{"id":"https://openalex.org/W2411267069","doi":"https://doi.org/10.1093/bioinformatics/btw323","title":"Prediction of conserved long-range RNA-RNA interactions in full viral genomes","display_name":"Prediction of conserved long-range RNA-RNA interactions in full viral genomes","publication_year":2016,"publication_date":"2016-06-10","ids":{"openalex":"https://openalex.org/W2411267069","doi":"https://doi.org/10.1093/bioinformatics/btw323","mag":"2411267069","pmid":"https://pubmed.ncbi.nlm.nih.gov/27288498"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw323","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/19/2928/25072544/btw323.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/19/2928/25072544/btw323.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028802154","display_name":"Markus Fricke","orcid":null},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Markus Fricke","raw_affiliation_strings":["1 Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041475009","display_name":"Manja Marz","orcid":"https://orcid.org/0000-0003-4783-8823"},"institutions":[{"id":"https://openalex.org/I315704651","display_name":"Leibniz Association","ror":"https://ror.org/01n6r0e97","country_code":"DE","type":"government","lineage":["https://openalex.org/I315704651"]},{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Manja Marz","raw_affiliation_strings":["1 Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany","2 FLI Leibniz Institute for Age Research, Jena, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany","institution_ids":["https://openalex.org/I76198965"]},{"raw_affiliation_string":"2 FLI Leibniz Institute for Age Research, Jena, Germany","institution_ids":["https://openalex.org/I315704651"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041475009"],"corresponding_institution_ids":["https://openalex.org/I315704651","https://openalex.org/I76198965"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.4515,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.82036355,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"32","issue":"19","first_page":"2928","last_page":"2935"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.11249999701976776,"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/T10604","display_name":"RNA Research and Splicing","score":0.11249999701976776,"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/T10166","display_name":"Mosquito-borne diseases and control","score":0.08950000256299973,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"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/T11668","display_name":"interferon and immune responses","score":0.07670000195503235,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"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/rna","display_name":"RNA","score":0.7783758640289307},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5421051383018494},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5331235527992249},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4938667416572571},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.4800487756729126},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4541544020175934},{"id":"https://openalex.org/keywords/rna-editing","display_name":"RNA editing","score":0.442655086517334},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.32269564270973206},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.180536150932312}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7783758640289307},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5421051383018494},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5331235527992249},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4938667416572571},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.4800487756729126},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4541544020175934},{"id":"https://openalex.org/C21786251","wikidata":"https://www.wikidata.org/wiki/Q14886350","display_name":"RNA editing","level":4,"score":0.442655086517334},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.32269564270973206},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.180536150932312},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw323","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/19/2928/25072544/btw323.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27288498","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27288498","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7189868","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7189868","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/19/2928","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/19/2928","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"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":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw323","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/19/2928/25072544/btw323.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2411267069.pdf"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1600974081","https://openalex.org/W1873547760","https://openalex.org/W1969057315","https://openalex.org/W1970294872","https://openalex.org/W1971141327","https://openalex.org/W1973783135","https://openalex.org/W1983815263","https://openalex.org/W1987263725","https://openalex.org/W1988081902","https://openalex.org/W2001580063","https://openalex.org/W2006099525","https://openalex.org/W2022687771","https://openalex.org/W2042844243","https://openalex.org/W2043653977","https://openalex.org/W2045864964","https://openalex.org/W2069642610","https://openalex.org/W2070896584","https://openalex.org/W2086561953","https://openalex.org/W2092267416","https://openalex.org/W2094253263","https://openalex.org/W2105538224","https://openalex.org/W2106927931","https://openalex.org/W2109098475","https://openalex.org/W2109402946","https://openalex.org/W2111272410","https://openalex.org/W2119340328","https://openalex.org/W2119896177","https://openalex.org/W2119905351","https://openalex.org/W2124995041","https://openalex.org/W2127774996","https://openalex.org/W2128880918","https://openalex.org/W2129706781","https://openalex.org/W2132885152","https://openalex.org/W2135086602","https://openalex.org/W2136046332","https://openalex.org/W2138085567","https://openalex.org/W2138532098","https://openalex.org/W2138819288","https://openalex.org/W2144775551","https://openalex.org/W2144979082","https://openalex.org/W2146277683","https://openalex.org/W2148346447","https://openalex.org/W2149824411","https://openalex.org/W2150882562","https://openalex.org/W2158589895","https://openalex.org/W2158804744","https://openalex.org/W2160515562","https://openalex.org/W2161159766","https://openalex.org/W2171586566","https://openalex.org/W4205477035","https://openalex.org/W6681367416"],"related_works":["https://openalex.org/W4239667766","https://openalex.org/W4248211466","https://openalex.org/W2998988912","https://openalex.org/W3083397822","https://openalex.org/W3045610206","https://openalex.org/W2162169386","https://openalex.org/W2893403792","https://openalex.org/W2022490671","https://openalex.org/W2410226897","https://openalex.org/W3027254392"],"abstract_inverted_index":{"MOTIVATION:":[0],"Long-range":[1],"RNA-RNA":[2],"interactions":[3,18],"(LRIs)":[4],"play":[5],"an":[6],"important":[7],"role":[8],"in":[9,47,71,93,116,149],"viral":[10,28,41,73,119],"replication,":[11],"however,":[12],"only":[13,22],"a":[14,24,39,65,77],"few":[15],"of":[16,27,85,96,130,140],"these":[17],"are":[19,52,113,164],"known":[20,50,88],"and":[21,89,100,112,138,152,156],"for":[23,43,67,144],"small":[25],"number":[26],"species.":[29],"Up":[30],"to":[31,37],"now,":[32],"it":[33],"has":[34],"been":[35],"impossible":[36],"screen":[38],"full":[40,72],"genome":[42,79,94],"LRIs":[44,51,92],"experimentally":[45,87],"or":[46],"silico":[48],"Most":[49],"cross-reacting":[53],"structures":[54],"(pseudoknots)":[55],"undetectable":[56],"by":[57],"most":[58],"bioinformatical":[59],"tools.":[60],"RESULTS:":[61],"We":[62,81,102],"present":[63],"LRIscan,":[64],"tool":[66],"the":[68,127],"LRI":[69],"prediction":[70],"genomes":[74],"based":[75],"on":[76,154],"multiple":[78],"alignment.":[80],"confirmed":[82],"14":[83],"out":[84],"16":[86],"evolutionary":[90],"conserved":[91,115],"alignments":[95],"HCV,":[97],"Tombusviruses,":[98],"Flaviviruses":[99],"HIV-1.":[101],"provide":[103,123],"several":[104],"promising":[105],"new":[106],"interactions,":[107],"which":[108],"include":[109],"compensatory":[110],"mutations":[111],"highly":[114],"all":[117],"considered":[118],"sequences.":[120],"Furthermore,":[121],"we":[122],"reactivity":[124],"plots":[125],"highlighting":[126],"hot":[128],"spots":[129],"predicted":[131],"LRIs.":[132],"AVAILABILITY":[133],"AND":[134],"IMPLEMENTATION:":[135],"Source":[136],"code":[137],"binaries":[139],"LRIscan":[141],"freely":[142],"available":[143,165],"download":[145],"at":[146,166],"http://www.rna.uni-jena.de/en/supplements/lriscan/,":[147],"implemented":[148],"Ruby/C":[150],"++":[151],"supported":[153],"Linux":[155],"Windows.":[157],"CONTACT:":[158],"manja@uni-jena.de":[159],"SUPPLEMENTARY":[160],"INFORMATION:":[161],"Supplementary":[162],"data":[163],"Bioinformatics":[167],"online.":[168]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
