{"id":"https://openalex.org/W2784113007","doi":"https://doi.org/10.1093/bib/bbx174","title":"Recent development of Ori-Finder system and DoriC database for microbial replication origins","display_name":"Recent development of Ori-Finder system and DoriC database for microbial replication origins","publication_year":2017,"publication_date":"2017-12-21","ids":{"openalex":"https://openalex.org/W2784113007","doi":"https://doi.org/10.1093/bib/bbx174","mag":"2784113007","pmid":"https://pubmed.ncbi.nlm.nih.gov/29329409"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbx174","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbx174","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":"review","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/A5009471000","display_name":"Hao Luo","orcid":"https://orcid.org/0000-0003-2714-8817"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hao Luo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016204750","display_name":"Chun\u2010Lan Quan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chun-Lan Quan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001804966","display_name":"Chong Peng","orcid":"https://orcid.org/0000-0002-7649-5551"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chong Peng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5074242312","display_name":"Feng Gao","orcid":"https://orcid.org/0000-0002-9563-3841"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Feng Gao","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-9563-3841","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5009471000"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.528,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.92890581,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"20","issue":"4","first_page":"1114","last_page":"1124"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9987000226974487,"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"}},"topics":[{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9987000226974487,"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"}},{"id":"https://openalex.org/T10123","display_name":"DNA Repair Mechanisms","score":0.9980999827384949,"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":0.989300012588501,"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/origin-of-replication","display_name":"Origin of replication","score":0.7393246293067932},{"id":"https://openalex.org/keywords/replication","display_name":"Replication (statistics)","score":0.728256344795227},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.712395191192627},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6433281898498535},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6006349921226501},{"id":"https://openalex.org/keywords/dna-replication","display_name":"DNA replication","score":0.5175156593322754},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4818328619003296},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4667750895023346},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.4356389045715332},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4163532555103302},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.3240041136741638},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.272047221660614},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.22960689663887024}],"concepts":[{"id":"https://openalex.org/C58337764","wikidata":"https://www.wikidata.org/wiki/Q976651","display_name":"Origin of replication","level":4,"score":0.7393246293067932},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.728256344795227},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.712395191192627},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6433281898498535},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6006349921226501},{"id":"https://openalex.org/C73573662","wikidata":"https://www.wikidata.org/wiki/Q130996","display_name":"DNA replication","level":3,"score":0.5175156593322754},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4818328619003296},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4667750895023346},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.4356389045715332},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4163532555103302},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3240041136741638},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.272047221660614},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.22960689663887024},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004261","descriptor_name":"DNA Replication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004261","descriptor_name":"DNA Replication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004261","descriptor_name":"DNA Replication","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbx174","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbx174","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:29329409","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29329409","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/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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":88,"referenced_works":["https://openalex.org/W626513392","https://openalex.org/W1931590386","https://openalex.org/W1967531530","https://openalex.org/W1971403296","https://openalex.org/W1988035696","https://openalex.org/W1990428134","https://openalex.org/W1994946291","https://openalex.org/W2008898045","https://openalex.org/W2015776846","https://openalex.org/W2016060560","https://openalex.org/W2019889601","https://openalex.org/W2020058603","https://openalex.org/W2025847444","https://openalex.org/W2026208100","https://openalex.org/W2026570450","https://openalex.org/W2027170016","https://openalex.org/W2033515367","https://openalex.org/W2036240398","https://openalex.org/W2048415203","https://openalex.org/W2051877145","https://openalex.org/W2057366479","https://openalex.org/W2062550534","https://openalex.org/W2066915800","https://openalex.org/W2068881314","https://openalex.org/W2082903017","https://openalex.org/W2084281933","https://openalex.org/W2086084754","https://openalex.org/W2088710021","https://openalex.org/W2092210299","https://openalex.org/W2096525273","https://openalex.org/W2097483331","https://openalex.org/W2099719926","https://openalex.org/W2101414295","https://openalex.org/W2104539744","https://openalex.org/W2105199251","https://openalex.org/W2118877430","https://openalex.org/W2124281279","https://openalex.org/W2125003792","https://openalex.org/W2128784723","https://openalex.org/W2130402515","https://openalex.org/W2130607415","https://openalex.org/W2131668304","https://openalex.org/W2132269330","https://openalex.org/W2134405043","https://openalex.org/W2140952049","https://openalex.org/W2141137078","https://openalex.org/W2145751704","https://openalex.org/W2146994562","https://openalex.org/W2147082907","https://openalex.org/W2149359491","https://openalex.org/W2149851064","https://openalex.org/W2151165630","https://openalex.org/W2152199066","https://openalex.org/W2157009395","https://openalex.org/W2157358322","https://openalex.org/W2158708753","https://openalex.org/W2161136014","https://openalex.org/W2161709031","https://openalex.org/W2163703477","https://openalex.org/W2166049912","https://openalex.org/W2166865790","https://openalex.org/W2167567837","https://openalex.org/W2172340082","https://openalex.org/W2179302559","https://openalex.org/W2197308808","https://openalex.org/W2220556288","https://openalex.org/W2265563546","https://openalex.org/W2334650965","https://openalex.org/W2337688411","https://openalex.org/W2338583862","https://openalex.org/W2345805394","https://openalex.org/W2412796905","https://openalex.org/W2418943590","https://openalex.org/W2461955027","https://openalex.org/W2519510067","https://openalex.org/W2549105671","https://openalex.org/W2557375457","https://openalex.org/W2558411436","https://openalex.org/W2585822716","https://openalex.org/W2593377842","https://openalex.org/W2593419675","https://openalex.org/W2750884682","https://openalex.org/W2751131112","https://openalex.org/W2899616402","https://openalex.org/W3198823065","https://openalex.org/W4234797890","https://openalex.org/W6693695204","https://openalex.org/W7075633510"],"related_works":["https://openalex.org/W2889029343","https://openalex.org/W2079327011","https://openalex.org/W2056973287","https://openalex.org/W2061340009","https://openalex.org/W3111025641","https://openalex.org/W3202542829","https://openalex.org/W1965562485","https://openalex.org/W2340204314","https://openalex.org/W1956137100","https://openalex.org/W2104081677"],"abstract_inverted_index":{"DNA":[0,46,121],"replication":[1,4,16,32,58,80,95,122,180,208],"begins":[2],"at":[3],"origins":[5,17,33,59,81,96,123,181,209],"in":[6,22,36,45,54,60,82,116,124,132,182,188,196,203,213],"all":[7],"three":[8],"domains":[9],"of":[10,15,30,41,57,70,120,129,141,152,207,221,241],"life.":[11],"Identification":[12],"and":[13,28,72,85,93,110,134,139,148,159,171,210,224,235,243],"characterization":[14],"are":[18,113,245],"important":[19],"not":[20],"only":[21],"providing":[23],"insights":[24],"into":[25,103],"the":[26,31,38,42,55,67,90,94,117,142,179,194,204,219,239],"structure":[27],"function":[29],"but":[34],"also":[35,246],"understanding":[37],"regulatory":[39],"mechanisms":[40],"initiation":[43],"step":[44],"replication.":[47],"The":[48],"Z-curve":[49,91],"method":[50],"has":[51,174],"been":[52,76,101,175,200],"used":[53,115,176,202],"identification":[56,128],"archaeal":[61,86,135],"genomes":[62,87],"successfully":[63],"since":[64],"2002.":[65],"Furthermore,":[66],"Web":[68],"servers":[69],"Ori-Finder":[71,73,108,164,172,222,242],"2":[74],"have":[75,100,199],"developed":[77],"to":[78,156,177],"predict":[79],"both":[83],"bacterial":[84,133,153],"based":[88],"on":[89],"method,":[92],"with":[97],"manual":[98],"curation":[99],"collected":[102],"an":[104],"online":[105],"database,":[106],"DoriC.":[107],"system":[109,165,173,223],"DoriC":[111,197,225,244],"database":[112,198,226],"currently":[114],"research":[118],"field":[119],"prokaryotes,":[125],"including:":[126],"(i)":[127],"oriC":[130,146],"regions":[131],"genomes;":[136],"(ii)":[137],"discovery":[138],"analysis":[140,151],"conserved":[143],"sequences":[144],"within":[145],"regions;":[147],"(iii)":[149],"strand-biased":[150],"genomes.":[154,215],"Up":[155],"now,":[157],"more":[158,160],"predicted":[161],"results":[162],"by":[163,168],"were":[166],"supported":[167],"subsequent":[169],"experiments,":[170],"identify":[178],">":[183],"100":[184],"newly":[185],"sequenced":[186],"prokaryotes":[187],"their":[189,230],"genome":[190],"reports.":[191],"In":[192],"addition,":[193],"data":[195],"widely":[201],"large-scale":[205],"analyses":[206],"strand":[211],"bias":[212],"prokaryotic":[214],"Here,":[216],"we":[217],"review":[218],"development":[220],"as":[227,229],"well":[228],"applications.":[231],"Some":[232],"future":[233],"directions":[234],"aspects":[236],"for":[237],"extending":[238],"application":[240],"presented.":[247]},"counts_by_year":[{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
