{"id":"https://openalex.org/W4293173874","doi":"https://doi.org/10.1109/tcbb.2022.3199758","title":"Predicting TF Proteins by Incorporating Evolution Information Through PSSM","display_name":"Predicting TF Proteins by Incorporating Evolution Information Through PSSM","publication_year":2022,"publication_date":"2022-08-25","ids":{"openalex":"https://openalex.org/W4293173874","doi":"https://doi.org/10.1109/tcbb.2022.3199758","pmid":"https://pubmed.ncbi.nlm.nih.gov/35981062"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3199758","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3199758","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/A5007272827","display_name":"Zhihua Du","orcid":"https://orcid.org/0000-0002-7213-2198"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhihua Du","raw_affiliation_strings":["Colleage of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong, China"],"raw_orcid":"https://orcid.org/0000-0002-7213-2198","affiliations":[{"raw_affiliation_string":"Colleage of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101032275","display_name":"Tianyou Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianyou Huang","raw_affiliation_strings":["Colleage of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Colleage of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083199032","display_name":"Vladimir N. Uversky","orcid":"https://orcid.org/0000-0002-4037-5857"},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]},{"id":"https://openalex.org/I4210140006","display_name":"USF Health Byrd Alzheimer's Institute","ror":"https://ror.org/048768v87","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210140006"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vladimir N. Uversky","raw_affiliation_strings":["Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-4037-5857","affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA","institution_ids":["https://openalex.org/I4210140006","https://openalex.org/I2613432"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100393871","display_name":"Jianqiang Li","orcid":"https://orcid.org/0000-0002-2208-962X"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianqiang Li","raw_affiliation_strings":["Colleage of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong, China"],"raw_orcid":"https://orcid.org/0000-0002-2208-962X","affiliations":[{"raw_affiliation_string":"Colleage of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007272827"],"corresponding_institution_ids":["https://openalex.org/I180726961"],"apc_list":null,"apc_paid":null,"fwci":0.3465,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.55598068,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"20","issue":"2","first_page":"1319","last_page":"1326"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9997000098228455,"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":0.9997000098228455,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9984999895095825,"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/encode","display_name":"ENCODE","score":0.714796245098114},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6091695427894592},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5920220017433167},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4445113241672516},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4395720958709717},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.42919081449508667},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4174906313419342},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.35791724920272827},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3523443341255188},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.323733925819397},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27431759238243103},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2225661277770996},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.0778723657131195}],"concepts":[{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.714796245098114},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6091695427894592},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5920220017433167},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4445113241672516},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4395720958709717},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.42919081449508667},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4174906313419342},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35791724920272827},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3523443341255188},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.323733925819397},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27431759238243103},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2225661277770996},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0778723657131195},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","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":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2022.3199758","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3199758","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:35981062","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35981062","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},{"id":"pmh:oai:digitalcommons.usf.edu:mme_facpub-2056","is_oa":false,"landing_page_url":"https://digitalcommons.usf.edu/mme_facpub/1038","pdf_url":null,"source":{"id":"https://openalex.org/S4377196272","display_name":"Digital Commons - University of South Florida (University of South Florida)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2613432","host_organization_name":"University of South Florida","host_organization_lineage":["https://openalex.org/I2613432"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Molecular Medicine Faculty Publications","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1366773193","display_name":null,"funder_award_id":"2019ZT08X603","funder_id":"https://openalex.org/F4320334009","funder_display_name":"Guangdong Provincial Pearl River Talents Program"},{"id":"https://openalex.org/G1860700528","display_name":null,"funder_award_id":"62006157","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3332848674","display_name":null,"funder_award_id":"R2020A045","funder_id":"https://openalex.org/F4320326705","funder_display_name":"Science, Technology and Innovation Commission of Shenzhen Municipality"},{"id":"https://openalex.org/G4429118438","display_name":null,"funder_award_id":"62073225","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5275301293","display_name":"\u9762\u5411AIoT\u667a\u80fd\u7269\u8054\u7f51\u7684\u4e91\u8fb9\u534f\u540c\u611f\u77e5\u7406\u8bba\u4e0e\u5173\u952e\u6280\u672f\u7814\u7a76","funder_award_id":"61972263","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6733505969","display_name":null,"funder_award_id":"U1713212","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6819557517","display_name":null,"funder_award_id":"2019A1515011608","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"},{"id":"https://openalex.org/G7097245526","display_name":"\u7c7b\u4eba\u4efb\u52a1\u89c4\u5212\u3001\u63a8\u7406\u53ca\u5176\u9a8c\u8bc1\u7cfb\u7edf\u7684\u7814\u7a76\u548c\u5e94\u7528","funder_award_id":"61836005","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7279309214","display_name":null,"funder_award_id":"62176164","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8217273170","display_name":"\u9762\u5411\u591a\u65b9\u9690\u79c1\u6570\u636e\u5b66\u4e60\u7684\u5206\u5e03\u5f0f\u9ad8\u65af\u8fc7\u7a0b\u7b97\u6cd5\u6846\u67b6\u7814\u7a76","funder_award_id":"62072315","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321921","display_name":"Natural Science Foundation of Guangdong Province","ror":null},{"id":"https://openalex.org/F4320326705","display_name":"Science, Technology and Innovation Commission of Shenzhen Municipality","ror":null},{"id":"https://openalex.org/F4320334009","display_name":"Guangdong Provincial Pearl River Talents Program","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1490161904","https://openalex.org/W1522301498","https://openalex.org/W1792685479","https://openalex.org/W2011983814","https://openalex.org/W2021312899","https://openalex.org/W2021632119","https://openalex.org/W2049476357","https://openalex.org/W2053724458","https://openalex.org/W2053820259","https://openalex.org/W2064675550","https://openalex.org/W2070126374","https://openalex.org/W2073200397","https://openalex.org/W2076063813","https://openalex.org/W2086802511","https://openalex.org/W2095705004","https://openalex.org/W2100198674","https://openalex.org/W2131774270","https://openalex.org/W2133564696","https://openalex.org/W2158714788","https://openalex.org/W2170747616","https://openalex.org/W2311607323","https://openalex.org/W2333587122","https://openalex.org/W2533355719","https://openalex.org/W2612935389","https://openalex.org/W2752782242","https://openalex.org/W2793344725","https://openalex.org/W2806884808","https://openalex.org/W2810756255","https://openalex.org/W2885815722","https://openalex.org/W2891678790","https://openalex.org/W2894749196","https://openalex.org/W2909854604","https://openalex.org/W2949275670","https://openalex.org/W2951793362","https://openalex.org/W2980975636","https://openalex.org/W2999481648","https://openalex.org/W3047670845","https://openalex.org/W3087240458","https://openalex.org/W3088671900","https://openalex.org/W3090491025","https://openalex.org/W3116625060","https://openalex.org/W3121554924","https://openalex.org/W3130970563","https://openalex.org/W3136918052","https://openalex.org/W3158808612","https://openalex.org/W3184265853","https://openalex.org/W6631190155","https://openalex.org/W6631943919","https://openalex.org/W6638444622","https://openalex.org/W6638667902","https://openalex.org/W6674330103","https://openalex.org/W6679434410","https://openalex.org/W6682889407","https://openalex.org/W6684191040"],"related_works":["https://openalex.org/W2468279273","https://openalex.org/W2354198838","https://openalex.org/W1989130879","https://openalex.org/W2103419012","https://openalex.org/W2988126442","https://openalex.org/W1974414866","https://openalex.org/W2063982682","https://openalex.org/W2338543196","https://openalex.org/W1544691147","https://openalex.org/W2039176012"],"abstract_inverted_index":{"Transcription":[0],"factors":[1],"(TFs)":[2],"are":[3,39],"DNA":[4,28],"binding":[5,25],"proteins":[6],"involved":[7],"in":[8,16,67,74,127,146],"the":[9,68,105,108,128,137],"regulation":[10],"of":[11,71,76,98,107],"gene":[12],"expression.":[13],"They":[14],"exist":[15],"all":[17],"organisms":[18],"and":[19,41,89,112,155],"activate":[20],"or":[21],"repress":[22],"transcription":[23],"by":[24,35],"to":[26,52,55,123,148],"specific":[27],"sequences.":[29,95],"Traditionally,":[30],"TFs":[31],"have":[32,49],"been":[33,50],"identified":[34],"experimental":[36],"methods":[37,48,118],"that":[38,86,136],"time-consuming":[40],"costly.":[42],"In":[43],"recent":[44],"years,":[45],"various":[46],"computational":[47,83],"developed":[51],"identify":[53],"TF":[54,91,110],"overcome":[56],"these":[57,72,99],"limitations.":[58],"However,":[59],"there":[60],"is":[61,101],"a":[62,81],"room":[63],"for":[64],"further":[65],"improvement":[66],"predictive":[69,139],"performance":[70,140],"tools":[73],"terms":[75],"accuracy.":[77],"We":[78],"report":[79],"here":[80],"novel":[82],"tool,":[84],"TFnet,":[85],"provides":[87],"accurate":[88],"comprehensive":[90],"predictions":[92,100],"from":[93,142],"protein":[94],"The":[96],"accuracy":[97],"substantially":[102],"better":[103],"than":[104],"results":[106],"existing":[109],"predictors":[111],"methods.":[113],"Especially,":[114],"it":[115],"outperforms":[116],"comparable":[117],"significantly":[119],"when":[120],"sequence":[121,150],"similarity":[122],"other":[124],"known":[125],"sequences":[126],"database":[129],"drops":[130],"below":[131],"40%.":[132],"Ablation":[133],"tests":[134],"reveal":[135],"high":[138],"stems":[141],"innovative":[143],"ways":[144],"used":[145],"TFnet":[147],"derive":[149],"Position-Specific":[151],"Scoring":[152],"Matrix":[153],"(PSSM)":[154],"encode":[156],"inputs.":[157]},"counts_by_year":[{"year":2024,"cited_by_count":4}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}