{"id":"https://openalex.org/W4400112290","doi":"https://doi.org/10.1109/tcbb.2024.3420430","title":"Haplotype Frequency Inference From Pooled Genetic Data With a Latent Multinomial Model","display_name":"Haplotype Frequency Inference From Pooled Genetic Data With a Latent Multinomial Model","publication_year":2024,"publication_date":"2024-06-28","ids":{"openalex":"https://openalex.org/W4400112290","doi":"https://doi.org/10.1109/tcbb.2024.3420430","pmid":"https://pubmed.ncbi.nlm.nih.gov/38941207"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3420430","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3420430","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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/A5037616253","display_name":"Yong See Foo","orcid":"https://orcid.org/0000-0003-3010-9106"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Yong See Foo","raw_affiliation_strings":["School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia"],"raw_orcid":"https://orcid.org/0000-0003-3010-9106","affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062407259","display_name":"Jennifer A. Flegg","orcid":"https://orcid.org/0000-0002-8809-726X"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jennifer Flegg","raw_affiliation_strings":["School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia"],"raw_orcid":"https://orcid.org/0000-0002-8809-726X","affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia","institution_ids":["https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I165779595"],"apc_list":null,"apc_paid":null,"fwci":0.3978,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.66507711,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"21","issue":"6","first_page":"1864","last_page":"1873"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9182999730110168,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9182999730110168,"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/inference","display_name":"Inference","score":0.7737555503845215},{"id":"https://openalex.org/keywords/multinomial-distribution","display_name":"Multinomial distribution","score":0.6485289335250854},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.6361606121063232},{"id":"https://openalex.org/keywords/genetic-data","display_name":"Genetic data","score":0.5126818418502808},{"id":"https://openalex.org/keywords/latent-variable-model","display_name":"Latent variable model","score":0.4306652247905731},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.4285759925842285},{"id":"https://openalex.org/keywords/latent-variable","display_name":"Latent variable","score":0.37601253390312195},{"id":"https://openalex.org/keywords/econometrics","display_name":"Econometrics","score":0.367683470249176},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3216784596443176},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27242380380630493},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.259803831577301},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2213735282421112},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20542165637016296},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.13402321934700012},{"id":"https://openalex.org/keywords/demography","display_name":"Demography","score":0.13366559147834778},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.0906355082988739}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7737555503845215},{"id":"https://openalex.org/C192065140","wikidata":"https://www.wikidata.org/wiki/Q1147928","display_name":"Multinomial distribution","level":2,"score":0.6485289335250854},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.6361606121063232},{"id":"https://openalex.org/C2993807623","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genetic data","level":3,"score":0.5126818418502808},{"id":"https://openalex.org/C65965080","wikidata":"https://www.wikidata.org/wiki/Q1806885","display_name":"Latent variable model","level":3,"score":0.4306652247905731},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.4285759925842285},{"id":"https://openalex.org/C51167844","wikidata":"https://www.wikidata.org/wiki/Q4422623","display_name":"Latent variable","level":2,"score":0.37601253390312195},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.367683470249176},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3216784596443176},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27242380380630493},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.259803831577301},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2213735282421112},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20542165637016296},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.13402321934700012},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.13366559147834778},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0906355082988739},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"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":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":"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":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3420430","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3420430","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38941207","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38941207","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2267882041","display_name":"Optimising progress towards elimination of malaria","funder_award_id":"DP200100747","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G3574404742","display_name":"Advances in data integration modelling for infectious disease response","funder_award_id":"FT210100034","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G3705808299","display_name":null,"funder_award_id":"APP2019093","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1535063149","https://openalex.org/W1584903252","https://openalex.org/W2033765726","https://openalex.org/W2102565381","https://openalex.org/W2109717210","https://openalex.org/W2129617669","https://openalex.org/W2135732313","https://openalex.org/W2158257880","https://openalex.org/W2167426038","https://openalex.org/W2217402295","https://openalex.org/W2906634067","https://openalex.org/W2913326851","https://openalex.org/W3152760956","https://openalex.org/W4390929398","https://openalex.org/W6638816469","https://openalex.org/W6641400130","https://openalex.org/W6652977711","https://openalex.org/W6653686852","https://openalex.org/W6664191588","https://openalex.org/W6675792658","https://openalex.org/W6675824659","https://openalex.org/W6679529799","https://openalex.org/W6762195253","https://openalex.org/W6784641772","https://openalex.org/W6793118012"],"related_works":["https://openalex.org/W2461917396","https://openalex.org/W2037497866","https://openalex.org/W4243467573","https://openalex.org/W1502435251","https://openalex.org/W62001224","https://openalex.org/W3032390039","https://openalex.org/W1584341211","https://openalex.org/W3122667150","https://openalex.org/W4393387622","https://openalex.org/W3145681568"],"abstract_inverted_index":{"In":[0],"genetic":[1,14,40,100,176],"association":[2],"studies,":[3],"haplotype":[4,36,96,119,156],"data":[5,11,41,101,153,157],"provide":[6,28],"more":[7,144,190],"refined":[8],"information":[9],"than":[10],"about":[12],"separate":[13],"markers.":[15],"However,":[16],"large-scale":[17],"studies":[18],"that":[19,42],"genotype":[20],"hundreds":[21],"to":[22,56,62,73,83,94,137,172,189],"thousands":[23],"of":[24,30,116,122,174,181,183],"individuals":[25],"may":[26],"only":[27],"results":[29,111],"pooled":[31,39,99,110,175],"data.":[32,64],"Methods":[33],"for":[34,151,155],"inferring":[35],"frequencies":[37,97],"from":[38,98,158],"scale":[43],"well":[44],"with":[45,135],"pool":[46,138],"size":[47],"rely":[48],"on":[49,103],"a":[50,104,179],"normal":[51,75],"approximation,":[52],"which":[53],"we":[54,89],"observe":[55],"produce":[57,143],"unreliable":[58],"inference":[59,146],"when":[60],"applied":[61,171],"real":[63],"We":[65,163],"illustrate":[66],"cases":[67],"where":[68,108],"the":[69,74,109,159],"approximation":[70],"fails,":[71],"due":[72],"covariance":[76],"matrix":[77],"being":[78],"near-singular.":[79],"As":[80],"an":[81],"alternative":[82],"approximate":[84,149],"methods,":[85,124],"in":[86],"this":[87],"paper":[88],"propose":[90],"two":[91],"exact":[92,141],"methods":[93,142,150,168,186],"infer":[95],"based":[102],"latent":[105,125],"multinomial":[106],"model,":[107],"are":[112,187],"considered":[113],"integer":[114],"combinations":[115],"latent,":[117],"unobserved":[118],"counts.":[120],"One":[121],"our":[123,167,185],"count":[126],"sampling":[127],"via":[128],"Markov":[129],"bases,":[130],"achieves":[131],"approximately":[132],"linear":[133],"runtime":[134],"respect":[136],"size.":[139],"Our":[140],"accurate":[145],"over":[147],"existing":[148],"synthetic":[152],"and":[154],"1000":[160],"Genomes":[161],"Project.":[162],"also":[164],"demonstrate":[165],"how":[166,184],"can":[169],"be":[170],"time-series":[173],"data,":[177],"as":[178,195],"proof":[180],"concept":[182],"relevant":[188],"complex":[191],"hierarchical":[192],"settings,":[193],"such":[194],"spatiotemporal":[196],"models.":[197]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-17T09:13:05.818461","created_date":"2025-10-10T00:00:00"}