{"id":"https://openalex.org/W3022711289","doi":"https://doi.org/10.1109/bibm.2010.5706632","title":"FluRF, an automated flu virus reassortment finder based on phylogenetic trees","display_name":"FluRF, an automated flu virus reassortment finder based on phylogenetic trees","publication_year":2010,"publication_date":"2010-12-01","ids":{"openalex":"https://openalex.org/W3022711289","doi":"https://doi.org/10.1109/bibm.2010.5706632","mag":"3022711289"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2010.5706632","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2010.5706632","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://infoscience.epfl.ch/record/178651","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085153139","display_name":"Alisa Yurovsky","orcid":"https://orcid.org/0000-0002-7500-7907"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Alisa Yurovsky","raw_affiliation_strings":["Laboratory of Computational Biology and Bioinformatics, Swiss Federal Institute of Technology, Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Biology and Bioinformatics, Swiss Federal Institute of Technology, Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059287546","display_name":"Bernard M. E. Moret","orcid":"https://orcid.org/0000-0003-1549-4544"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Bernard M.E. Moret","raw_affiliation_strings":["Laboratory of Computational Biology and Bioinformatics, Swiss Federal Institute of Technology, Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Biology and Bioinformatics, Swiss Federal Institute of Technology, Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5085153139"],"corresponding_institution_ids":["https://openalex.org/I5124864"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.32480046,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"3","issue":null,"first_page":"579","last_page":"584"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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":0.9986000061035156,"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/T10167","display_name":"Influenza Virus Research Studies","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9854999780654907,"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/reassortment","display_name":"Reassortment","score":0.952857255935669},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8229356408119202},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.6490276455879211},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6192842125892639},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5679539442062378},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5317441821098328},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4114955961704254},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3319966793060303},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2415279746055603},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22439002990722656},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.21493303775787354}],"concepts":[{"id":"https://openalex.org/C16154277","wikidata":"https://www.wikidata.org/wiki/Q2004399","display_name":"Reassortment","level":5,"score":0.952857255935669},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8229356408119202},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.6490276455879211},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6192842125892639},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5679539442062378},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5317441821098328},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4114955961704254},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3319966793060303},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2415279746055603},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22439002990722656},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.21493303775787354},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm.2010.5706632","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2010.5706632","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:infoscience.tind.io:178651","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/178651","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://infoscience.epfl.ch/record/178651","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:infoscience.tind.io:178651","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/178651","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://infoscience.epfl.ch/record/178651","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8500000238418579,"display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310419","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1539801472","https://openalex.org/W1979158913","https://openalex.org/W1996189748","https://openalex.org/W1999291172","https://openalex.org/W2020891730","https://openalex.org/W2023890904","https://openalex.org/W2029402506","https://openalex.org/W2065461553","https://openalex.org/W2101106298","https://openalex.org/W2101970047","https://openalex.org/W2127774996","https://openalex.org/W2127847431","https://openalex.org/W2162275552","https://openalex.org/W2164239649","https://openalex.org/W2166261520","https://openalex.org/W2169702034","https://openalex.org/W4238181735","https://openalex.org/W6632235526"],"related_works":["https://openalex.org/W2962788624","https://openalex.org/W2151403144","https://openalex.org/W2092353756","https://openalex.org/W3013637395","https://openalex.org/W1963675143","https://openalex.org/W2582734947","https://openalex.org/W2616854082","https://openalex.org/W2809882059","https://openalex.org/W2096085713","https://openalex.org/W2892235577"],"abstract_inverted_index":{"Reassortments":[0],"are":[1,52,68,206,221],"events":[2],"in":[3,17,218],"the":[4,7,22,88,97,102,106,124,190,209,213,228],"evolution":[5,115,134],"of":[6,9,21,49,101,148,161,175,189,199,230,252],"genome":[8],"influenza":[10],"(flu).":[11],"As":[12],"reassortments":[13,156,176,184,241,266],"have":[14,243],"been":[15],"implicated":[16],"major":[18],"human":[19],"pandemics":[20],"last":[23],"century,":[24],"their":[25],"identification":[26,34,63,93],"has":[27],"become":[28],"a":[29,39,43,77,112,139,186],"health":[30],"priority.":[31],"While":[32],"such":[33],"can":[35],"be":[36],"done":[37],"on":[38],"small":[40],"dataset":[41],"by":[42,87,131,158,185],"biologist":[44],"(using":[45],"phylogenetic":[46,99,194],"trees),":[47],"databases":[48],"flu":[50,80,114,133,167],"sequences":[51],"growing":[53],"exponentially,":[54],"so":[55],"that":[56,205],"it":[57],"is":[58,85,261,275],"imperative":[59],"to":[60,70,91,118,122,223,264],"develop":[61],"automated":[62,79],"methods.":[64],"However,":[65],"current":[66],"methods":[67],"limited":[69,263],"pairwise":[71],"segment":[72,247],"comparisons.":[73],"We":[74,109],"present":[75,111],"FluRF,":[76,136],"fully":[78],"virus":[81],"reassortment":[82,92],"finder.":[83],"FluRF":[84,125,152,182,249],"inspired":[86],"visual":[89,159],"approach":[90],"and":[94,105,171,192,256,260],"thus":[95],"uses":[96],"reconstructed":[98],"trees":[100,195],"individual":[103],"segments":[104],"full":[107],"genome.":[108],"also":[110],"simple":[113],"simulator,":[116,135],"used":[117],"produce":[119],"synthetic":[120,128],"datasets":[121,129],"tune":[123],"parameters.":[126],"On":[127],"produced":[130],"our":[132],"tuned":[137],"for":[138,196,254],"0%":[140],"false":[141,145],"positive":[142],"rate,":[143],"yielded":[144],"negative":[146],"rates":[147],"10%":[149],"or":[150,201],"less.":[151],"corroborated":[153],"two":[154],"new":[155],"identified":[157],"analysis":[160],"75":[162],"Human":[163],"H3N2":[164],"New":[165],"York":[166],"strains":[168],"from":[169,208,212,277],"2005-2008":[170],"gave":[172],"partial":[173],"verification":[174],"found":[177],"using":[178,227],"another":[179],"bioinformatics":[180],"method.":[181],"finds":[183],"bottom-up":[187],"search":[188],"full-genome":[191],"segment-based":[193],"candidate":[197],"clades-groups":[198],"one":[200],"more":[202],"sampled":[203],"viruses":[204],"separated":[207],"other":[210,236],"variants":[211],"same":[214],"season.":[215],"Candidate":[216],"clades":[217,239],"each":[219],"tree":[220,237],"tested":[222],"guarantee":[224],"confidence":[225],"values,":[226],"lengths":[229],"key":[231],"edges":[232],"as":[233,235],"well":[234],"parameters;":[238],"with":[240,267],"must":[242],"validated":[244],"incongruencies":[245],"among":[246],"trees.":[248],"demonstrates":[250],"robustness":[251],"prediction":[253],"geographically":[255],"temporally":[257],"expanded":[258],"datasets,":[259],"not":[262],"finding":[265],"previously":[268],"collected":[269],"sequences.":[270],"The":[271],"complete":[272],"source":[273],"code":[274],"available":[276],"lcbb.epfl.ch/software.html.":[278]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2020-05-13T00:00:00"}