{"id":"https://openalex.org/W3161188131","doi":"https://doi.org/10.3390/a14050136","title":"Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination","display_name":"Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination","publication_year":2021,"publication_date":"2021-04-25","ids":{"openalex":"https://openalex.org/W3161188131","doi":"https://doi.org/10.3390/a14050136","mag":"3161188131"},"language":"en","primary_location":{"id":"doi:10.3390/a14050136","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a14050136","pdf_url":"https://www.mdpi.com/1999-4893/14/5/136/pdf?version=1619422549","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1999-4893/14/5/136/pdf?version=1619422549","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037001958","display_name":"Aritra Bose","orcid":"https://orcid.org/0000-0002-8665-056X"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aritra Bose","raw_affiliation_strings":["Computational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USA"],"affiliations":[{"raw_affiliation_string":"Computational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USA","institution_ids":["https://openalex.org/I4210114115"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068361263","display_name":"Filippo Utro","orcid":"https://orcid.org/0000-0003-3226-7642"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Filippo Utro","raw_affiliation_strings":["Computational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USA"],"affiliations":[{"raw_affiliation_string":"Computational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USA","institution_ids":["https://openalex.org/I4210114115"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085036471","display_name":"Daniel E. Platt","orcid":"https://orcid.org/0000-0002-6826-928X"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel E. Platt","raw_affiliation_strings":["Computational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USA"],"affiliations":[{"raw_affiliation_string":"Computational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USA","institution_ids":["https://openalex.org/I4210114115"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025497346","display_name":"Laxmi Parida","orcid":"https://orcid.org/0000-0002-7872-5074"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Laxmi Parida","raw_affiliation_strings":["Computational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USA"],"affiliations":[{"raw_affiliation_string":"Computational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USA","institution_ids":["https://openalex.org/I4210114115"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025497346"],"corresponding_institution_ids":["https://openalex.org/I4210114115"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05012101,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"14","issue":"5","first_page":"136","last_page":"136"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9997000098228455,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9944000244140625,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9743000268936157,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/coalescent-theory","display_name":"Coalescent theory","score":0.9420216679573059},{"id":"https://openalex.org/keywords/epistasis","display_name":"Epistasis","score":0.8585885167121887},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5679358839988708},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.49431848526000977},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4837341606616974},{"id":"https://openalex.org/keywords/recombination","display_name":"Recombination","score":0.44750508666038513},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4344535768032074},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3587123453617096},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.35863667726516724},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15573650598526},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14789816737174988},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.13028398156166077}],"concepts":[{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.9420216679573059},{"id":"https://openalex.org/C61727976","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Epistasis","level":3,"score":0.8585885167121887},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5679358839988708},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.49431848526000977},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4837341606616974},{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.44750508666038513},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4344535768032074},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3587123453617096},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.35863667726516724},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15573650598526},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14789816737174988},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.13028398156166077},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/a14050136","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a14050136","pdf_url":"https://www.mdpi.com/1999-4893/14/5/136/pdf?version=1619422549","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:a7784e066b244a989a5060a1b11a9dab","is_oa":true,"landing_page_url":"https://doaj.org/article/a7784e066b244a989a5060a1b11a9dab","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms, Vol 14, Iss 5, p 136 (2021)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1999-4893/14/5/136/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/a14050136","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms; Volume 14; Issue 5; Pages: 136","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/a14050136","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a14050136","pdf_url":"https://www.mdpi.com/1999-4893/14/5/136/pdf?version=1619422549","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3161188131.pdf","grobid_xml":"https://content.openalex.org/works/W3161188131.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W114397555","https://openalex.org/W1853989166","https://openalex.org/W1990275569","https://openalex.org/W2007650268","https://openalex.org/W2025522412","https://openalex.org/W2040640649","https://openalex.org/W2101549247","https://openalex.org/W2103985888","https://openalex.org/W2118335985","https://openalex.org/W2120296271","https://openalex.org/W2131210485","https://openalex.org/W2131839922","https://openalex.org/W2135151038","https://openalex.org/W2144658220","https://openalex.org/W2147476214","https://openalex.org/W2147911093","https://openalex.org/W2147985011","https://openalex.org/W2149220842","https://openalex.org/W2165141658","https://openalex.org/W2170055238","https://openalex.org/W2278447904","https://openalex.org/W2290749117","https://openalex.org/W2319462502","https://openalex.org/W2429185183","https://openalex.org/W2559403778","https://openalex.org/W2789124133","https://openalex.org/W2951621382","https://openalex.org/W2951641704","https://openalex.org/W3187962553","https://openalex.org/W4256073354","https://openalex.org/W6654510979"],"related_works":["https://openalex.org/W2952954362","https://openalex.org/W3093602888","https://openalex.org/W2762052495","https://openalex.org/W3156045358","https://openalex.org/W2921578049","https://openalex.org/W2581424563","https://openalex.org/W2020089203","https://openalex.org/W4392111346","https://openalex.org/W4300980709","https://openalex.org/W2104334254"],"abstract_inverted_index":{"As":[0],"studies":[1],"move":[2],"into":[3],"deeper":[4],"characterization":[5],"of":[6,9,38,95,111,131,147,163,178],"the":[7,36,72,93,112,129,132,135,139,161,164,186],"impact":[8],"selection":[10,21,101],"through":[11,168],"non-neutral":[12],"mutations":[13],"in":[14,34,92,150,176,183],"whole":[15],"genome":[16],"population":[17],"genetics,":[18],"modeling":[19],"for":[20,58,86],"becomes":[22],"crucial.":[23],"Moreover,":[24],"epistasis":[25,57,149],"has":[26],"long":[27],"been":[28],"recognized":[29],"as":[30,124],"a":[31,44,108,117,125,144,151],"significant":[32],"component":[33],"understanding":[35],"evolution":[37],"complex":[39,89],"genetic":[40],"systems.":[41],"We":[42,105,137,166],"present":[43,107],"backward":[45],"coalescent":[46,81,113,152],"model,":[47],"EpiSimRA,":[48],"that":[49,142,171],"accommodates":[50],"multiple":[51],"loci":[52],"selection,":[53],"with":[54,67,102,154,158],"multi-way":[55],"(k-way)":[56],"any":[59],"arbitrary":[60,64],"k.":[61],"Starting":[62],"from":[63],"extant":[65],"populations":[66],"epistatic":[68],"sites,":[69],"we":[70,122],"trace":[71],"Ancestral":[73],"Recombination":[74],"Graph":[75],"(ARG),":[76],"sampling":[77],"relevant":[78],"recombination":[79],"and":[80,99],"events.":[82],"Our":[83],"framework":[84,141],"allows":[85,143],"studying":[87],"different":[88],"evolutionary":[90],"scenarios":[91],"presence":[94],"selective":[96],"sweeps,":[97],"positive":[98],"negative":[100],"multiway":[103,148],"epistasis.":[104],"also":[106],"forward":[109,156,187],"counterpart":[110,157],"model":[114,188],"based":[115],"on":[116,191],"Wright-Fisher":[118],"(WF)":[119],"process,":[120],"which":[121],"use":[123],"validation":[126],"framework,":[127],"comparing":[128],"hallmarks":[130,162],"ARG":[133],"between":[134],"two.":[136],"provide":[138],"first":[140],"nose-to-nose":[145],"comparison":[146,184],"simulator":[153],"its":[155,192],"respect":[159],"to":[160,185],"ARG.":[165],"demonstrate,":[167],"extensive":[169],"experiments,":[170],"EpiSimRA":[172],"is":[173],"consistently":[174],"superior":[175],"terms":[177],"performance":[179],"(seconds":[180],"vs.":[181],"hours)":[182],"without":[189],"compromising":[190],"accuracy.":[193]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2021-05-24T00:00:00"}