{"id":"https://openalex.org/W3081538984","doi":"https://doi.org/10.1093/bib/bbaa182","title":"Ori-Finder 3: a web server for genome-wide prediction of replication origins in <i>Saccharomyces cerevisiae</i>","display_name":"Ori-Finder 3: a web server for genome-wide prediction of replication origins in <i>Saccharomyces cerevisiae</i>","publication_year":2020,"publication_date":"2020-07-15","ids":{"openalex":"https://openalex.org/W3081538984","doi":"https://doi.org/10.1093/bib/bbaa182","mag":"3081538984","pmid":"https://pubmed.ncbi.nlm.nih.gov/34020544"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa182","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa182","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/A5100411859","display_name":"Dan Wang","orcid":"https://orcid.org/0000-0002-8583-448X"},"institutions":[{"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":"Dan Wang","raw_affiliation_strings":["Department of Physics, School of Science, Tianjin University"],"affiliations":[{"raw_affiliation_string":"Department of Physics, School of Science, Tianjin University","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/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 University"],"affiliations":[{"raw_affiliation_string":"Department of Physics, School of Science, Tianjin University","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/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Feng Gao","raw_affiliation_strings":["Department of Physics, School of Science, and the Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University"],"affiliations":[{"raw_affiliation_string":"Department of Physics, School of Science, and the Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University","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/I162868743"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.58,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.65022801,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"22","issue":"3","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":0.9987999796867371,"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":0.9987999796867371,"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":0.9977999925613403,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/origin-of-replication","display_name":"Origin of replication","score":0.6537624597549438},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6353123784065247},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.6255122423171997},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5917419195175171},{"id":"https://openalex.org/keywords/replication","display_name":"Replication (statistics)","score":0.5440170168876648},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.52409428358078},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.511293888092041},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43435728549957275},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4273444414138794},{"id":"https://openalex.org/keywords/dna-replication","display_name":"DNA replication","score":0.4171893894672394},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39883100986480713},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.27322715520858765},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.18717893958091736},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15637508034706116},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.11633354425430298},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07993173599243164}],"concepts":[{"id":"https://openalex.org/C58337764","wikidata":"https://www.wikidata.org/wiki/Q976651","display_name":"Origin of replication","level":4,"score":0.6537624597549438},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6353123784065247},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.6255122423171997},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5917419195175171},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.5440170168876648},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.52409428358078},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.511293888092041},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43435728549957275},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4273444414138794},{"id":"https://openalex.org/C73573662","wikidata":"https://www.wikidata.org/wiki/Q130996","display_name":"DNA replication","level":3,"score":0.4171893894672394},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39883100986480713},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.27322715520858765},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.18717893958091736},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15637508034706116},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.11633354425430298},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07993173599243164},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine 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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa182","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa182","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:34020544","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34020544","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":[],"awards":[{"id":"https://openalex.org/G1710608835","display_name":null,"funder_award_id":"2018YFA0903700","funder_id":"https://openalex.org/F4320335613","funder_display_name":"State Key Laboratory of Biochemical Engineering"},{"id":"https://openalex.org/G202076348","display_name":null,"funder_award_id":"91746119","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7243257119","display_name":null,"funder_award_id":"21621004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8573908226","display_name":null,"funder_award_id":"31171238","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/F4320335613","display_name":"State Key Laboratory of Biochemical Engineering","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1594639112","https://openalex.org/W1952444787","https://openalex.org/W1971894358","https://openalex.org/W1973070150","https://openalex.org/W1976791027","https://openalex.org/W1987168746","https://openalex.org/W1993623149","https://openalex.org/W2008486131","https://openalex.org/W2021823827","https://openalex.org/W2027170016","https://openalex.org/W2034285658","https://openalex.org/W2048620141","https://openalex.org/W2053775943","https://openalex.org/W2056298514","https://openalex.org/W2057587708","https://openalex.org/W2059594509","https://openalex.org/W2061449183","https://openalex.org/W2068881314","https://openalex.org/W2075320162","https://openalex.org/W2087909839","https://openalex.org/W2096954920","https://openalex.org/W2101234009","https://openalex.org/W2102221598","https://openalex.org/W2110643123","https://openalex.org/W2114850508","https://openalex.org/W2119544261","https://openalex.org/W2121168511","https://openalex.org/W2121980126","https://openalex.org/W2134421533","https://openalex.org/W2142294062","https://openalex.org/W2147082907","https://openalex.org/W2147835058","https://openalex.org/W2148373857","https://openalex.org/W2148771849","https://openalex.org/W2153635508","https://openalex.org/W2156125289","https://openalex.org/W2157009395","https://openalex.org/W2165234308","https://openalex.org/W2166459599","https://openalex.org/W2171460421","https://openalex.org/W2171582839","https://openalex.org/W2214602901","https://openalex.org/W2328176404","https://openalex.org/W2409368645","https://openalex.org/W2473838984","https://openalex.org/W2784113007","https://openalex.org/W2804489036","https://openalex.org/W2810211328","https://openalex.org/W2901754076","https://openalex.org/W2949485484","https://openalex.org/W2970965315","https://openalex.org/W3007150491","https://openalex.org/W6675354045","https://openalex.org/W6785705305"],"related_works":["https://openalex.org/W2123987161","https://openalex.org/W2082627754","https://openalex.org/W2043025987","https://openalex.org/W2122909165","https://openalex.org/W84663166","https://openalex.org/W2059208699","https://openalex.org/W2084837006","https://openalex.org/W2155705928","https://openalex.org/W2092686644","https://openalex.org/W4284970895"],"abstract_inverted_index":{"DNA":[0,88],"replication":[1,22,76],"is":[2],"a":[3,66,143,153,161],"fundamental":[4],"process":[5],"in":[6,27,78,113,150],"all":[7],"organisms;":[8],"this":[9,31],"event":[10],"initiates":[11],"at":[12,81,105,180],"sites":[13],"termed":[14],"origins":[15,23,77],"of":[16,20,47,75,122,145],"replication.":[17],"The":[18,90],"characteristics":[19],"eukaryotic":[21],"are":[24,55],"best":[25],"understood":[26],"Saccharomyces":[28],"cerevisiae.":[29],"For":[30,109],"species,":[32],"origin":[33],"prediction":[34,74,168],"algorithms":[35],"or":[36],"web":[37,163],"servers":[38],"have":[39],"been":[40],"developed":[41,160],"based":[42,85],"on":[43,87,137],"the":[44,61,72,82,106,110,114,123,131,146,166,171],"sequence":[45,100],"features":[46],"autonomously":[48],"replicating":[49],"sequences":[50],"(ARSs).":[51],"However,":[52],"their":[53],"performances":[54],"far":[56],"from":[57],"satisfactory.":[58],"By":[59],"utilizing":[60],"Z-curve":[62],"methodology,":[63],"we":[64,140,159],"present":[65],"novel":[67],"pipeline,":[68],"Ori-Finder":[69,138],"3,":[70,139],"for":[71],"computational":[73],"S.":[79,115,155],"cerevisiae":[80,116,156],"genome-wide":[83],"level":[84],"solely":[86],"sequences.":[89],"ARS":[91,98,133,167],"exhibiting":[92],"both":[93],"an":[94],"AT-rich":[95],"stretch":[96],"and":[97,120,126,170],"consensus":[99],"element":[101],"can":[102,176],"be":[103,177],"predicted":[104,147,172],"single-nucleotide":[107],"level.":[108],"identified":[111,149],"ARSs":[112,148,173],"reference":[117],"genome,":[118],"83":[119],"60%":[121],"top":[124,127],"100":[125],"300":[128],"predictions":[129],"matched":[130],"known":[132],"records,":[134],"respectively.":[135],"Based":[136],"subsequently":[141],"built":[142],"database":[144],"more":[151],"than":[152],"hundred":[154],"genomes.":[157],"Consequently,":[158],"user-friendly":[162],"server":[164],"including":[165],"pipeline":[169],"database,":[174],"which":[175],"freely":[178],"accessed":[179],"http://tubic.tju.edu.cn/Ori-Finder3.":[181]},"counts_by_year":[{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2020-09-08T00:00:00"}
