{"id":"https://openalex.org/W2119897585","doi":"https://doi.org/10.1093/bioinformatics/bts033","title":"Exact coalescent simulation of new haplotype data from existing reference haplotypes","display_name":"Exact coalescent simulation of new haplotype data from existing reference haplotypes","publication_year":2012,"publication_date":"2012-01-17","ids":{"openalex":"https://openalex.org/W2119897585","doi":"https://doi.org/10.1093/bioinformatics/bts033","mag":"2119897585","pmid":"https://pubmed.ncbi.nlm.nih.gov/22257666"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts033","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts033","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/838/48874949/bioinformatics_28_6_838.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/838/48874949/bioinformatics_28_6_838.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027744715","display_name":"Chul Joo Kang","orcid":"https://orcid.org/0000-0003-0463-4935"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chul Joo Kang","raw_affiliation_strings":["Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079125457","display_name":"Paul Marjoram","orcid":"https://orcid.org/0000-0003-0824-7449"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Marjoram","raw_affiliation_strings":["Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5027744715"],"corresponding_institution_ids":["https://openalex.org/I1174212"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2044,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.63471259,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"28","issue":"6","first_page":"838","last_page":"844"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.920199990272522,"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":0.920199990272522,"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/T10885","display_name":"Gene expression and cancer classification","score":0.012400000356137753,"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/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.009100000374019146,"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":0.933666467666626},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.9214606285095215},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4475923478603363},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4049423933029175},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.376817524433136},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3576597571372986},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3515273332595825},{"id":"https://openalex.org/keywords/genealogy","display_name":"Genealogy","score":0.32108092308044434},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15433654189109802},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.1499910056591034},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.13136297464370728},{"id":"https://openalex.org/keywords/history","display_name":"History","score":0.08426353335380554}],"concepts":[{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.933666467666626},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.9214606285095215},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4475923478603363},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4049423933029175},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.376817524433136},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3576597571372986},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3515273332595825},{"id":"https://openalex.org/C53553401","wikidata":"https://www.wikidata.org/wiki/Q47307","display_name":"Genealogy","level":1,"score":0.32108092308044434},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15433654189109802},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.1499910056591034},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.13136297464370728},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.08426353335380554}],"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":"D000465","descriptor_name":"Algorithms","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044382","descriptor_name":"Population Groups","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044382","descriptor_name":"Population Groups","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044382","descriptor_name":"Population Groups","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts033","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts033","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/838/48874949/bioinformatics_28_6_838.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22257666","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22257666","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:2594589","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3307111","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts033","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts033","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/838/48874949/bioinformatics_28_6_838.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4041035839","display_name":null,"funder_award_id":"MH084678","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2119897585.pdf","grobid_xml":"https://content.openalex.org/works/W2119897585.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1962960380","https://openalex.org/W1975060110","https://openalex.org/W1978124765","https://openalex.org/W2009596137","https://openalex.org/W2082967637","https://openalex.org/W2083277053","https://openalex.org/W2107916366","https://openalex.org/W2114010745","https://openalex.org/W2120296271","https://openalex.org/W2131210485","https://openalex.org/W2134599124","https://openalex.org/W2141672406","https://openalex.org/W2147985011","https://openalex.org/W2161102342","https://openalex.org/W2162530578","https://openalex.org/W2167638767","https://openalex.org/W2171777347","https://openalex.org/W2885727518","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2952954362","https://openalex.org/W3093602888","https://openalex.org/W3156045358","https://openalex.org/W2921578049","https://openalex.org/W2581424563","https://openalex.org/W2020599444","https://openalex.org/W2762052495","https://openalex.org/W1969590299","https://openalex.org/W4300980709","https://openalex.org/W2104334254"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"We":[2,100],"introduce":[3],"a":[4,16,38,108,114],"coalescent-based":[5],"method":[6,106],"(RECOAL)":[7],"for":[8,24,134],"the":[9,25,32,45,63,73,76,102,123],"simulation":[10,84],"of":[11,19,62,75,85,104,110],"new":[12,50,54,68,86],"haplotype":[13,27,51,55,87],"data":[14,28,56,111,121,143],"from":[15,31,122],"reference":[17,26],"population":[18],"haplotypes.":[20],"A":[21],"coalescent":[22,39,78,83,115],"genealogy":[23,40,47],"is":[29,41,131],"sampled":[30,46],"appropriate":[33],"posterior":[34],"probability":[35],"distribution,":[36],"then":[37],"simulated":[42,77,112],"which":[43,93],"extends":[44],"to":[48,120],"include":[49],"data.":[52],"The":[53,128],"will,":[57],"therefore,":[58],"contain":[59],"both":[60],"some":[61],"existing":[64],"polymorphic":[65],"sites":[66],"and":[67],"polymorphisms":[69],"added":[70],"based":[71],"on":[72],"structure":[74],"genealogy.":[79],"This":[80],"allows":[81],"exact":[82],"data,":[88],"compared":[89],"with":[90],"other":[91],"methods":[92],"are":[94,144],"more":[95],"approximate":[96],"in":[97],"nature.":[98],"Results:":[99],"demonstrate":[101],"performance":[103],"our":[105],"using":[107],"variety":[109],"under":[113],"model,":[116],"before":[117],"applying":[118],"it":[119],"1000":[124],"Genomes":[125],"project.":[126],"Availability:":[127],"source":[129],"code":[130],"freely":[132],"available":[133,145],"download":[135],"at":[136,146],"ftp://popgen.usc.edu":[137],"Contact:":[138],"chulkang@usc.edu":[139],"Supplementary":[140,142],"information:":[141],"Bioinformatics":[147],"online.":[148]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}