{"id":"https://openalex.org/W2972870121","doi":"https://doi.org/10.1145/3307339.3343478","title":"Pangenome-Wide Association Studies with Frequented Regions","display_name":"Pangenome-Wide Association Studies with Frequented Regions","publication_year":2019,"publication_date":"2019-09-04","ids":{"openalex":"https://openalex.org/W2972870121","doi":"https://doi.org/10.1145/3307339.3343478","mag":"2972870121"},"language":"en","primary_location":{"id":"doi:10.1145/3307339.3343478","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3307339.3343478","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3307339.3343478","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3307339.3343478","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089523904","display_name":"Buwani Manuweera","orcid":null},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Buwani Manuweera","raw_affiliation_strings":["Montana State University, Bozeman, MT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Montana State University, Bozeman, MT, USA","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071538924","display_name":"Joann Mudge","orcid":"https://orcid.org/0000-0002-2972-1640"},"institutions":[{"id":"https://openalex.org/I1310183320","display_name":"National Center for Genome Resources","ror":"https://ror.org/01p4cne93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1310183320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joann Mudge","raw_affiliation_strings":["National Center for Genome Resources, Santa Fe, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Genome Resources, Santa Fe, NM, USA","institution_ids":["https://openalex.org/I1310183320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010719226","display_name":"Indika Kahanda","orcid":"https://orcid.org/0000-0002-4536-6917"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Indika Kahanda","raw_affiliation_strings":["Montana State University, Bozeman, MT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Montana State University, Bozeman, MT, USA","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084888509","display_name":"Brendan Mumey","orcid":"https://orcid.org/0000-0001-7151-2124"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brendan Mumey","raw_affiliation_strings":["Montana State University, Bozeman, MT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Montana State University, Bozeman, MT, USA","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083833340","display_name":"Thiruvarangan Ramaraj","orcid":"https://orcid.org/0000-0002-7333-1041"},"institutions":[{"id":"https://openalex.org/I1310183320","display_name":"National Center for Genome Resources","ror":"https://ror.org/01p4cne93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1310183320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thiruvarangan Ramaraj","raw_affiliation_strings":["National Center for Genome Resources, Santa Fe, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Genome Resources, Santa Fe, NM, USA","institution_ids":["https://openalex.org/I1310183320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012589523","display_name":"Alan Cleary","orcid":"https://orcid.org/0000-0002-6567-5346"},"institutions":[{"id":"https://openalex.org/I1310183320","display_name":"National Center for Genome Resources","ror":"https://ror.org/01p4cne93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1310183320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alan Cleary","raw_affiliation_strings":["National Center for Genome Resources, Santa Fe, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Genome Resources, Santa Fe, NM, USA","institution_ids":["https://openalex.org/I1310183320"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"627","last_page":"632"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9987999796867371,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9987999796867371,"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":0.9987999796867371,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9987000226974487,"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/genome-wide-association-study","display_name":"Genome-wide association study","score":0.7696674466133118},{"id":"https://openalex.org/keywords/genetic-association","display_name":"Genetic association","score":0.5804711580276489},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.5356687307357788},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5352165699005127},{"id":"https://openalex.org/keywords/genetic-variation","display_name":"Genetic variation","score":0.48057985305786133},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4755915403366089},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4227636456489563},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39688512682914734},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.30197763442993164},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26314592361450195}],"concepts":[{"id":"https://openalex.org/C106208931","wikidata":"https://www.wikidata.org/wiki/Q1098876","display_name":"Genome-wide association study","level":5,"score":0.7696674466133118},{"id":"https://openalex.org/C186413461","wikidata":"https://www.wikidata.org/wiki/Q744727","display_name":"Genetic association","level":5,"score":0.5804711580276489},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.5356687307357788},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5352165699005127},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.48057985305786133},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4755915403366089},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4227636456489563},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39688512682914734},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.30197763442993164},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26314592361450195},{"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":1,"locations":[{"id":"doi:10.1145/3307339.3343478","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3307339.3343478","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3307339.3343478","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3307339.3343478","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3307339.3343478","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3307339.3343478","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[{"score":0.5,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G5991752279","display_name":null,"funder_award_id":"DBI-1759522","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8076972632","display_name":"Collaborative Research:  Innovation: Pioneering New Approaches to Explore Pangenomic Space at Scale","funder_award_id":"1759522","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2972870121.pdf","grobid_xml":"https://content.openalex.org/works/W2972870121.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1492273171","https://openalex.org/W1520812622","https://openalex.org/W1979914496","https://openalex.org/W1998231903","https://openalex.org/W2091374137","https://openalex.org/W2101234009","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2118685291","https://openalex.org/W2128207034","https://openalex.org/W2150550043","https://openalex.org/W2152116196","https://openalex.org/W2162995709","https://openalex.org/W2272733715","https://openalex.org/W2725988230","https://openalex.org/W2747043344","https://openalex.org/W2767785164","https://openalex.org/W2776539412","https://openalex.org/W2807938045","https://openalex.org/W2884924725","https://openalex.org/W2891275623","https://openalex.org/W2897587353","https://openalex.org/W2912816423","https://openalex.org/W2950299756","https://openalex.org/W2962931338","https://openalex.org/W2979304081","https://openalex.org/W2997591727","https://openalex.org/W3033648611"],"related_works":["https://openalex.org/W2587112589","https://openalex.org/W2065120962","https://openalex.org/W4223972846","https://openalex.org/W2517753256","https://openalex.org/W2069221540","https://openalex.org/W2094455802","https://openalex.org/W4306392993","https://openalex.org/W2092398847","https://openalex.org/W2884987722","https://openalex.org/W2057390011"],"abstract_inverted_index":{"Connecting":[0],"genetic":[1,16,30,48,172],"variation":[2,6,31,131,173],"(genotype)":[3],"to":[4,27,32,84,92,119,170,183,202,238,248],"trait":[5],"(phenotype)":[7],"is":[8,23,41,66],"a":[9,24,85,133,140,147,166,188,255],"critical":[10],"but":[11],"often":[12],"difficult":[13],"step":[14],"in":[15,43,69,112,228],"research.":[17],"A":[18],"genome-wide":[19],"association":[20,196],"study":[21,171],"(GWAS)":[22],"common":[25],"approach":[26],"connect":[28],"underlying":[29,57],"complex":[33,53,155,249],"phenotypic":[34,38,250,275],"traits,":[35],"allowing":[36],"for":[37,51,149,187,217,273],"prediction.":[39],"GWAS":[40,65,96,201],"important":[42,58],"many":[44],"disciplines,":[45],"including":[46],"identifying":[47,55,150,225],"risk":[49],"factors":[50],"common,":[52],"diseases,":[54],"genes":[56],"traits":[59],"and":[60,94,130,160,207,224],"predicting":[61,274],"phenotypes":[62],"from":[63,97],"genotypes.":[64],"limited,":[67],"though,":[68],"that":[70,153,162,199,231,246,262],"the":[71,120,126],"types":[72],"of":[73,104,132,139,191,213,258],"variations":[74,156],"typically":[75],"studied":[76],"are":[77,135],"single":[78,86],"nucleotide":[79],"polymorphisms":[80],"(SNPs)":[81],"identified":[82],"relative":[83],"reference":[87],"genome.":[88],"These":[89],"limitations":[90],"lead":[91],"bias":[93],"preclude":[95],"studies":[98,197],"across":[99,208],"related":[100],"species.":[101,209],"The":[102],"advent":[103],"next-generation":[105],"sequencing":[106],"has":[107,117],"brought":[108],"an":[109],"exponential":[110],"growth":[111],"DNA":[113],"sequence":[114,128],"data.":[115],"This":[116,177],"led":[118],"more":[121,167],"comprehensive":[122],"pangenomics":[123],"approach,":[124],"where":[125],"entire":[127],"content":[129],"population":[134],"succinctly":[136],"represented":[137],"independent":[138],"reference.":[141],"In":[142],"prior":[143],"work,":[144],"we":[145],"developed":[146,215],"method":[148],"genomic":[151,192],"regions":[152,164,227],"characterize":[154],"within":[157,206],"pangenomic":[158,240],"data":[159],"showed":[161],"these":[163,229],"provide":[165,266],"general":[168],"way":[169],"than":[174,271],"existing":[175],"approaches.":[176],"work":[178],"describes":[179],"our":[180],"initial":[181],"results":[182,253],"develop":[184],"new":[185,189],"methods":[186],"branch":[190],"analysis":[193],"called":[194],"pangenome-wide":[195],"(PWAS)":[198],"generalizes":[200],"pangenome":[203,256],"datasets":[204],"both":[205],"We":[210],"make":[211],"use":[212],"recently":[214],"algorithms":[216],"fast":[218],"compressed":[219],"De":[220],"Bruijn":[221],"graph":[222],"construction":[223],"frequented":[226,263],"graphs":[230],"can":[232],"be":[233],"used":[234],"as":[235],"machine-learning":[236,268],"features":[237,265],"identify":[239],"regions,":[241],"overlaid":[242],"with":[243],"gene":[244],"annotations,":[245],"relate":[247],"traits.":[251,276],"Initial":[252],"on":[254],"composed":[257],"100":[259],"yeast":[260],"indicate":[261],"region":[264],"better":[267],"regression":[269],"models":[270],"SNPs":[272]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}