{"id":"https://openalex.org/W4206129384","doi":"https://doi.org/10.1093/bib/bbac001","title":"ORI-Deep: improving the accuracy for predicting origin of replication sites by using a blend of features and long short-term memory network","display_name":"ORI-Deep: improving the accuracy for predicting origin of replication sites by using a blend of features and long short-term memory network","publication_year":2022,"publication_date":"2022-01-03","ids":{"openalex":"https://openalex.org/W4206129384","doi":"https://doi.org/10.1093/bib/bbac001","pmid":"https://pubmed.ncbi.nlm.nih.gov/35048955"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac001","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac001","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084390005","display_name":"Mahwish Shahid","orcid":"https://orcid.org/0000-0002-2928-3716"},"institutions":[{"id":"https://openalex.org/I87482320","display_name":"University of Management and Technology","ror":"https://ror.org/0095xcq10","country_code":"PK","type":"education","lineage":["https://openalex.org/I87482320"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Mahwish Shahid","raw_affiliation_strings":["School of Systems and Technologies, University of Management and Technology, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Systems and Technologies, University of Management and Technology, Lahore, Pakistan","institution_ids":["https://openalex.org/I87482320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112730236","display_name":"M. Ilyas","orcid":null},"institutions":[{"id":"https://openalex.org/I87482320","display_name":"University of Management and Technology","ror":"https://ror.org/0095xcq10","country_code":"PK","type":"education","lineage":["https://openalex.org/I87482320"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Maham Ilyas","raw_affiliation_strings":["University of Management and Technology, Lahore, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Management and Technology, Lahore, Pakistan","institution_ids":["https://openalex.org/I87482320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073505552","display_name":"Waqar Hussain","orcid":"https://orcid.org/0000-0001-8991-9424"},"institutions":[{"id":"https://openalex.org/I87482320","display_name":"University of Management and Technology","ror":"https://ror.org/0095xcq10","country_code":"PK","type":"education","lineage":["https://openalex.org/I87482320"]}],"countries":["PK"],"is_corresponding":true,"raw_author_name":"Waqar Hussain","raw_affiliation_strings":["University of Management and Technology, Lahore, Pakistan"],"raw_orcid":"https://orcid.org/0000-0001-8991-9424","affiliations":[{"raw_affiliation_string":"University of Management and Technology, Lahore, Pakistan","institution_ids":["https://openalex.org/I87482320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075858344","display_name":"Yaser Daanial Khan","orcid":"https://orcid.org/0000-0002-2482-275X"},"institutions":[{"id":"https://openalex.org/I87482320","display_name":"University of Management and Technology","ror":"https://ror.org/0095xcq10","country_code":"PK","type":"education","lineage":["https://openalex.org/I87482320"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Yaser Daanial Khan","raw_affiliation_strings":["Department of Computer Science, University of Management and Technology, Lahore, Pakistan"],"raw_orcid":"https://orcid.org/0000-0002-2482-275X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Management and Technology, Lahore, Pakistan","institution_ids":["https://openalex.org/I87482320"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5073505552"],"corresponding_institution_ids":["https://openalex.org/I87482320"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.6788,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.83727991,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"23","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976999759674072,"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/computer-science","display_name":"Computer science","score":0.7343195676803589},{"id":"https://openalex.org/keywords/origin-of-replication","display_name":"Origin of replication","score":0.7129566073417664},{"id":"https://openalex.org/keywords/replication","display_name":"Replication (statistics)","score":0.7048478722572327},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6267361044883728},{"id":"https://openalex.org/keywords/dna-replication","display_name":"DNA replication","score":0.5384838581085205},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5057711601257324},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4849146008491516},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45810815691947937},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4120084047317505},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3212466239929199},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26604318618774414},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2041139304637909},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.198476642370224}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7343195676803589},{"id":"https://openalex.org/C58337764","wikidata":"https://www.wikidata.org/wiki/Q976651","display_name":"Origin of replication","level":4,"score":0.7129566073417664},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.7048478722572327},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6267361044883728},{"id":"https://openalex.org/C73573662","wikidata":"https://www.wikidata.org/wiki/Q130996","display_name":"DNA replication","level":3,"score":0.5384838581085205},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5057711601257324},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4849146008491516},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45810815691947937},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4120084047317505},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3212466239929199},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26604318618774414},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2041139304637909},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.198476642370224},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008570","descriptor_name":"Memory, Short-Term","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008570","descriptor_name":"Memory, Short-Term","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018741","descriptor_name":"Replication Origin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018741","descriptor_name":"Replication Origin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018741","descriptor_name":"Replication Origin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018741","descriptor_name":"Replication Origin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac001","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac001","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35048955","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35048955","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6100000143051147}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":68,"referenced_works":["https://openalex.org/W1579409894","https://openalex.org/W1644997609","https://openalex.org/W1680797894","https://openalex.org/W1996986783","https://openalex.org/W2022965734","https://openalex.org/W2025847444","https://openalex.org/W2050297026","https://openalex.org/W2064675550","https://openalex.org/W2066915800","https://openalex.org/W2073223847","https://openalex.org/W2104216356","https://openalex.org/W2104539744","https://openalex.org/W2145957695","https://openalex.org/W2147082907","https://openalex.org/W2149359491","https://openalex.org/W2160257187","https://openalex.org/W2161621183","https://openalex.org/W2165710627","https://openalex.org/W2315593216","https://openalex.org/W2344859163","https://openalex.org/W2411639680","https://openalex.org/W2520682509","https://openalex.org/W2755050428","https://openalex.org/W2771200722","https://openalex.org/W2792363117","https://openalex.org/W2800333284","https://openalex.org/W2804489036","https://openalex.org/W2884524796","https://openalex.org/W2900891475","https://openalex.org/W2901754076","https://openalex.org/W2905276595","https://openalex.org/W2906411860","https://openalex.org/W2924377282","https://openalex.org/W2934605085","https://openalex.org/W2969134071","https://openalex.org/W2969438243","https://openalex.org/W2972319401","https://openalex.org/W2979665139","https://openalex.org/W2982150996","https://openalex.org/W3002225207","https://openalex.org/W3005096604","https://openalex.org/W3007150491","https://openalex.org/W3016736146","https://openalex.org/W3022821485","https://openalex.org/W3047705148","https://openalex.org/W3094020344","https://openalex.org/W3094567318","https://openalex.org/W3096599651","https://openalex.org/W3112172360","https://openalex.org/W3112601518","https://openalex.org/W3159663509","https://openalex.org/W3169622143","https://openalex.org/W3189610884","https://openalex.org/W3197735129","https://openalex.org/W3199924206","https://openalex.org/W3203395656","https://openalex.org/W3204658953","https://openalex.org/W3209675702","https://openalex.org/W3212066946","https://openalex.org/W3214729651","https://openalex.org/W4210395023","https://openalex.org/W4213283310","https://openalex.org/W4237222478","https://openalex.org/W4246084279","https://openalex.org/W4251881819","https://openalex.org/W4292671038","https://openalex.org/W6663309430","https://openalex.org/W6801332211"],"related_works":["https://openalex.org/W2329795915","https://openalex.org/W1970722699","https://openalex.org/W1981922425","https://openalex.org/W2102366565","https://openalex.org/W2082627754","https://openalex.org/W2123987161","https://openalex.org/W2043025987","https://openalex.org/W84663166","https://openalex.org/W2059208699","https://openalex.org/W2084837006"],"abstract_inverted_index":{"Replication":[0,34],"of":[1,35,38,50,57,59,133,148,165,221],"DNA":[2,36,61,225],"is":[3,54,98,115,138,151,196,233,240],"an":[4],"important":[5],"process":[6],"for":[7,83,89,125,143,186,231],"the":[8,48,55,60,72,90,104,144,163,166,183,192,208,219],"cell":[9,106],"division":[10],"cycle,":[11],"gene":[12],"expression":[13],"regulation":[14],"and":[15,32,45,146,150,182,191,203],"other":[16],"biological":[17],"evolution":[18],"processes.":[19],"It":[20],"also":[21],"has":[22],"a":[23,27,94,118,135,155],"crucial":[24],"role":[25],"in":[26,71,224],"living":[28],"organism's":[29],"physical":[30],"growth":[31],"structure.":[33],"comprises":[37],"three":[39],"stages":[40],"known":[41],"as":[42],"initiation,":[43],"elongation":[44],"termination,":[46],"whereas":[47,237],"origin":[49,222],"replication":[51,62,223],"sites":[52,220],"(ORI)":[53],"location":[56],"initiation":[58],"process.":[63],"There":[64],"exist":[65],"various":[66],"methodologies":[67],"to":[68,100,122,154,177,198],"identify":[69,101,123],"ORIs":[70,102,124],"genomic":[73,108],"sequences,":[74],"however,":[75],"these":[76],"methods":[77],"have":[78,86],"used":[79],"either":[80],"extensive":[81],"computations":[82],"execution,":[84],"or":[85],"limited":[87],"optimization":[88],"large":[91],"datasets.":[92],"Herein,":[93],"model":[95],"called":[96],"ORI-Deep":[97,215,232],"proposed":[99,116,167],"from":[103],"multiple":[105],"type":[107],"sequence":[109,226],"benchmark":[110],"data.":[111],"An":[112],"efficient":[113],"method":[114],"using":[117,140],"deep":[119],"neural":[120],"network":[121],"four":[126],"different":[127,175],"eukaryotic":[128],"species.":[129],"For":[130],"better":[131],"representation":[132],"data,":[134],"feature":[136],"vector":[137],"constructed":[139],"statistical":[141],"moments":[142],"training":[145],"testing":[147],"data":[149],"further":[152],"fed":[153],"long":[156],"short-term":[157],"memory":[158],"(LSTM)":[159],"network.":[160],"To":[161],"prove":[162],"effectiveness":[164],"model,":[168],"we":[169],"applied":[170],"several":[171],"validation":[172],"techniques":[173],"at":[174,235,242],"levels":[176],"obtain":[178],"seven":[179],"accuracy":[180,184],"metrics,":[181],"score":[185],"self-consistency,":[187],"10-fold":[188],"cross-validation,":[189],"jackknife":[190],"independent":[193],"set":[194],"test":[195],"observed":[197],"be":[199,212],"0.977,":[200,204],"0.948,":[201],"0.976":[202],"respectively.":[205],"Based":[206],"on":[207],"results,":[209],"it":[210],"can":[211,216],"concluded":[213],"that":[214],"efficiently":[217],"predict":[218],"with":[227],"high":[228],"accuracy.":[229],"Webserver":[230],"available":[234,241],"(https://share.streamlit.io/waqarhusain/orideep/main/app.py),":[236],"source":[238],"code":[239],"(https://github.com/WaqarHusain/OriDeep).":[243]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
