{"id":"https://openalex.org/W4389010890","doi":"https://doi.org/10.1093/bib/bbad432","title":"Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis","display_name":"Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis","publication_year":2023,"publication_date":"2023-11-22","ids":{"openalex":"https://openalex.org/W4389010890","doi":"https://doi.org/10.1093/bib/bbad432","pmid":"https://pubmed.ncbi.nlm.nih.gov/38008420"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad432","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad432/53810825/bbad432.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad432/53810825/bbad432.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016130330","display_name":"Zhen-Ning Yin","orcid":"https://orcid.org/0009-0001-0715-717X"},"institutions":[{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]},{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen-Ning Yin","raw_affiliation_strings":["Department of Physics , School of Science, , Tianjin 300072 , China","Tianjin University , School of Science, , Tianjin 300072 , China","Department of Physics, School of Science, Tianjin University, Tianjin 300072, China"],"affiliations":[{"raw_affiliation_string":"Department of Physics , School of Science, , Tianjin 300072 , China","institution_ids":["https://openalex.org/I132369690"]},{"raw_affiliation_string":"Tianjin University , School of Science, , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"Department of Physics, School of Science, Tianjin University, Tianjin 300072, China","institution_ids":["https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044024642","display_name":"Fei-Liao Lai","orcid":null},"institutions":[{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]},{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei-Liao Lai","raw_affiliation_strings":["Department of Physics , School of Science, , Tianjin 300072 , China","Tianjin University , School of Science, , Tianjin 300072 , China","Department of Physics, School of Science, Tianjin University, Tianjin 300072, China"],"affiliations":[{"raw_affiliation_string":"Department of Physics , School of Science, , Tianjin 300072 , China","institution_ids":["https://openalex.org/I132369690"]},{"raw_affiliation_string":"Tianjin University , School of Science, , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"Department of Physics, School of Science, Tianjin University, Tianjin 300072, China","institution_ids":["https://openalex.org/I162868743"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074242312","display_name":"Feng Gao","orcid":"https://orcid.org/0000-0002-9563-3841"},"institutions":[{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]},{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]},{"id":"https://openalex.org/I4210151209","display_name":"Collaborative Innovation Center of Chemical Science and Engineering Tianjin","ror":"https://ror.org/0225a5s12","country_code":"CN","type":"facility","lineage":["https://openalex.org/I162868743","https://openalex.org/I205237279","https://openalex.org/I4210151209"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Feng Gao","raw_affiliation_strings":["Department of Physics , School of Science, , Tianjin 300072 , China","Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University , Tianjin 300072 , China","SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300072 , China","Tianjin University , School of Science, , Tianjin 300072 , China","Department of Physics, School of Science, Tianjin University, Tianjin 300072, China","Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China"],"affiliations":[{"raw_affiliation_string":"Department of Physics , School of Science, , Tianjin 300072 , China","institution_ids":["https://openalex.org/I132369690"]},{"raw_affiliation_string":"Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300072 , China","institution_ids":["https://openalex.org/I4210151209"]},{"raw_affiliation_string":"Tianjin University , School of Science, , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"Department of Physics, School of Science, Tianjin University, Tianjin 300072, China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China","institution_ids":["https://openalex.org/I162868743"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074242312"],"corresponding_institution_ids":["https://openalex.org/I132369690","https://openalex.org/I162868743","https://openalex.org/I4210151209"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.0562,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.78016629,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"25","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9979000091552734,"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":0.9979000091552734,"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":0.9943000078201294,"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":0.9843000173568726,"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/replication","display_name":"Replication (statistics)","score":0.8241451978683472},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6408437490463257},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5880846977233887},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5865179896354675},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39857766032218933},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36830610036849976},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20679953694343567},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.13400784134864807}],"concepts":[{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.8241451978683472},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6408437490463257},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5880846977233887},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5865179896354675},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39857766032218933},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36830610036849976},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20679953694343567},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.13400784134864807}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad432","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad432/53810825/bbad432.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38008420","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38008420","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10676776","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10676776","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10676776/pdf/bbad432.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad432","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad432/53810825/bbad432.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G518651691","display_name":null,"funder_award_id":"2018YFA0903700","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5865461599","display_name":null,"funder_award_id":"2018YFA0903700","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G932100424","display_name":null,"funder_award_id":"32270692","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G999540423","display_name":null,"funder_award_id":"31571358","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/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4389010890.pdf"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W176093406","https://openalex.org/W1709815505","https://openalex.org/W1976456142","https://openalex.org/W2005530496","https://openalex.org/W2021823827","https://openalex.org/W2036240398","https://openalex.org/W2056298514","https://openalex.org/W2068881314","https://openalex.org/W2083158919","https://openalex.org/W2088819045","https://openalex.org/W2099929096","https://openalex.org/W2134179844","https://openalex.org/W2147082907","https://openalex.org/W2148771849","https://openalex.org/W2155695990","https://openalex.org/W2165710627","https://openalex.org/W2166459599","https://openalex.org/W2170747616","https://openalex.org/W2234143669","https://openalex.org/W2238758434","https://openalex.org/W2318228043","https://openalex.org/W2502949459","https://openalex.org/W2509863861","https://openalex.org/W2517008357","https://openalex.org/W2770178180","https://openalex.org/W2784113007","https://openalex.org/W2898439045","https://openalex.org/W2949485484","https://openalex.org/W2989747508","https://openalex.org/W3007150491","https://openalex.org/W3016489761","https://openalex.org/W3023962428","https://openalex.org/W3027404681","https://openalex.org/W3094704314","https://openalex.org/W3096599651","https://openalex.org/W3136851266","https://openalex.org/W4243013257","https://openalex.org/W4306393225","https://openalex.org/W4307468135","https://openalex.org/W4307655495","https://openalex.org/W4310494148","https://openalex.org/W4321480048","https://openalex.org/W4366210809","https://openalex.org/W6725701304"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W2961085424","https://openalex.org/W3215138031","https://openalex.org/W4306674287","https://openalex.org/W3009238340","https://openalex.org/W4321369474","https://openalex.org/W4360585206","https://openalex.org/W4285208911","https://openalex.org/W3046775127","https://openalex.org/W3082895349"],"abstract_inverted_index":{"Accurate":[0],"identification":[1],"of":[2,15,38,68,92,120,160],"replication":[3],"origins":[4],"(ORIs)":[5],"is":[6],"crucial":[7],"for":[8,70,107,133,152],"a":[9,25,82,88,100,117],"comprehensive":[10,150],"investigation":[11],"into":[12],"the":[13,35,43,62,121,158],"progression":[14],"human":[16,36],"cell":[17,72,135],"growth":[18],"and":[19,32,139,149],"cancer":[20],"therapy.":[21],"Here,":[22],"we":[23,79],"proposed":[24],"computational":[26],"approach":[27,143],"Ori-FinderH,":[28],"which":[29,86],"can":[30],"efficiently":[31],"precisely":[33],"predict":[34],"ORIs":[37],"various":[39],"lengths":[40],"by":[41],"combining":[42],"Z-curve":[44],"method":[45],"with":[46,51],"deep":[47],"learning":[48],"approach.":[49],"Compared":[50],"existing":[52],"methods,":[53],"Ori-FinderH":[54],"exhibits":[55],"superior":[56],"performance,":[57],"achieving":[58],"an":[59],"area":[60],"under":[61],"receiver":[63],"operating":[64],"characteristic":[65],"curve":[66],"(AUC)":[67],"0.9616":[69],"K562":[71],"line":[73],"in":[74],"10-fold":[75],"cross-validation.":[76],"In":[77],"addition,":[78],"also":[80],"established":[81],"cross-cell-line":[83],"predictive":[84],"model,":[85],"yielded":[87],"further":[89,156],"improved":[90],"AUC":[91],"0.9706.":[93],"The":[94],"model":[95],"was":[96],"subsequently":[97],"employed":[98],"as":[99],"fitness":[101],"function":[102],"to":[103],"support":[104],"genetic":[105],"algorithm":[106],"generating":[108],"artificial":[109],"ORIs.":[110],"Sequence":[111],"analysis":[112],"through":[113],"iORI-Euk":[114],"revealed":[115],"that":[116],"vast":[118],"majority":[119],"created":[122],"sequences,":[123],"specifically":[124],"98%":[125],"or":[126],"more,":[127],"incorporate":[128],"at":[129],"least":[130],"one":[131],"ORI":[132],"three":[134],"lines":[136],"(Hela,":[137],"MCF7":[138],"K562).":[140],"This":[141],"innovative":[142],"could":[144],"provide":[145],"more":[146],"efficient,":[147],"accurate":[148],"information":[151],"experimental":[153],"investigation,":[154],"thereby":[155],"advancing":[157],"development":[159],"this":[161],"field.":[162]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
