{"id":"https://openalex.org/W2888599454","doi":"https://doi.org/10.1093/bioinformatics/bty735","title":"Haplotype matching in large cohorts using the Li and Stephens model","display_name":"Haplotype matching in large cohorts using the Li and Stephens model","publication_year":2018,"publication_date":"2018-08-23","ids":{"openalex":"https://openalex.org/W2888599454","doi":"https://doi.org/10.1093/bioinformatics/bty735","mag":"2888599454","pmid":"https://pubmed.ncbi.nlm.nih.gov/30165547"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty735","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty735","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/798/48966042/bioinformatics_35_5_798.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/798/48966042/bioinformatics_35_5_798.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062526316","display_name":"Gerton Lunter","orcid":"https://orcid.org/0000-0002-3798-2058"},"institutions":[{"id":"https://openalex.org/I1336263701","display_name":"Centre for Human Genetics","ror":"https://ror.org/01rjnta51","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Gerton Lunter","raw_affiliation_strings":["University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK"],"raw_orcid":"https://orcid.org/0000-0002-3798-2058","affiliations":[{"raw_affiliation_string":"University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK","institution_ids":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5062526316"],"corresponding_institution_ids":["https://openalex.org/I1336263701","https://openalex.org/I40120149"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":2051,"currency":"EUR","value_usd":2212},"fwci":1.6633,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.85203312,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"35","issue":"5","first_page":"798","last_page":"806"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9995999932289124,"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":0.9995999932289124,"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/T10351","display_name":"Liver Disease Diagnosis and Treatment","score":0.9958000183105469,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9921000003814697,"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/matching","display_name":"Matching (statistics)","score":0.7137218117713928},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.6603625416755676},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47263476252555847},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.38791993260383606},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2523421049118042},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2192016839981079},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2081930935382843},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.09706130623817444}],"concepts":[{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.7137218117713928},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.6603625416755676},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47263476252555847},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.38791993260383606},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2523421049118042},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2192016839981079},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2081930935382843},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.09706130623817444},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"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":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015331","descriptor_name":"Cohort Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015331","descriptor_name":"Cohort Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015331","descriptor_name":"Cohort Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bty735","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty735","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/798/48966042/bioinformatics_35_5_798.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30165547","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30165547","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:5389909","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6394399","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6394399","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6394399","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:cfbc4f57-6760-4e36-8f11-639168362fa1","is_oa":true,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:cfbc4f57-6760-4e36-8f11-639168362fa1","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty735","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty735","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/798/48966042/bioinformatics_35_5_798.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7004411822","display_name":"Understanding the genetic basis of common human diseases: core funding for the Wellcome Trust Centre for Human Genetics.","funder_award_id":"090532","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G8946600302","display_name":"Understanding the genetic basis of common human diseases: core funding for the Wellcome Trust Centre for Human Genetics.","funder_award_id":"090532/Z/09/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G8975541179","display_name":null,"funder_award_id":"090532/Z/09/","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2888599454.pdf","grobid_xml":"https://content.openalex.org/works/W2888599454.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1962960380","https://openalex.org/W1992436001","https://openalex.org/W2019956985","https://openalex.org/W2091705028","https://openalex.org/W2103441770","https://openalex.org/W2124985265","https://openalex.org/W2134783591","https://openalex.org/W2147477044","https://openalex.org/W2166879882","https://openalex.org/W2167030304","https://openalex.org/W2217809488","https://openalex.org/W2319462502","https://openalex.org/W4247464444"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W3146762847","https://openalex.org/W2398263405","https://openalex.org/W2056886854","https://openalex.org/W2025446304","https://openalex.org/W2166354960","https://openalex.org/W1888102361","https://openalex.org/W2131321814","https://openalex.org/W2171251480","https://openalex.org/W1492100763"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"Li":[2,76],"and":[3,24,55,77,80,126],"Stephens":[4,78],"model,":[5],"which":[6],"approximates":[7],"the":[8,11,33,44,75,85,88,97,100,104,118],"coalescent":[9],"describing":[10],"pattern":[12],"of":[13,21,37,84,87,99],"variation":[14],"in":[15,26],"a":[16,19,68,113],"population,":[17],"underpins":[18],"range":[20],"key":[22],"tools":[23],"results":[25],"genetics.":[27],"Although":[28],"highly":[29],"efficient":[30],"compared":[31],"to":[32,52,60,92,106],"coalescent,":[34],"standard":[35],"implementations":[36,57],"this":[38,94],"model":[39,79],"still":[40],"cannot":[41],"deal":[42],"with":[43],"very":[45,123],"large":[46],"reference":[47,89],"cohorts":[48],"that":[49,73,117],"are":[50],"starting":[51],"become":[53],"available,":[54],"practical":[56],"use":[58,98],"heuristics":[59],"achieve":[61],"reasonable":[62],"runtimes.":[63],"RESULTS:":[64],"Here":[65],"I":[66,115],"describe":[67],"new,":[69],"exact":[70],"algorithm":[71,105],"('fastLS')":[72],"implements":[74],"achieves":[81],"runtimes":[82],"independent":[83],"size":[86],"cohort.":[90,114],"Key":[91],"achieving":[93],"runtime":[95],"is":[96,122],"Burrows-Wheeler":[101,130],"transform,":[102],"allowing":[103],"efficiently":[107],"identify":[108],"partial":[109],"haplotype":[110],"matches":[111],"across":[112],"show":[116],"proposed":[119],"data":[120],"structure":[121],"similar":[124],"to,":[125],"generalizes,":[127],"Durbin's":[128],"positional":[129],"transform.":[131]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
