{"id":"https://openalex.org/W2954842515","doi":"https://doi.org/10.1371/journal.pcbi.1008030","title":"A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis","display_name":"A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis","publication_year":2020,"publication_date":"2020-08-17","ids":{"openalex":"https://openalex.org/W2954842515","doi":"https://doi.org/10.1371/journal.pcbi.1008030","mag":"2954842515","pmid":"https://pubmed.ncbi.nlm.nih.gov/32804924"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008030","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008030","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008030&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008030&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064391693","display_name":"Amrit Dhar","orcid":"https://orcid.org/0000-0003-3353-9996"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amrit Dhar","raw_affiliation_strings":["Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","Department of Statistics, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Department of Statistics, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085169998","display_name":"Duncan Ralph","orcid":"https://orcid.org/0000-0002-2527-8610"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Duncan K. Ralph","raw_affiliation_strings":["Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089671301","display_name":"Vladimir N. Minin","orcid":"https://orcid.org/0000-0002-1917-9288"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Vladimir N. Minin","raw_affiliation_strings":["Department of Statistics, University of California, Irvine, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of California, Irvine, California, United States of America","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084752404","display_name":"F. A. Matsen","orcid":"https://orcid.org/0000-0003-0607-6025"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Frederick A. Matsen","raw_affiliation_strings":["Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5084752404","https://openalex.org/A5089671301"],"corresponding_institution_ids":["https://openalex.org/I204250578","https://openalex.org/I4210089486"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.7076,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.84686512,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"16","issue":"8","first_page":"e1008030","last_page":"e1008030"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9883000254631042,"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/T11725","display_name":"Immunodeficiency and Autoimmune Disorders","score":0.964900016784668,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8000805377960205},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6766200661659241},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5128645896911621},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.49176910519599915},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4897179901599884},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4276784658432007},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4215685725212097},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3959333598613739},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.16700655221939087},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15966114401817322},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1543213427066803}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8000805377960205},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6766200661659241},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5128645896911621},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.49176910519599915},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4897179901599884},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4276784658432007},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4215685725212097},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3959333598613739},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.16700655221939087},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15966114401817322},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1543213427066803}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"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":"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":"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":"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":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015322","descriptor_name":"Gene Rearrangement, B-Lymphocyte","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015322","descriptor_name":"Gene Rearrangement, B-Lymphocyte","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015322","descriptor_name":"Gene Rearrangement, B-Lymphocyte","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015322","descriptor_name":"Gene Rearrangement, B-Lymphocyte","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015322","descriptor_name":"Gene Rearrangement, B-Lymphocyte","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":"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":"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":"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":"D027041","descriptor_name":"Somatic Hypermutation, Immunoglobulin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027041","descriptor_name":"Somatic Hypermutation, Immunoglobulin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027041","descriptor_name":"Somatic Hypermutation, Immunoglobulin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027041","descriptor_name":"Somatic Hypermutation, Immunoglobulin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027041","descriptor_name":"Somatic Hypermutation, Immunoglobulin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1008030","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008030","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008030&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:32804924","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32804924","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:arXiv.org:1906.11982","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1906.11982","pdf_url":"https://arxiv.org/pdf/1906.11982","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},{"id":"pmh:oai:RePEc:plo:pcbi00:1008030","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008030","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:b8b464fde53b4a1ba513628dc21726dd","is_oa":true,"landing_page_url":"https://doaj.org/article/b8b464fde53b4a1ba513628dc21726dd","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 8, p e1008030 (2020)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt62j344xw","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/62j344xw","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"PLoS computational biology, vol 16, iss 8","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7451993","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7451993","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008030","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008030","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008030&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8100000023841858,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G1737146978","display_name":null,"funder_award_id":"AI146028","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1885104655","display_name":null,"funder_award_id":"IGERT DGE-1258485","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2335442534","display_name":null,"funder_award_id":"multiple","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3808495251","display_name":null,"funder_award_id":"1564137","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4352710008","display_name":null,"funder_award_id":"CISE-1564137","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5119375280","display_name":"IGERT-CIF21: Big Data U: A Program for Integrated Multidisciplinary Education and Research for Big Data Science","funder_award_id":"1258485","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5594358474","display_name":null,"funder_award_id":"multiple","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5762190694","display_name":"III: AF: Medium: Collaborative Research: Enabling Phylogenetic Inference for Modern Data Sets","funder_award_id":"1561334","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6637464624","display_name":null,"funder_award_id":"GM113246","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7150081037","display_name":null,"funder_award_id":"CISE-1561334","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7378993406","display_name":null,"funder_award_id":"AI138709","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8006612767","display_name":null,"funder_award_id":"DGE-1258485","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8164471825","display_name":null,"funder_award_id":"IGERT","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332169","display_name":"Directorate for Computer and Information Science and Engineering","ror":"https://ror.org/025kzpk63"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2954842515.pdf","grobid_xml":"https://content.openalex.org/works/W2954842515.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W416847175","https://openalex.org/W577575140","https://openalex.org/W1501586228","https://openalex.org/W1539673959","https://openalex.org/W1565321014","https://openalex.org/W1593676244","https://openalex.org/W1700611987","https://openalex.org/W1802312377","https://openalex.org/W1901318710","https://openalex.org/W1968294650","https://openalex.org/W1978398372","https://openalex.org/W1980811933","https://openalex.org/W1993476635","https://openalex.org/W1997064329","https://openalex.org/W2001914359","https://openalex.org/W2003302807","https://openalex.org/W2010959676","https://openalex.org/W2020596573","https://openalex.org/W2031611770","https://openalex.org/W2042296034","https://openalex.org/W2045656233","https://openalex.org/W2061140759","https://openalex.org/W2063195211","https://openalex.org/W2075032293","https://openalex.org/W2091933470","https://openalex.org/W2093296692","https://openalex.org/W2098613108","https://openalex.org/W2102424972","https://openalex.org/W2105329815","https://openalex.org/W2105594594","https://openalex.org/W2113557726","https://openalex.org/W2122796331","https://openalex.org/W2124790653","https://openalex.org/W2127346557","https://openalex.org/W2137603774","https://openalex.org/W2147660889","https://openalex.org/W2148294135","https://openalex.org/W2156125289","https://openalex.org/W2158266834","https://openalex.org/W2171634310","https://openalex.org/W2235599671","https://openalex.org/W2259225862","https://openalex.org/W2294858472","https://openalex.org/W2317651087","https://openalex.org/W2332774781","https://openalex.org/W2408731419","https://openalex.org/W2561038494","https://openalex.org/W2580067296","https://openalex.org/W2615390960","https://openalex.org/W2736535424","https://openalex.org/W2770988077","https://openalex.org/W2915177470","https://openalex.org/W2945941055","https://openalex.org/W2949537553","https://openalex.org/W2963777440","https://openalex.org/W2977367481","https://openalex.org/W2979682945","https://openalex.org/W3139821851","https://openalex.org/W3199943451","https://openalex.org/W4233815609","https://openalex.org/W4235232179","https://openalex.org/W4238387639","https://openalex.org/W4248681815","https://openalex.org/W4298440781","https://openalex.org/W4388323202"],"related_works":["https://openalex.org/W2053269318","https://openalex.org/W2364370872","https://openalex.org/W2097963413","https://openalex.org/W2294335174","https://openalex.org/W2025614924","https://openalex.org/W3145575561","https://openalex.org/W2001275470","https://openalex.org/W2144958703","https://openalex.org/W2080410528","https://openalex.org/W2529820324"],"abstract_inverted_index":{"The":[0,26],"human":[1],"body":[2],"generates":[3],"a":[4,145,159,170,175],"diverse":[5],"set":[6],"of":[7,14,29,87,120,137],"high":[8],"affinity":[9],"antibodies,":[10],"the":[11,73,84,98,107,117,121,131,135,193],"soluble":[12],"form":[13],"B":[15,102],"cell":[16,103],"receptors":[17],"(BCRs),":[18],"that":[19,155],"bind":[20],"to":[21,36,82,130,148],"and":[22,46,59,128],"neutralize":[23],"invading":[24],"pathogens.":[25],"natural":[27],"development":[28],"BCRs":[30],"must":[31],"be":[32],"understood":[33],"in":[34,188],"order":[35],"design":[37],"vaccines":[38],"for":[39,65,152,178,186],"highly":[40],"mutable":[41],"pathogens":[42],"such":[43,105],"as":[44,106],"influenza":[45],"HIV.":[47],"BCR":[48,66,88,153,179],"diversity":[49],"is":[50,156],"induced":[51],"by":[52],"naturally":[53,184],"occurring":[54],"combinatorial":[55],"\"V(D)J\"":[56],"rearrangement,":[57],"mutation,":[58],"selection":[60],"processes.":[61,75],"Most":[62],"current":[63],"methods":[64,78],"sequence":[67,89,125,180],"analysis":[68],"focus":[69],"on":[70,158],"separately":[71],"modeling":[72],"above":[74],"Statistical":[76],"phylogenetic":[77,114,150,160,176,194],"are":[79],"often":[80],"used":[81],"model":[83,163,173,177],"mutational":[85],"dynamics":[86],"data,":[90],"but":[91,182],"these":[92],"techniques":[93],"do":[94],"not":[95,167],"consider":[96],"all":[97,189],"complexities":[99,136],"associated":[100],"with":[101,174],"diversification":[104],"V(D)J":[108,138],"rearrangement":[109,172],"process.":[110],"In":[111,140],"particular,":[112],"standard":[113],"approaches":[115],"assume":[116],"DNA":[118],"bases":[119],"progenitor":[122],"(or":[123],"\"naive\")":[124],"arise":[126],"independently":[127],"according":[129],"same":[132],"distribution,":[133],"ignoring":[134],"rearrangement.":[139],"this":[141],"paper,":[142],"we":[143],"introduce":[144],"novel":[146],"approach":[147],"Bayesian":[149],"inference":[151],"sequences":[154],"based":[157],"hidden":[161],"Markov":[162],"(phylo-HMM).":[164],"This":[165],"technique":[166],"only":[168],"integrates":[169],"naive":[171],"evolution":[181],"also":[183],"accounts":[185],"uncertainty":[187],"unobserved":[190],"variables,":[191],"including":[192],"tree,":[195],"via":[196],"posterior":[197],"distribution":[198],"sampling.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":6}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
