{"id":"https://openalex.org/W1993983922","doi":"https://doi.org/10.1089/cmb.2009.0185","title":"Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data","display_name":"Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data","publication_year":2010,"publication_date":"2010-03-01","ids":{"openalex":"https://openalex.org/W1993983922","doi":"https://doi.org/10.1089/cmb.2009.0185","mag":"1993983922","pmid":"https://pubmed.ncbi.nlm.nih.gov/20377461"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.2009.0185","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2009.0185","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/A5027970835","display_name":"Suzanne Sindi","orcid":"https://orcid.org/0000-0003-2742-4332"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suzanne S. Sindi","raw_affiliation_strings":["Department of Computer Science, Brown University, Providence, Rhode Island","Division of Applied Mathematics, Brown University, Providence, Rhode Island"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Brown University, Providence, Rhode Island","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Division of Applied Mathematics, Brown University, Providence, Rhode Island","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025899028","display_name":"Benjamin J. Raphael","orcid":"https://orcid.org/0000-0003-1274-048X"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benjamin J. Raphael","raw_affiliation_strings":["Center for Computational Molecular Biology, Brown University, Providence, Rhode Island","Department of Computer Science, Brown University, Providence, Rhode Island"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Molecular Biology, Brown University, Providence, Rhode Island","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Department of Computer Science, Brown University, Providence, Rhode Island","institution_ids":["https://openalex.org/I27804330"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5025899028"],"corresponding_institution_ids":["https://openalex.org/I27804330"],"apc_list":null,"apc_paid":null,"fwci":1.8707,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.86117346,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"3","first_page":"517","last_page":"531"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9998999834060669,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9998999834060669,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.994700014591217,"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/international-hapmap-project","display_name":"International HapMap Project","score":0.8186048269271851},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.5942406058311462},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5707154870033264},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5538260340690613},{"id":"https://openalex.org/keywords/chromosomal-inversion","display_name":"Chromosomal inversion","score":0.5273662209510803},{"id":"https://openalex.org/keywords/1000-genomes-project","display_name":"1000 Genomes Project","score":0.50434410572052},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.49350202083587646},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4760477542877197},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4750288128852844},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4585984945297241},{"id":"https://openalex.org/keywords/inversion","display_name":"Inversion (geology)","score":0.4516909122467041},{"id":"https://openalex.org/keywords/breakpoint","display_name":"Breakpoint","score":0.4351046085357666},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.42797890305519104},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3282940685749054},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.1516537070274353},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14202794432640076},{"id":"https://openalex.org/keywords/karyotype","display_name":"Karyotype","score":0.0818776786327362}],"concepts":[{"id":"https://openalex.org/C177580304","wikidata":"https://www.wikidata.org/wiki/Q1147298","display_name":"International HapMap Project","level":5,"score":0.8186048269271851},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.5942406058311462},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5707154870033264},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5538260340690613},{"id":"https://openalex.org/C165984737","wikidata":"https://www.wikidata.org/wiki/Q1070877","display_name":"Chromosomal inversion","level":5,"score":0.5273662209510803},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.50434410572052},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.49350202083587646},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4760477542877197},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4750288128852844},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4585984945297241},{"id":"https://openalex.org/C1893757","wikidata":"https://www.wikidata.org/wiki/Q3653001","display_name":"Inversion (geology)","level":3,"score":0.4516909122467041},{"id":"https://openalex.org/C206936463","wikidata":"https://www.wikidata.org/wiki/Q634179","display_name":"Breakpoint","level":4,"score":0.4351046085357666},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.42797890305519104},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3282940685749054},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.1516537070274353},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14202794432640076},{"id":"https://openalex.org/C53226629","wikidata":"https://www.wikidata.org/wiki/Q189967","display_name":"Karyotype","level":4,"score":0.0818776786327362},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.0},{"id":"https://openalex.org/C138626823","wikidata":"https://www.wikidata.org/wiki/Q916504","display_name":"Chromosomal translocation","level":3,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C109007969","wikidata":"https://www.wikidata.org/wiki/Q749565","display_name":"Structural basin","level":2,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D007446","descriptor_name":"Chromosome Inversion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007446","descriptor_name":"Chromosome Inversion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007446","descriptor_name":"Chromosome Inversion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019457","descriptor_name":"Chromosome Breakage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019457","descriptor_name":"Chromosome Breakage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019457","descriptor_name":"Chromosome Breakage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1089/cmb.2009.0185","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2009.0185","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:20377461","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20377461","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":[],"funders":[{"id":"https://openalex.org/F4320306133","display_name":"Burroughs Wellcome Fund","ror":"https://ror.org/01d35cw23"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1504977184","https://openalex.org/W1508985588","https://openalex.org/W1973769499","https://openalex.org/W2013221974","https://openalex.org/W2020953156","https://openalex.org/W2032247293","https://openalex.org/W2037454239","https://openalex.org/W2047361940","https://openalex.org/W2049633694","https://openalex.org/W2053600190","https://openalex.org/W2085755265","https://openalex.org/W2087261765","https://openalex.org/W2089251117","https://openalex.org/W2098126593","https://openalex.org/W2098187463","https://openalex.org/W2103241734","https://openalex.org/W2113649367","https://openalex.org/W2116753165","https://openalex.org/W2119279196","https://openalex.org/W2129637418","https://openalex.org/W2133112449","https://openalex.org/W2134783591","https://openalex.org/W2135732313","https://openalex.org/W2140869203","https://openalex.org/W2142642738","https://openalex.org/W2144690533","https://openalex.org/W2144958703","https://openalex.org/W2147039800","https://openalex.org/W2153822291","https://openalex.org/W2156341632","https://openalex.org/W2157752701","https://openalex.org/W2158489424","https://openalex.org/W2159091117","https://openalex.org/W2161409513","https://openalex.org/W2161641617","https://openalex.org/W2161644980","https://openalex.org/W2163938152"],"related_works":["https://openalex.org/W2017753262","https://openalex.org/W4365445324","https://openalex.org/W4308645533","https://openalex.org/W2112030661","https://openalex.org/W2415408935","https://openalex.org/W2012768882","https://openalex.org/W2056001048","https://openalex.org/W2122946544","https://openalex.org/W2160838129","https://openalex.org/W2793353350"],"abstract_inverted_index":{"Structural":[0],"rearrangements,":[1],"including":[2],"copy-number":[3],"alterations":[4],"and":[5,54,84,87,117,137,162],"inversions,":[6],"are":[7,21],"increasingly":[8],"recognized":[9],"as":[10,35,79,110,112],"an":[11],"important":[12],"contributor":[13],"to":[14,40,50,75,146,153],"human":[15,128],"genetic":[16],"variation.":[17],"Copy":[18],"number":[19],"variants":[20,33],"readily":[22,62],"measured":[23],"via":[24],"array-based":[25],"techniques":[26],"like":[27],"comparative":[28],"genomic":[29],"hybridization,":[30],"but":[31],"copy-neutral":[32],"such":[34],"inversion":[36,52,98,120,139,165],"polymorphisms":[37,53,140],"remain":[38],"difficult":[39],"identify":[41,51],"without":[42],"whole":[43],"genome":[44],"sequencing.":[45],"We":[46],"introduce":[47],"a":[48,59,72,77,80,123],"method":[49,70,104],"estimate":[55],"their":[56],"frequency":[57,142],"in":[58,94,114],"population":[60,78,116],"using":[61],"available":[63],"single":[64],"nucleotide":[65],"polymorphism":[66],"(SNP)":[67],"data.":[68],"Our":[69],"uses":[71],"probabilistic":[73],"model":[74],"describe":[76],"mixture":[81],"of":[82,150],"forward":[83],"inverted":[85],"chromosomes":[86],"identifies":[88],"putative":[89],"inversions":[90,107,155],"by":[91],"characteristic":[92],"differences":[93],"haplotype":[95],"frequencies":[96,109,121,166],"around":[97],"breakpoints.":[99],"On":[100,126],"simulated":[101],"data,":[102,132],"our":[103],"accurately":[105],"predicts":[106],"with":[108,141,169],"low":[111],"25%":[113],"the":[115,127,163,170],"reliably":[118],"estimates":[119],"over":[122],"wide":[124],"range.":[125],"HapMap":[129],"Phase":[130],"2":[131],"we":[133],"predict":[134],"between":[135],"88":[136],"142":[138],"ranging":[143],"from":[144],"20":[145],"81":[147],"percent.":[148],"Many":[149],"these":[151],"correspond":[152],"known":[154],"or":[156],"have":[157],"other":[158],"evidence":[159],"supporting":[160],"them,":[161],"predicted":[164],"largely":[167],"agree":[168],"limited":[171],"information":[172],"presently":[173],"available.":[174]},"counts_by_year":[{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":7}],"updated_date":"2025-12-23T23:11:35.936235","created_date":"2025-10-10T00:00:00"}