{"id":"https://openalex.org/W7130694430","doi":"https://doi.org/10.1177/15578666261424921","title":"A REsampling and Visual EvALuation Method to Detect and Map Local Model Violations During Biomolecular Sequence Analysis","display_name":"A REsampling and Visual EvALuation Method to Detect and Map Local Model Violations During Biomolecular Sequence Analysis","publication_year":2026,"publication_date":"2026-02-20","ids":{"openalex":"https://openalex.org/W7130694430","doi":"https://doi.org/10.1177/15578666261424921","pmid":"https://pubmed.ncbi.nlm.nih.gov/41719082"},"language":"en","primary_location":{"id":"doi:10.1177/15578666261424921","is_oa":false,"landing_page_url":"https://doi.org/10.1177/15578666261424921","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","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/A5043783006","display_name":"Meijun Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Meijun Gao","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, USA"],"raw_orcid":"https://orcid.org/0000-0002-2584-5718","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5126492075","display_name":"Kevin J. Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kevin J. Liu","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, USA","Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA","Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan, USA","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5126492075"],"corresponding_institution_ids":["https://openalex.org/I87216513"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.30260885,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"33","issue":"4","first_page":"482","last_page":"498"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5407000184059143,"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":0.5407000184059143,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.06790000200271606,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.04390000179409981,"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/resampling","display_name":"Resampling","score":0.7330999970436096},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5935999751091003},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5313000082969666},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.48820000886917114},{"id":"https://openalex.org/keywords/generalizability-theory","display_name":"Generalizability theory","score":0.48489999771118164},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"Phylogenomics","score":0.46619999408721924},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4643000066280365},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4097000062465668},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.361299991607666}],"concepts":[{"id":"https://openalex.org/C150921843","wikidata":"https://www.wikidata.org/wiki/Q1170431","display_name":"Resampling","level":2,"score":0.7330999970436096},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6664999723434448},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5935999751091003},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5313000082969666},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.48820000886917114},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.48489999771118164},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4733000099658966},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.46619999408721924},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4643000066280365},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45910000801086426},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.436599999666214},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4097000062465668},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.361299991607666},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.3546999990940094},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.33869999647140503},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.3264000117778778},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.3109000027179718},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.29820001125335693},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.2948000133037567},{"id":"https://openalex.org/C149904235","wikidata":"https://www.wikidata.org/wiki/Q7049620","display_name":"Nonsynonymous substitution","level":4,"score":0.29249998927116394},{"id":"https://openalex.org/C177774035","wikidata":"https://www.wikidata.org/wiki/Q1246948","display_name":"Granularity","level":2,"score":0.29179999232292175},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2897999882698059},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.2888000011444092},{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.2736000120639801},{"id":"https://openalex.org/C40696583","wikidata":"https://www.wikidata.org/wiki/Q989120","display_name":"Type I and type II errors","level":2,"score":0.27320000529289246},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.2653000056743622}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1177/15578666261424921","is_oa":false,"landing_page_url":"https://doi.org/10.1177/15578666261424921","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:41719082","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41719082","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1815845794","display_name":null,"funder_award_id":"2144121","funder_id":"https://openalex.org/F4320337398","funder_display_name":"Division of Biological Infrastructure"},{"id":"https://openalex.org/G3978997456","display_name":null,"funder_award_id":"1714417","funder_id":"https://openalex.org/F4320337387","funder_display_name":"Division of Computing and Communication Foundations"},{"id":"https://openalex.org/G7891425602","display_name":null,"funder_award_id":"2214038","funder_id":"https://openalex.org/F4320337398","funder_display_name":"Division of Biological Infrastructure"}],"funders":[{"id":"https://openalex.org/F4320337387","display_name":"Division of Computing and Communication Foundations","ror":"https://ror.org/01mng8331"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W17481062","https://openalex.org/W1977169047","https://openalex.org/W1981662601","https://openalex.org/W2007668764","https://openalex.org/W2030966943","https://openalex.org/W2039155573","https://openalex.org/W2042982067","https://openalex.org/W2091472740","https://openalex.org/W2131400772","https://openalex.org/W2134599124","https://openalex.org/W2147461064","https://openalex.org/W2150413224","https://openalex.org/W2154160289","https://openalex.org/W2157552136","https://openalex.org/W2159368494","https://openalex.org/W2168830571","https://openalex.org/W2169537477","https://openalex.org/W2896510193","https://openalex.org/W2973028429","https://openalex.org/W3008479721","https://openalex.org/W3179455538","https://openalex.org/W3190559456","https://openalex.org/W3197367468","https://openalex.org/W4226246331","https://openalex.org/W4382631978","https://openalex.org/W4385880802","https://openalex.org/W4388322114","https://openalex.org/W4391985212"],"related_works":[],"abstract_inverted_index":{"A":[0],"fundamental":[1],"assumption":[2,31],"in":[3,24,35,40,51,112,212,262],"phylogenetics":[4],"and":[5,48,59,91,99,108,167,185,217,221,234,255,264],"phylogenomics":[6],"is":[7,32],"that":[8,158,240],"a":[9,25,55,102,137,253],"single,":[10],"global":[11,127],"evolutionary":[12,41,92,201],"model":[13,46,76,110,150,207,238,260],"can":[14],"adequately":[15],"characterize":[16],"the":[17,142,146],"substitution":[18],"processes":[19],"operating":[20],"across":[21,88,199],"all":[22],"sites":[23],"molecular":[26],"sequence":[27,114,143,215],"alignment.":[28],"However,":[29],"this":[30,68],"frequently":[33],"violated":[34],"practice":[36],"due":[37],"to":[38,44,66,125,135,229],"heterogeneity":[39],"processes,":[42],"leading":[43],"local":[45,138],"mis-specification":[47,111],"potential":[49],"bias":[50],"downstream":[52],"inference.":[53],"While":[54],"variety":[56],"of":[57,148,163,173,187,206,214,219],"statistical":[58,104,133],"machine":[60],"learning-based":[61],"approaches":[62],"have":[63],"been":[64],"developed":[65],"address":[67],"issue,":[69],"these":[70],"methods":[71],"often":[72],"rely":[73],"on":[74],"restrictive":[75],"assumptions":[77,121],"or":[78,183,197],"are":[79,241],"designed":[80],"for":[81,106,258],"narrowly":[82],"scoped":[83],"applications,":[84],"limiting":[85],"their":[86],"generalizability":[87],"diverse":[89,200],"datasets":[90],"contexts.":[93],"Here,":[94],"we":[95,156],"present":[96],"REVEAL":[97,116,159,228,251],"(\u201cREsampling":[98],"Visual":[100],"EvALuation\u201d),":[101],"general-purpose":[103],"framework":[105],"detecting":[107],"localizing":[109],"biomolecular":[113],"data.":[115],"operates":[117],"without":[118],"introducing":[119],"additional":[120],"beyond":[122],"those":[123],"inherent":[124],"standard":[126],"model-based":[128],"analyses.":[129,266],"It":[130],"employs":[131],"sequence-aware":[132],"resampling":[134],"construct":[136],"support":[139],"matrix":[140],"along":[141],"alignment,":[144],"facilitating":[145],"identification":[147],"site-level":[149],"violations.":[151],"Through":[152],"extensive":[153],"simulation":[154],"experiments,":[155],"demonstrate":[157],"achieves":[160],"robust":[161],"control":[162],"both":[164],"type":[165,168],"I":[166],"II":[169],"errors,":[170],"with":[171,243],"precision":[172],"<mml:math":[174,188],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[175,189],"display=\"inline\"":[176,190],"overflow=\"scroll\">":[177,191],"<mml:mrow>":[178,192],"<mml:mn>90</mml:mn>":[179],"<mml:mi>%</mml:mi>":[180,194],"</mml:mrow>":[181,195],"</mml:math>":[182,196],"greater":[184,198],"recall":[186],"<mml:mn>85</mml:mn>":[193],"scenarios":[202],"involving":[203],"different":[204],"sources":[205],"heterogeneity,":[208],"varying":[209],"dataset":[210],"sizes":[211],"terms":[213],"length":[216],"number":[218],"taxa,":[220],"other":[222],"experimental":[223],"factors.":[224],"We":[225],"further":[226],"apply":[227],"genomic":[230],"data":[231],"from":[232],"mouse":[233],"mosquito,":[235],"uncovering":[236],"localized":[237],"violations":[239],"consistent":[242],"previously":[244],"reported":[245],"biological":[246],"signals.":[247],"These":[248],"results":[249],"establish":[250],"as":[252],"flexible":[254],"effective":[256],"tool":[257],"evaluating":[259],"adequacy":[261],"phylogenetic":[263],"phylogenomic":[265]},"counts_by_year":[],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2026-02-21T00:00:00"}