{"id":"https://openalex.org/W2101769535","doi":"https://doi.org/10.1287/ijoc.1090.0360","title":"Least-Squares Support Vector Machine Approach to Viral Replication Origin Prediction","display_name":"Least-Squares Support Vector Machine Approach to Viral Replication Origin Prediction","publication_year":2009,"publication_date":"2009-10-03","ids":{"openalex":"https://openalex.org/W2101769535","doi":"https://doi.org/10.1287/ijoc.1090.0360","mag":"2101769535","pmid":"https://pubmed.ncbi.nlm.nih.gov/20729987"},"language":"en","primary_location":{"id":"doi:10.1287/ijoc.1090.0360","is_oa":false,"landing_page_url":"https://doi.org/10.1287/ijoc.1090.0360","pdf_url":null,"source":{"id":"https://openalex.org/S165318533","display_name":"INFORMS journal on computing","issn_l":"1091-9856","issn":["1091-9856","1526-5528"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315699","host_organization_name":"Institute for Operations Research and the Management Sciences","host_organization_lineage":["https://openalex.org/P4310315699"],"host_organization_lineage_names":["Institute for Operations Research and the Management Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"INFORMS Journal on Computing","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/A5059475820","display_name":"Raul Cruz\u2010Cano","orcid":"https://orcid.org/0000-0001-7715-1198"},"institutions":[{"id":"https://openalex.org/I51380931","display_name":"Texas A&M University \u2013 Texarkana","ror":"https://ror.org/01x3z9745","country_code":"US","type":"education","lineage":["https://openalex.org/I51380931"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Raul Cruz-Cano","raw_affiliation_strings":["Department of Computer Science, Texas A&M University\u2013Texarkana, Texarkana, Texas 75505","Department of Computer Science, Texas A&M University--Texarkana, Texarkana, Texas 75505#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A&M University\u2013Texarkana, Texarkana, Texas 75505","institution_ids":["https://openalex.org/I51380931"]},{"raw_affiliation_string":"Department of Computer Science, Texas A&M University--Texarkana, Texarkana, Texas 75505#TAB#","institution_ids":["https://openalex.org/I51380931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036089466","display_name":"David S. H. Chew","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["SG","US"],"is_corresponding":false,"raw_author_name":"David S. H. Chew","raw_affiliation_strings":["Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore, and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089"],"affiliations":[{"raw_affiliation_string":"Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore, and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089","institution_ids":["https://openalex.org/I165932596","https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022585038","display_name":"Kwok-Pui Choi","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Kwok-Pui Choi","raw_affiliation_strings":["Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore"],"affiliations":[{"raw_affiliation_string":"Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040135909","display_name":"Ming\u2010Ying Leung","orcid":"https://orcid.org/0000-0003-2035-1214"},"institutions":[{"id":"https://openalex.org/I164936912","display_name":"The University of Texas at El Paso","ror":"https://ror.org/04d5vba33","country_code":"US","type":"education","lineage":["https://openalex.org/I164936912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ming-Ying Leung","raw_affiliation_strings":["Bioinformatics Program and Department of Mathematical Sciences, University of Texas at El Paso, El Paso, Texas 79968","Bioinformatics Program and Department of Mathematical Sciences, University of Texas at El Paso, El Paso, Texas 79968#TAB#"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Program and Department of Mathematical Sciences, University of Texas at El Paso, El Paso, Texas 79968","institution_ids":["https://openalex.org/I164936912"]},{"raw_affiliation_string":"Bioinformatics Program and Department of Mathematical Sciences, University of Texas at El Paso, El Paso, Texas 79968#TAB#","institution_ids":["https://openalex.org/I164936912"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5059475820"],"corresponding_institution_ids":["https://openalex.org/I51380931"],"apc_list":null,"apc_paid":null,"fwci":0.3706,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.68237716,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"22","issue":"3","first_page":"457","last_page":"470"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10625","display_name":"Herpesvirus Infections and Treatments","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10625","display_name":"Herpesvirus Infections and Treatments","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10981","display_name":"Cytomegalovirus and herpesvirus research","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/replication","display_name":"Replication (statistics)","score":0.8169277906417847},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.6969965696334839},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.632357120513916},{"id":"https://openalex.org/keywords/origin-of-replication","display_name":"Origin of replication","score":0.5372405648231506},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4619605243206024},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4400044083595276},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.42518261075019836},{"id":"https://openalex.org/keywords/viral-replication","display_name":"Viral replication","score":0.42210841178894043},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40808048844337463},{"id":"https://openalex.org/keywords/dna-replication","display_name":"DNA replication","score":0.35014793276786804},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32309389114379883},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2780008018016815},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17179334163665771},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.16103798151016235},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.15233197808265686},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.10042962431907654}],"concepts":[{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.8169277906417847},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.6969965696334839},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.632357120513916},{"id":"https://openalex.org/C58337764","wikidata":"https://www.wikidata.org/wiki/Q976651","display_name":"Origin of replication","level":4,"score":0.5372405648231506},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4619605243206024},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4400044083595276},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.42518261075019836},{"id":"https://openalex.org/C140704245","wikidata":"https://www.wikidata.org/wiki/Q3933202","display_name":"Viral replication","level":3,"score":0.42210841178894043},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40808048844337463},{"id":"https://openalex.org/C73573662","wikidata":"https://www.wikidata.org/wiki/Q130996","display_name":"DNA replication","level":3,"score":0.35014793276786804},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32309389114379883},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2780008018016815},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17179334163665771},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.16103798151016235},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.15233197808265686},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.10042962431907654},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1287/ijoc.1090.0360","is_oa":false,"landing_page_url":"https://doi.org/10.1287/ijoc.1090.0360","pdf_url":null,"source":{"id":"https://openalex.org/S165318533","display_name":"INFORMS journal on computing","issn_l":"1091-9856","issn":["1091-9856","1526-5528"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315699","host_organization_name":"Institute for Operations Research and the Management Sciences","host_organization_lineage":["https://openalex.org/P4310315699"],"host_organization_lineage_names":["Institute for Operations Research and the Management Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"INFORMS Journal on Computing","raw_type":"journal-article"},{"id":"pmid:20729987","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20729987","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":"INFORMS journal on computing","raw_type":null},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/105193","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/105193","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus","raw_type":"Article"},{"id":"pmh:oai:RePEc:inm:orijoc:v:22:y:2010:i:3:p:457-470","is_oa":false,"landing_page_url":"http://doi.org/10.1287/ijoc.1090.0360","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2111535","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2923853","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320698","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W11319819","https://openalex.org/W146900863","https://openalex.org/W190813328","https://openalex.org/W202837327","https://openalex.org/W1496317909","https://openalex.org/W1506780151","https://openalex.org/W1596717185","https://openalex.org/W1731704781","https://openalex.org/W1789174141","https://openalex.org/W1801988245","https://openalex.org/W1832545641","https://openalex.org/W1868857024","https://openalex.org/W1888245696","https://openalex.org/W1982227872","https://openalex.org/W1988377515","https://openalex.org/W2019360170","https://openalex.org/W2030976750","https://openalex.org/W2034285658","https://openalex.org/W2041387425","https://openalex.org/W2052812603","https://openalex.org/W2056308182","https://openalex.org/W2060878103","https://openalex.org/W2072556121","https://openalex.org/W2090432153","https://openalex.org/W2096207715","https://openalex.org/W2097839764","https://openalex.org/W2098276784","https://openalex.org/W2099564671","https://openalex.org/W2109681606","https://openalex.org/W2110709196","https://openalex.org/W2113362355","https://openalex.org/W2119387367","https://openalex.org/W2120669962","https://openalex.org/W2121519777","https://openalex.org/W2140211206","https://openalex.org/W2142705391","https://openalex.org/W2143426320","https://openalex.org/W2145872581","https://openalex.org/W2150025400","https://openalex.org/W2151388232","https://openalex.org/W2153635508","https://openalex.org/W2156909104","https://openalex.org/W2161327845","https://openalex.org/W2161694749","https://openalex.org/W2164191424","https://openalex.org/W2170146596","https://openalex.org/W2413535096","https://openalex.org/W2492794003","https://openalex.org/W4246285604"],"related_works":["https://openalex.org/W2329795915","https://openalex.org/W1981922425","https://openalex.org/W2102366565","https://openalex.org/W2082627754","https://openalex.org/W2123987161","https://openalex.org/W2043025987","https://openalex.org/W2122909165","https://openalex.org/W84663166","https://openalex.org/W2059208699","https://openalex.org/W2084837006"],"abstract_inverted_index":{"Replication":[0],"of":[1,12,24,31,40,58,87,97,152,171,183],"their":[2],"DNA":[3,26],"genomes":[4],"is":[5],"a":[6,63,85,164],"central":[7],"step":[8],"in":[9,187],"the":[10,25,36,56,79,95,115,124,129,133,142,148,153,160,169,181],"reproduction":[11],"many":[13],"viruses.":[14,42],"Procedures":[15],"to":[16,111,168],"find":[17,147],"replication":[18,27,48,135,176],"origins,":[19],"which":[20],"are":[21,29],"initiation":[22],"sites":[23],"process,":[28],"therefore":[30],"great":[32],"importance":[33],"for":[34,46,132,174],"controlling":[35],"growth":[37],"and":[38,72,104,179],"spread":[39],"such":[41],"Existing":[43],"computational":[44,172],"methods":[45],"viral":[47,92,175],"origin":[49,177],"prediction":[50,130,178],"have":[51],"mostly":[52],"been":[53],"tested":[54],"within":[55],"family":[57,81],"herpesviruses.":[59],"This":[60],"paper":[61],"proposes":[62],"new":[64],"approach":[65,101,126],"by":[66,114,138],"least-squares":[67],"support":[68],"vector":[69],"machines":[70],"(LS-SVMs)":[71],"tests":[73],"its":[74],"performance":[75],"not":[76],"only":[77],"on":[78,84],"herpes":[80],"but":[82],"also":[83,145],"collection":[86],"caudoviruses":[88],"coming":[89],"from":[90],"three":[91],"families":[93],"under":[94],"order":[96],"caudovirales.":[98],"The":[99,156],"LS-SVM":[100,125,143],"provides":[102],"sensitivities":[103],"positive":[105],"predictive":[106],"values":[107],"superior":[108],"or":[109],"comparable":[110],"those":[112],"given":[113],"previous":[116,122],"methods.":[117],"When":[118],"suitably":[119],"combined":[120],"with":[121],"methods,":[123],"further":[127],"improves":[128],"accuracy":[131],"herpesvirus":[134],"origins.":[136],"Furthermore,":[137],"recursive":[139],"feature":[140],"elimination,":[141],"has":[144],"helped":[146],"most":[149],"significant":[150],"features":[151],"data":[154],"sets.":[155],"results":[157],"suggest":[158],"that":[159],"LS-SVMs":[161],"will":[162],"be":[163],"highly":[165],"useful":[166],"addition":[167],"set":[170],"tools":[173],"illustrate":[180],"value":[182],"optimization-based":[184],"computing":[185],"techniques":[186],"biomedical":[188],"applications.":[189]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
