{"id":"https://openalex.org/W2118700281","doi":"https://doi.org/10.1109/ipdpsw.2012.84","title":"Parallel Pair-HMM SNP Detection","display_name":"Parallel Pair-HMM SNP Detection","publication_year":2012,"publication_date":"2012-05-01","ids":{"openalex":"https://openalex.org/W2118700281","doi":"https://doi.org/10.1109/ipdpsw.2012.84","mag":"2118700281"},"language":"en","primary_location":{"id":"doi:10.1109/ipdpsw.2012.84","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdpsw.2012.84","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops &amp; PhD Forum","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5021267323","display_name":"Nathan Clement","orcid":"https://orcid.org/0000-0002-7533-625X"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan L. Clement","raw_affiliation_strings":["Department of Computer Science, University of Texas, Austin, Austin, TX, USA","Department of Computer Science, University of Texas at Austin, Austin, TX, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Texas, Austin, Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Department of Computer Science, University of Texas at Austin, Austin, TX, USA#TAB#","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089714323","display_name":"Brent A. Shepherd","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brent A. Shepherd","raw_affiliation_strings":["Department of Statistics, Brigham Young University, Provo, UT, USA","Dept. of Stat., Brigham Young Univ., Provo, UT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"Dept. of Stat., Brigham Young Univ., Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090402063","display_name":"Paul Bodily","orcid":"https://orcid.org/0000-0002-5941-0069"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Bodily","raw_affiliation_strings":["Department of Computer Science, Brigham Young University, Provo, UT, USA","[Department of Computer Science, Brigham Young University, Provo, UT, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"[Department of Computer Science, Brigham Young University, Provo, UT, USA]","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009384411","display_name":"Sukhbat Tumur-Ochir","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sukhbat Tumur-Ochir","raw_affiliation_strings":["Department of Computer Science, Brigham Young University, Provo, UT, USA","[Department of Computer Science, Brigham Young University, Provo, UT, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"[Department of Computer Science, Brigham Young University, Provo, UT, USA]","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069418802","display_name":"Younghoon Gim","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Younghoon Gim","raw_affiliation_strings":["Department of Computer Science, Brigham Young University, Provo, UT, USA","[Department of Computer Science, Brigham Young University, Provo, UT, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"[Department of Computer Science, Brigham Young University, Provo, UT, USA]","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064637082","display_name":"Quinn Snell","orcid":"https://orcid.org/0000-0002-0579-612X"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Quinn Snell","raw_affiliation_strings":["Department of Computer Science, Brigham Young University, Provo, UT, USA","[Department of Computer Science, Brigham Young University, Provo, UT, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"[Department of Computer Science, Brigham Young University, Provo, UT, USA]","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058435710","display_name":"Mark Clement","orcid":"https://orcid.org/0000-0003-4902-3521"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark J. Clement","raw_affiliation_strings":["Department of Computer Science, Brigham Young University, Provo, UT, USA","[Department of Computer Science, Brigham Young University, Provo, UT, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"[Department of Computer Science, Brigham Young University, Provo, UT, USA]","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021633597","display_name":"W. Evan Johnson","orcid":"https://orcid.org/0000-0002-6247-6595"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. Evan Johnson","raw_affiliation_strings":["Department of Medicine, Boston University, Boston, MA, USA","Dept. of Med., Boston Univ., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Boston University, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Dept. of Med., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"675","last_page":"683"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987000226974487,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9976999759674072,"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/computer-science","display_name":"Computer science","score":0.7491924166679382},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.6123119592666626},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.564383864402771},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.542071521282196},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.5214319229125977},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4125817120075226},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3225064277648926},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28597235679626465},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.16868317127227783},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1571003496646881},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10687491297721863}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7491924166679382},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6123119592666626},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.564383864402771},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.542071521282196},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.5214319229125977},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4125817120075226},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3225064277648926},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28597235679626465},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.16868317127227783},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1571003496646881},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10687491297721863},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/ipdpsw.2012.84","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdpsw.2012.84","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops &amp; PhD Forum","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.5099999904632568}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1990073900","https://openalex.org/W2001725958","https://openalex.org/W2009570821","https://openalex.org/W2028709282","https://openalex.org/W2043186892","https://openalex.org/W2048818637","https://openalex.org/W2074231493","https://openalex.org/W2097986534","https://openalex.org/W2112113834","https://openalex.org/W2119501327","https://openalex.org/W2124960286","https://openalex.org/W2138270253","https://openalex.org/W2140872496","https://openalex.org/W2165863545","https://openalex.org/W2171657939","https://openalex.org/W2492715936","https://openalex.org/W2612812586","https://openalex.org/W2914081640"],"related_works":["https://openalex.org/W2053269318","https://openalex.org/W2364370872","https://openalex.org/W2097963413","https://openalex.org/W2025614924","https://openalex.org/W2002739602","https://openalex.org/W2345647014","https://openalex.org/W2201192772","https://openalex.org/W3136891595","https://openalex.org/W2535030201","https://openalex.org/W1964819397"],"abstract_inverted_index":{"I.":[0],"MOTIVATION:":[1],"Due":[2],"to":[3,69],"the":[4,63,113,136,161,187,225],"massive":[5],"amounts":[6],"of":[7,38,60,115,202],"data":[8],"generated":[9],"from":[10],"each":[11],"instrument":[12],"run,":[13],"next":[14,51,118],"generation":[15,52,119],"sequencing":[16,53,120],"technologies":[17],"have":[18,103],"presented":[19],"researchers":[20,84],"with":[21,85,173],"unique":[22],"analytical":[23],"challenges":[24],"which":[25,67,106,163,194],"require":[26],"innovative,":[27],"computationally":[28],"efficient":[29],"statistical":[30,182,192],"solutions.":[31],"Here":[32],"we":[33,179],"present":[34],"a":[35,39,78,92,96,108,124,181,222],"parallel":[36,200],"implementation":[37,201],"probabilistic":[40,126,227],"Pair-Hidden":[41,127],"Markov":[42,128],"Model":[43],"for":[44,112,133,186,235],"base":[45,64],"calling":[46,65,88,204],"and":[47,157],"SNP":[48,87,203],"detection":[49],"in":[50,117,135,144,167,171,224],"data.":[54,121],"Our":[55,148],"approach":[56,76,111],"incorporates":[57],"multiple":[58],"sources":[59],"error":[61],"into":[62],"procedure":[66],"leads":[68],"more":[70],"accurate":[71,110],"results.":[72,198],"In":[73,177],"addition,":[74,178],"our":[75],"applies":[77],"likelihood":[79],"ratio":[80],"test":[81],"that":[82,151,184],"provides":[83],"straight-forward":[86],"cutoffs":[89,193],"based":[90],"on":[91,209],"p-value":[93],"cutoff":[94],"or":[95,170,212],"false":[97],"discovery":[98],"control.":[99],"II.":[100],"RESULTS:":[101],"We":[102],"developed":[104],"GNUMAP-SNP,":[105],"is":[107,164,219,232],"highly":[109],"identification":[114],"SNPs":[116],"By":[122],"utilizing":[123],"novel":[125],"Model,":[129],"GNUMAP-SNP":[130,152,218],"effectively":[131],"accounts":[132,185],"uncertainty":[134],"read":[137,142,175,228],"calls":[138],"as":[139,141,221],"well":[140],"mapping":[143,229],"an":[145],"unbiased":[146],"fashion.":[147],"results":[149],"show":[150],"has":[153],"both":[154],"high":[155,158],"sensitivity":[156],"specificity":[159],"throughout":[160],"genome,":[162],"especially":[165],"true":[166],"repeat":[168],"regions":[169],"areas":[172],"low":[174],"coverage.":[176],"propose":[180],"framework":[183],"background":[188],"noise":[189],"using":[190],"straightforward":[191],"filters":[195],"out":[196],"false-positive":[197],"The":[199],"achieves":[205],"near":[206],"linear":[207],"speedup":[208],"distributed":[210],"memory":[211,214],"shared":[213],"platforms.":[215],"III.":[216],"AVAILABILITY:":[217],"available":[220,234],"module":[223],"GNUMAP":[226,231],"software.":[230],"freely":[233],"download":[236],"at:":[237],"http://dna.cs.byu.edu/gnumap/.":[238]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
