{"id":"https://openalex.org/W2172245210","doi":"https://doi.org/10.1099/vir.0.80141-0","title":"Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods","display_name":"Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods","publication_year":2004,"publication_date":"2004-09-24","ids":{"openalex":"https://openalex.org/W2172245210","doi":"https://doi.org/10.1099/vir.0.80141-0","mag":"2172245210","pmid":"https://pubmed.ncbi.nlm.nih.gov/15448367"},"language":"en","primary_location":{"id":"doi:10.1099/vir.0.80141-0","doi":"https://doi.org/10.1099/vir.0.80141-0","is_oa":false,"landing_page_url":"https://doi.org/10.1099/vir.0.80141-0","pdf_url":null,"source":{"id":"https://openalex.org/S103035011","display_name":"Journal of General Virology","issn_l":"0022-1317","issn":["0022-1317","1465-2099"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320497","host_organization_name":"Microbiology Society","host_organization_lineage":["https://openalex.org/P4310320497"],"host_organization_lineage_names":["Microbiology Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of General Virology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"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/A5075427321","display_name":"Andrew K. Tuplin","orcid":"https://orcid.org/0000-0003-2524-707X","observed_orcids":["https://orcid.org/0000-0003-2524-707X"]},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"A. Tuplin","raw_affiliation_strings":["Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, Scotland, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085745151","display_name":"David John Evans","orcid":"https://orcid.org/0000-0002-1315-4258","observed_orcids":["https://orcid.org/0000-0002-1315-4258"]},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"D. J. Evans","raw_affiliation_strings":["Department of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, Scotland, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070291466","display_name":"Peter Simmonds K","orcid":"https://orcid.org/0000-0002-7964-4700","observed_orcids":["https://orcid.org/0000-0002-7964-4700"]},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"P. Simmonds","raw_affiliation_strings":["Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, Scotland, UK","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.3592,"has_fulltext":false,"cited_by_count":114,"citation_normalized_percentile":{"value":0.89010989,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"85","issue":"10","first_page":"3037","last_page":"3047"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10151","display_name":"Hepatitis C virus research","score":0.7387999892234802,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"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/T10151","display_name":"Hepatitis C virus research","score":0.7387999892234802,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.2409999966621399,"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/T11495","display_name":"Animal Virus Infections Studies","score":0.003700000001117587,"subfield":{"id":"https://openalex.org/subfields/1103","display_name":"Animal Science and Zoology"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hepatitis-c-virus","display_name":"hepatitis C virus","score":0.9990000128746033},{"id":"https://openalex.org/keywords/rna-secondary-structure","display_name":"RNA secondary structure","score":0.9900000095367432},{"id":"https://openalex.org/keywords/core-area","display_name":"core area","score":0.7400000095367432},{"id":"https://openalex.org/keywords/ns5b-region","display_name":"NS5B region","score":0.9819999933242798},{"id":"https://openalex.org/keywords/cis-acting-replication-element","display_name":"cis-acting replication element","score":0.9399999976158142},{"id":"https://openalex.org/keywords/stem-loop-structure","display_name":"stem-loop structure","score":0.8640000224113464},{"id":"https://openalex.org/keywords/hcv-genotypes","display_name":"HCV genotypes","score":0.8309999704360962},{"id":"https://openalex.org/keywords/single-stranded-regions","display_name":"single-stranded regions","score":0.7279999852180481},{"id":"https://openalex.org/keywords/translation-initiation","display_name":"translation initiation","score":0.7170000076293945},{"id":"https://openalex.org/keywords/host-persistence","display_name":"host persistence","score":0.6169999837875366},{"id":"https://openalex.org/keywords/positive-strand-rna-viruses","display_name":"positive-strand RNA viruses","score":0.7540000081062317}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7930777668952942},{"id":"https://openalex.org/C2781426373","wikidata":"https://www.wikidata.org/wiki/Q24766653","display_name":"NS5B","level":5,"score":0.7640094757080078},{"id":"https://openalex.org/C10879258","wikidata":"https://www.wikidata.org/wiki/Q76826611","display_name":"RNase P","level":4,"score":0.705581784248352},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.6916688084602356},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6151876449584961},{"id":"https://openalex.org/C175156509","wikidata":"https://www.wikidata.org/wiki/Q1990218","display_name":"Cleavage (geology)","level":3,"score":0.6134141087532043},{"id":"https://openalex.org/C69766542","wikidata":"https://www.wikidata.org/wiki/Q3430179","display_name":"RNase H","level":5,"score":0.6091234683990479},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4636003077030182},{"id":"https://openalex.org/C2776408679","wikidata":"https://www.wikidata.org/wiki/Q708693","display_name":"Hepatitis C virus","level":3,"score":0.3993417024612427},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.37799105048179626},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3398194909095764},{"id":"https://openalex.org/C2781463415","wikidata":"https://www.wikidata.org/wiki/Q2082778","display_name":"Hepacivirus","level":4,"score":0.29292231798171997},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22376862168312073},{"id":"https://openalex.org/C43369102","wikidata":"https://www.wikidata.org/wiki/Q2307625","display_name":"Fracture (geology)","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012260","descriptor_name":"Ribonucleases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012324","descriptor_name":"RNA-Dependent RNA Polymerase","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017361","descriptor_name":"Viral Nonstructural Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1099/vir.0.80141-0","doi":"https://doi.org/10.1099/vir.0.80141-0","is_oa":false,"landing_page_url":"https://doi.org/10.1099/vir.0.80141-0","pdf_url":null,"source":{"id":"https://openalex.org/S103035011","display_name":"Journal of General Virology","issn_l":"0022-1317","issn":["0022-1317","1465-2099"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320497","host_organization_name":"Microbiology Society","host_organization_lineage":["https://openalex.org/P4310320497"],"host_organization_lineage_names":["Microbiology Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of General Virology","raw_type":"journal-article"},{"id":"pmid:15448367","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15448367","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,"listed_in":[],"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":"The Journal of general virology","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.334.338","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.334.338","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://vir.sgmjournals.org/content/85/10/3037.full.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1486369891","https://openalex.org/W1519015484","https://openalex.org/W1776345984","https://openalex.org/W1836032532","https://openalex.org/W1902706292","https://openalex.org/W1914838920","https://openalex.org/W1914884504","https://openalex.org/W1966297612","https://openalex.org/W1969728880","https://openalex.org/W1972610030","https://openalex.org/W1973417881","https://openalex.org/W1976341528","https://openalex.org/W1976707255","https://openalex.org/W1984987205","https://openalex.org/W1991274836","https://openalex.org/W1996208605","https://openalex.org/W2005674957","https://openalex.org/W2008557779","https://openalex.org/W2012033859","https://openalex.org/W2021447506","https://openalex.org/W2036456126","https://openalex.org/W2053238170","https://openalex.org/W2089829321","https://openalex.org/W2093191777","https://openalex.org/W2106132583","https://openalex.org/W2108218303","https://openalex.org/W2112363848","https://openalex.org/W2118727579","https://openalex.org/W2124220387","https://openalex.org/W2125908595","https://openalex.org/W2131522965","https://openalex.org/W2132034333","https://openalex.org/W2133609692","https://openalex.org/W2138172337","https://openalex.org/W2141157874","https://openalex.org/W2143153134","https://openalex.org/W2147427891","https://openalex.org/W2148510296","https://openalex.org/W2149294770","https://openalex.org/W2153293128","https://openalex.org/W2167222139","https://openalex.org/W2168694015","https://openalex.org/W2169757199","https://openalex.org/W6681666782","https://openalex.org/W6685098520"],"related_works":["https://openalex.org/W2147427891","https://openalex.org/W2158589895","https://openalex.org/W4400255619","https://openalex.org/W2053238170","https://openalex.org/W2169218501","https://openalex.org/W2132034333","https://openalex.org/W2087021327","https://openalex.org/W1969742464","https://openalex.org/W2136377885","https://openalex.org/W7057524345"],"abstract_inverted_index":{"There":[0],"is":[1,161,217,241],"accumulating":[2],"evidence":[3,185],"from":[4,99],"bioinformatic":[5,88],"studies":[6,28],"that":[7,51,111,129,240],"hepatitis":[8],"C":[9],"virus":[10],"(HCV)":[11],"possesses":[12],"extensive":[13],"RNA":[14,81,97,109,227,238],"secondary":[15],"structure":[16,34],"in":[17,35,79,114,132,175,197,224],"the":[18,24,36,61,100,108,122,155,167,176,198,233],"core":[19,101,215],"and":[20,102,179,205,214],"NS5B-encoding":[21],"regions":[22,104],"of":[23,64,76,96,124,148,154,169,189,208,210,232,235],"genome.":[25],"Recent":[26],"functional":[27],"have":[29,90],"defined":[30],"one":[31,147],"such":[32],"stem-loop":[33,66,201],"NS5B":[37,103,213],"region":[38,153],"as":[39,139,141],"an":[40],"essential":[41],"cis-acting":[42],"replication":[43],"element":[44],"(CRE).":[45],"A":[46],"program":[47],"was":[48,183],"developed":[49],"(STRUCTUR_DIST)":[50],"analyses":[52],"multiple":[53],"rna-folding":[54],"patterns":[55],"predicted":[56,65,80,200],"by":[57,69],"mfold":[58],"to":[59,73,105,157],"determine":[60],"evolutionary":[62],"conservation":[63,172],"structures":[67,110,216],"and,":[68],"a":[70,152,229],"new":[71],"method,":[72],"analyse":[74],"frequencies":[75],"covariant":[77],"sites":[78,196],"folding":[82],"between":[83,173],"HCV":[84,134,177],"genotypes.":[85],"These":[86],"novel":[87],"methods":[89,120],"been":[91],"combined":[92],"with":[93,151,221,243],"enzymic":[94],"mapping":[95],"transcripts":[98],"precisely":[106],"delineate":[107],"are":[112,130],"present":[113],"these":[115,119,211],"genomic":[116],"regions.":[117],"Together,":[118],"predict":[121],"existence":[123,168],"multiple,":[125],"often":[126],"juxtaposed":[127],"stem-loops":[128],"found":[131],"all":[133],"genotypes":[135,174],"throughout":[136],"both":[137],"regions,":[138,146,181],"well":[140],"several":[142],"strikingly":[143],"conserved":[144],"single-stranded":[145,180],"which":[149,158],"coincides":[150],"genome":[156],"ribosomal":[159],"access":[160],"required":[162],"for":[163,186],"translation":[164],"initiation.":[165],"Despite":[166],"marked":[170],"sequence":[171],"CRE":[178],"there":[182],"no":[184],"comparable":[187],"suppression":[188],"variability":[190,207],"at":[191],"either":[192],"synonymous":[193],"or":[194],"non-synonymous":[195],"other":[199,212],"structures.":[202],"The":[203],"configuration":[204,231],"genetic":[206],"many":[209,236],"perhaps":[218],"more":[219],"consistent":[220],"their":[222],"involvement":[223],"genome-scale":[225],"ordered":[226],"structure,":[228],"structural":[230],"genomes":[234],"positive-stranded":[237],"viruses":[239],"associated":[242],"host":[244],"persistence.":[245]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2016-06-24T00:00:00"}