{"id":"https://openalex.org/W2565865891","doi":"https://doi.org/10.1093/bioinformatics/btw728","title":"A comprehensive benchmark of RNA\u2013RNA interaction prediction tools for all domains of life","display_name":"A comprehensive benchmark of RNA\u2013RNA interaction prediction tools for all domains of life","publication_year":2016,"publication_date":"2016-11-16","ids":{"openalex":"https://openalex.org/W2565865891","doi":"https://doi.org/10.1093/bioinformatics/btw728","mag":"2565865891","pmid":"https://pubmed.ncbi.nlm.nih.gov/27993777"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw728","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw728","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/988/25149806/btw728.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/33/7/988/25149806/btw728.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017558790","display_name":"Sinan U. Umu","orcid":"https://orcid.org/0000-0001-8081-7819"},"institutions":[{"id":"https://openalex.org/I185492890","display_name":"University of Canterbury","ror":"https://ror.org/03y7q9t39","country_code":"NZ","type":"education","lineage":["https://openalex.org/I185492890"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"Sinan U\u011fur Umu","raw_affiliation_strings":["Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand","School of Biological Sciences, University of Canterbury, Christchurch, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand","institution_ids":["https://openalex.org/I185492890"]},{"raw_affiliation_string":"School of Biological Sciences, University of Canterbury, Christchurch, New Zealand","institution_ids":["https://openalex.org/I185492890"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067459027","display_name":"Paul P. Gardner","orcid":"https://orcid.org/0000-0002-7808-1213"},"institutions":[{"id":"https://openalex.org/I185492890","display_name":"University of Canterbury","ror":"https://ror.org/03y7q9t39","country_code":"NZ","type":"education","lineage":["https://openalex.org/I185492890"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Paul P Gardner","raw_affiliation_strings":["Bio-Protection Research Centre, University of Canterbury, Christchurch, New Zealand","Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand","School of Biological Sciences, University of Canterbury, Christchurch, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bio-Protection Research Centre, University of Canterbury, Christchurch, New Zealand","institution_ids":["https://openalex.org/I185492890"]},{"raw_affiliation_string":"Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand","institution_ids":["https://openalex.org/I185492890"]},{"raw_affiliation_string":"School of Biological Sciences, University of Canterbury, Christchurch, New Zealand","institution_ids":["https://openalex.org/I185492890"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017558790"],"corresponding_institution_ids":["https://openalex.org/I185492890"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.6556,"has_fulltext":false,"cited_by_count":76,"citation_normalized_percentile":{"value":0.93411372,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"7","first_page":"988","last_page":"996"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.8216000199317932,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.8216000199317932,"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/T11482","display_name":"RNA modifications and cancer","score":0.09399999678134918,"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/T10604","display_name":"RNA Research and Splicing","score":0.03139999881386757,"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/benchmark","display_name":"Benchmark (surveying)","score":0.7892998456954956},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.675218939781189},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5856783986091614},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4642537236213684},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32697200775146484},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22511902451515198},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15142366290092468},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08733147382736206}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7892998456954956},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.675218939781189},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5856783986091614},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4642537236213684},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32697200775146484},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22511902451515198},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15142366290092468},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08733147382736206},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw728","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw728","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/988/25149806/btw728.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:27993777","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27993777","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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5408919","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5408919","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw728","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw728","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/988/25149806/btw728.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":[{"id":"https://openalex.org/F4320334429","display_name":"Biomolecular Interaction Centre, University of Canterbury","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":135,"referenced_works":["https://openalex.org/W165054072","https://openalex.org/W1501627602","https://openalex.org/W1531414226","https://openalex.org/W1534710388","https://openalex.org/W1536601791","https://openalex.org/W1543796220","https://openalex.org/W1965955186","https://openalex.org/W1967735923","https://openalex.org/W1968698890","https://openalex.org/W1976342457","https://openalex.org/W1977384011","https://openalex.org/W1980900189","https://openalex.org/W1982501766","https://openalex.org/W1982660543","https://openalex.org/W1983811755","https://openalex.org/W1983815263","https://openalex.org/W1984675364","https://openalex.org/W1992102098","https://openalex.org/W1997639391","https://openalex.org/W1999530403","https://openalex.org/W2000191287","https://openalex.org/W2012706864","https://openalex.org/W2014372073","https://openalex.org/W2014946489","https://openalex.org/W2015292449","https://openalex.org/W2017910292","https://openalex.org/W2022523272","https://openalex.org/W2025763720","https://openalex.org/W2027941418","https://openalex.org/W2030047242","https://openalex.org/W2031014255","https://openalex.org/W2033907622","https://openalex.org/W2036456126","https://openalex.org/W2040191060","https://openalex.org/W2042068730","https://openalex.org/W2043653977","https://openalex.org/W2046374424","https://openalex.org/W2050110866","https://openalex.org/W2050256969","https://openalex.org/W2053783019","https://openalex.org/W2054697783","https://openalex.org/W2055043387","https://openalex.org/W2057519110","https://openalex.org/W2061158331","https://openalex.org/W2062469063","https://openalex.org/W2062896692","https://openalex.org/W2066498236","https://openalex.org/W2068242488","https://openalex.org/W2073858449","https://openalex.org/W2074990432","https://openalex.org/W2077327925","https://openalex.org/W2078849828","https://openalex.org/W2082946618","https://openalex.org/W2083381199","https://openalex.org/W2085534636","https://openalex.org/W2086561953","https://openalex.org/W2089142809","https://openalex.org/W2089499735","https://openalex.org/W2089971639","https://openalex.org/W2091356219","https://openalex.org/W2094253263","https://openalex.org/W2096240879","https://openalex.org/W2097016050","https://openalex.org/W2098508116","https://openalex.org/W2098553089","https://openalex.org/W2098571862","https://openalex.org/W2100932663","https://openalex.org/W2102017611","https://openalex.org/W2109553965","https://openalex.org/W2110919406","https://openalex.org/W2112821430","https://openalex.org/W2116661471","https://openalex.org/W2117165052","https://openalex.org/W2117431427","https://openalex.org/W2117453516","https://openalex.org/W2119086628","https://openalex.org/W2119340328","https://openalex.org/W2121936213","https://openalex.org/W2124756133","https://openalex.org/W2124995041","https://openalex.org/W2125489084","https://openalex.org/W2129375421","https://openalex.org/W2129706781","https://openalex.org/W2130168792","https://openalex.org/W2131527797","https://openalex.org/W2131567601","https://openalex.org/W2136145671","https://openalex.org/W2137356209","https://openalex.org/W2138122982","https://openalex.org/W2141521804","https://openalex.org/W2142972222","https://openalex.org/W2144671815","https://openalex.org/W2145476823","https://openalex.org/W2146339022","https://openalex.org/W2147225758","https://openalex.org/W2148393113","https://openalex.org/W2149748804","https://openalex.org/W2150882562","https://openalex.org/W2151804955","https://openalex.org/W2153081647","https://openalex.org/W2156154309","https://openalex.org/W2159444732","https://openalex.org/W2160515562","https://openalex.org/W2160945322","https://openalex.org/W2161159766","https://openalex.org/W2162537420","https://openalex.org/W2162866469","https://openalex.org/W2164700062","https://openalex.org/W2165089971","https://openalex.org/W2166268906","https://openalex.org/W2166802510","https://openalex.org/W2169471376","https://openalex.org/W2174181728","https://openalex.org/W2174734928","https://openalex.org/W2175411040","https://openalex.org/W2233449657","https://openalex.org/W2312194337","https://openalex.org/W2341424800","https://openalex.org/W2383534773","https://openalex.org/W2387926211","https://openalex.org/W2388201280","https://openalex.org/W2400250419","https://openalex.org/W2952333148","https://openalex.org/W4236154753","https://openalex.org/W4241736596","https://openalex.org/W4293196852","https://openalex.org/W6606772280","https://openalex.org/W6669614655","https://openalex.org/W6683716841","https://openalex.org/W6684319383","https://openalex.org/W6685253900","https://openalex.org/W6685401528","https://openalex.org/W6703735664","https://openalex.org/W6711526205","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W2087343574"],"abstract_inverted_index":{"Motivation:":[0],"The":[1,38,86],"aim":[2],"of":[3,11,19,31,80,91],"this":[4],"study":[5],"is":[6],"to":[7,49,95,102,112],"assess":[8],"the":[9,32,50,81],"performance":[10],"RNA-RNA":[12],"interaction":[13,35],"prediction":[14,36],"tools":[15,40],"for":[16,133],"all":[17,69],"domains":[18],"life.":[20],"Results:":[21],"Minimum":[22],"free":[23],"energy":[24,54],"(MFE)":[25],"and":[26,47,98,117,124],"alignment":[27,99],"methods":[28,100],"constitute":[29],"most":[30],"current":[33],"RNA":[34],"algorithms.":[37],"MFE":[39],"that":[41,88],"include":[42,89],"accessibility":[43,113],"(i.e.":[44],"RNAup,":[45],"IntaRNA":[46],"RNAplex)":[48],"final":[51],"predicted":[52],"binding":[53,93],"have":[55,103],"better":[56],"true":[57],"positive":[58,64],"rates":[59],"(TPRs)":[60],"with":[61],"a":[62],"high":[63,104],"predictive":[65],"values":[66],"(PPVs)":[67],"in":[68],"datasets":[70,125],"than":[71],"other":[72],"methods.":[73,115],"They":[74],"can":[75],"also":[76],"differentiate":[77],"almost":[78],"half":[79],"native":[82],"interactions":[83],"from":[84],"background.":[85],"algorithms":[87],"effects":[90],"internal":[92],"energies":[94],"their":[96],"model":[97],"seem":[101],"TPR":[105],"but":[106],"relatively":[107],"low":[108],"associated":[109],"PPV":[110],"compared":[111],"based":[114],"Availability":[116],"Implementation:":[118],"We":[119],"shared":[120],"our":[121],"wrapper":[122],"scripts":[123],"at":[126,144],"Github":[127],"(github.com/UCanCompBio/RNA_Interactions_Benchmark).":[128],"All":[129],"parameters":[130],"are":[131,142],"documented":[132],"personal":[134],"use.":[135],"Contact:":[136],"sinan.umu@pg.canterbury.ac.nz.":[137],"Supplementary":[138,140],"information:":[139],"data":[141],"available":[143],"Bioinformatics":[145],"online.":[146]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-26T13:28:51.108037","created_date":"2025-10-10T00:00:00"}
