":[137],"dataset.":[138],"This":[139],"process":[140],"involves":[141],"two":[142],"steps:":[143],"a)":[144],"are":[149],"capable":[150],"identifying":[152],"useful":[153,175],"TF":[154,188],"binding":[155,176,189],"site":[156,177],"by":[157,178],"using":[158,179],"MEME":[159],"technique,":[160],"b)":[162],"computing":[163],"score":[165,190],"indicating":[166],"likelihood":[168],"given":[171],"sequence":[172],"being":[173],"CNN":[180],"technique.":[181],"The":[182],"proposed":[183],"CnNet":[184],"predicts":[186],"much":[192],"better":[193],"accuracy":[194],"compared":[195],"existing":[197],"approaches.":[198]},"counts_by_year":[],"updated_date":"2026-04-04T08:04:53.788161","created_date":"2025-10-10T00:00:00"}