{"id":"https://openalex.org/W2148889460","doi":"https://doi.org/10.1093/bioinformatics/bti1128","title":"Recovering haplotype structure through recombination and gene conversion","display_name":"Recovering haplotype structure through recombination and gene conversion","publication_year":2005,"publication_date":"2005-09-01","ids":{"openalex":"https://openalex.org/W2148889460","doi":"https://doi.org/10.1093/bioinformatics/bti1128","mag":"2148889460","pmid":"https://pubmed.ncbi.nlm.nih.gov/16204098"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti1128","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1128","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/suppl_2/ii173/6686154/bti1128.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/21/suppl_2/ii173/6686154/bti1128.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029451334","display_name":"Mathieu Lajoie","orcid":"https://orcid.org/0000-0001-9162-086X"},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Mathieu Lajoie","raw_affiliation_strings":["D\u00e9partement d'Informatique et de Recherche Op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al CP 6128 Succursale Centre-ville, Montr\u00e9al, QC H3C 3J7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement d'Informatique et de Recherche Op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al CP 6128 Succursale Centre-ville, Montr\u00e9al, QC H3C 3J7, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041470344","display_name":"Nadia El-Mabrouk","orcid":"https://orcid.org/0000-0002-5385-1015"},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nadia El-Mabrouk","raw_affiliation_strings":["D\u00e9partement d'Informatique et de Recherche Op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al CP 6128 Succursale Centre-ville, Montr\u00e9al, QC H3C 3J7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement d'Informatique et de Recherche Op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al CP 6128 Succursale Centre-ville, Montr\u00e9al, QC H3C 3J7, Canada","institution_ids":["https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5029451334"],"corresponding_institution_ids":["https://openalex.org/I70931966"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9338,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.76855406,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"suppl_2","first_page":"ii173","last_page":"ii179"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.8339999914169312,"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":0.8339999914169312,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.019500000402331352,"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":0.018300000578165054,"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/haplotype","display_name":"Haplotype","score":0.8611382246017456},{"id":"https://openalex.org/keywords/recombination","display_name":"Recombination","score":0.7434918880462646},{"id":"https://openalex.org/keywords/gene-conversion","display_name":"Gene conversion","score":0.669340968132019},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5184697508811951},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4791630804538727},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4418724477291107},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3969746232032776},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37682536244392395},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.15830302238464355}],"concepts":[{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.8611382246017456},{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.7434918880462646},{"id":"https://openalex.org/C112212490","wikidata":"https://www.wikidata.org/wiki/Q471134","display_name":"Gene conversion","level":4,"score":0.669340968132019},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5184697508811951},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4791630804538727},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4418724477291107},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3969746232032776},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37682536244392395},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.15830302238464355}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005785","descriptor_name":"Gene Conversion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005785","descriptor_name":"Gene Conversion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005785","descriptor_name":"Gene Conversion","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":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bti1128","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1128","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/suppl_2/ii173/6686154/bti1128.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:16204098","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16204098","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:CiteSeerX.psu:10.1.1.541.2127","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.541.2127","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.iro.umontreal.ca/~major/Journal Club/ISMB-2005-submitted.pdf","raw_type":"text"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:278084","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference Paper"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti1128","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1128","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/suppl_2/ii173/6686154/bti1128.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":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1502232315","https://openalex.org/W1891283710","https://openalex.org/W1965804318","https://openalex.org/W1974475064","https://openalex.org/W1979900996","https://openalex.org/W1984324163","https://openalex.org/W1987646246","https://openalex.org/W1992249022","https://openalex.org/W2008323735","https://openalex.org/W2027778251","https://openalex.org/W2037655215","https://openalex.org/W2047222949","https://openalex.org/W2054547415","https://openalex.org/W2083878136","https://openalex.org/W2094540363","https://openalex.org/W2098544478","https://openalex.org/W2103225712","https://openalex.org/W2105253498","https://openalex.org/W2106549255","https://openalex.org/W2109347434","https://openalex.org/W2110755408","https://openalex.org/W2111107841","https://openalex.org/W2116652744","https://openalex.org/W2124554062","https://openalex.org/W2130133796","https://openalex.org/W2134599124","https://openalex.org/W2146022716","https://openalex.org/W2146820632","https://openalex.org/W2152490971","https://openalex.org/W2152664025","https://openalex.org/W2161186860","https://openalex.org/W2161425930","https://openalex.org/W2161676423","https://openalex.org/W2165671666","https://openalex.org/W2180470233"],"related_works":["https://openalex.org/W2000602789","https://openalex.org/W1997899882","https://openalex.org/W2152490525","https://openalex.org/W1970732273","https://openalex.org/W1982537316","https://openalex.org/W2057219715","https://openalex.org/W2087920981","https://openalex.org/W2163957985","https://openalex.org/W2802021930","https://openalex.org/W2025497764"],"abstract_inverted_index":{"MOTIVATION:":[0],"Understanding":[1],"haplotype":[2,75],"evolution":[3],"subject":[4],"to":[5,13,32,72,120,149,169],"mutation,":[6],"recombination":[7],"and":[8,20,45,68,117,124,138,157,184],"gene":[9,69,106],"conversion":[10],"is":[11,31,92],"fundamental":[12],"understand":[14],"genetic":[15],"specificities":[16],"of":[17,23,28,40,48,65,76,82,96,115,152,173],"human":[18],"populations":[19],"hereditary":[21],"bases":[22],"complex":[24],"disorders.":[25],"The":[26,58,108,177],"goal":[27],"this":[29],"project":[30],"develop":[33],"new":[34,56],"algorithmic":[35],"tools":[36],"assisting":[37],"the":[38,46,93,146,150,171],"reconstruction":[39],"historical":[41],"relationships":[42],"between":[43],"haplotypes":[44,49,154],"inference":[47],"from":[50,79,155],"genotypes.":[51],"RESULTS:":[52],"We":[53,144],"present":[54],"two":[55],"algorithms.":[57],"first":[59],"one":[60,110,148],"finds":[61,111],"an":[62,112,165],"optimal":[63,113],"pathway":[64,114],"mutations,":[66],"recombinations":[67,118],"conversions":[70],"leading":[71,119],"a":[73,80,104,121,134,140],"given":[74,122],"size":[77],"m":[78],"population":[81],"h":[83],"haplotypes.":[84],"It":[85],"runs":[86,125],"in":[87,103,126,182],"time":[88,127],"O(mhs(2)),":[89],"where":[90],"s":[91],"maximum":[94],"number":[95],"contiguous":[97],"sites":[98],"that":[99],"can":[100,161],"be":[101,162],"exchanged":[102],"single":[105],"conversion.":[107],"second":[109,147],"mutations":[116],"genotype,":[123],"O(mh(2)).":[128],"Both":[129],"algorithms":[130,178],"are":[131,185],"based":[132],"on":[133,187],"penalty":[135],"score":[136],"model":[137],"use":[139],"dynamic":[141],"programming":[142],"approach.":[143],"apply":[145],"problem":[151],"inferring":[153],"genotypes,":[156],"show":[158],"how":[159],"it":[160],"used":[163],"as":[164],"independent":[166],"tool,":[167],"or":[168],"improve":[170],"performance":[172],"existing":[174],"methods.":[175],"AVAILABILITY:":[176],"have":[179],"been":[180],"implemented":[181],"JAVA":[183],"available":[186],"request.":[188]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}