{"id":"https://openalex.org/W2894351956","doi":"https://doi.org/10.1371/journal.pcbi.1006534","title":"A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation","display_name":"A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation","publication_year":2019,"publication_date":"2019-04-22","ids":{"openalex":"https://openalex.org/W2894351956","doi":"https://doi.org/10.1371/journal.pcbi.1006534","mag":"2894351956","pmid":"https://pubmed.ncbi.nlm.nih.gov/31009452"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006534","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006534","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006534&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":["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.1006534&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049670721","display_name":"Marko J\u00e4rvenp\u00e4\u00e4","orcid":"https://orcid.org/0000-0002-9578-9272"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","US"],"is_corresponding":false,"raw_author_name":"Marko J\u00e4rvenp\u00e4\u00e4","raw_affiliation_strings":["Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA","Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland","institution_ids":["https://openalex.org/I32943570","https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001817555","display_name":"Mohamad Sater","orcid":"https://orcid.org/0000-0003-1912-0590"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohamad R. Abdul Sater","raw_affiliation_strings":["Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA"],"raw_orcid":"https://orcid.org/0000-0003-1912-0590","affiliations":[{"raw_affiliation_string":"Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011687012","display_name":"Georgia Lagoudas","orcid":null},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I4210110987","display_name":"IIT@MIT","ror":"https://ror.org/01wp8zh54","country_code":"US","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210110987"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Georgia K. Lagoudas","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA, USA","Department of Biological Engineering, MIT, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0002-3165-7801","affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Biological Engineering, MIT, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210110987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024611841","display_name":"Paul C. Blainey","orcid":"https://orcid.org/0000-0002-4889-8783"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I4210110987","display_name":"IIT@MIT","ror":"https://ror.org/01wp8zh54","country_code":"US","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210110987"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul C. Blainey","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA, USA","Department of Biological Engineering, MIT, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0002-4889-8783","affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Biological Engineering, MIT, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210110987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016777889","display_name":"Loren G. Miller","orcid":"https://orcid.org/0000-0003-0487-1711"},"institutions":[{"id":"https://openalex.org/I2801403999","display_name":"UCLA Medical Center","ror":"https://ror.org/04vq5kb54","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799798094","https://openalex.org/I2801403999"]},{"id":"https://openalex.org/I4210105266","display_name":"Biomed Research Institute","ror":"https://ror.org/00tfz0s96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210105266"]},{"id":"https://openalex.org/I4210165985","display_name":"Harbor\u2013UCLA Medical Center","ror":"https://ror.org/05h4zj272","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1328359107","https://openalex.org/I4210165985"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Loren G. Miller","raw_affiliation_strings":["Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Diseases, LA Biomed Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA","Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Diseases, LA Biomed Research Institute at Harbor\u2013UCLA Medical Center, Torrance, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Diseases, LA Biomed Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA","institution_ids":["https://openalex.org/I4210105266","https://openalex.org/I2801403999"]},{"raw_affiliation_string":"Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Diseases, LA Biomed Research Institute at Harbor\u2013UCLA Medical Center, Torrance, CA, USA","institution_ids":["https://openalex.org/I4210105266","https://openalex.org/I4210165985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052781570","display_name":"James A. McKinnell","orcid":null},"institutions":[{"id":"https://openalex.org/I2801403999","display_name":"UCLA Medical Center","ror":"https://ror.org/04vq5kb54","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799798094","https://openalex.org/I2801403999"]},{"id":"https://openalex.org/I4210105266","display_name":"Biomed Research Institute","ror":"https://ror.org/00tfz0s96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210105266"]},{"id":"https://openalex.org/I4210165985","display_name":"Harbor\u2013UCLA Medical Center","ror":"https://ror.org/05h4zj272","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1328359107","https://openalex.org/I4210165985"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James A. McKinnell","raw_affiliation_strings":["Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Diseases, LA Biomed Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA","Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Diseases, LA Biomed Research Institute at Harbor\u2013UCLA Medical Center, Torrance, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Diseases, LA Biomed Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA","institution_ids":["https://openalex.org/I4210105266","https://openalex.org/I2801403999"]},{"raw_affiliation_string":"Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Diseases, LA Biomed Research Institute at Harbor\u2013UCLA Medical Center, Torrance, CA, USA","institution_ids":["https://openalex.org/I4210105266","https://openalex.org/I4210165985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046304079","display_name":"Susan S. Huang","orcid":"https://orcid.org/0000-0001-6748-3447"},"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":false,"raw_author_name":"Susan S. Huang","raw_affiliation_strings":["Division of Infectious Diseases and Health Policy Research Institute, University of California, Irvine School of Medicine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Diseases and Health Policy Research Institute, University of California, Irvine School of Medicine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015588148","display_name":"Yonatan H. Grad","orcid":"https://orcid.org/0000-0001-5646-1314"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yonatan H. Grad","raw_affiliation_strings":["Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089920272","display_name":"Pekka Marttinen","orcid":"https://orcid.org/0000-0001-7078-7927"},"institutions":[{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Pekka Marttinen","raw_affiliation_strings":["Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland"],"raw_orcid":"https://orcid.org/0000-0001-7078-7927","affiliations":[{"raw_affiliation_string":"Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland","institution_ids":["https://openalex.org/I32943570","https://openalex.org/I9927081"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5015588148","https://openalex.org/A5089920272"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I32943570","https://openalex.org/I9927081"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2150,"currency":"EUR","value_usd":2318},"fwci":0.71,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.68156512,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"15","issue":"4","first_page":"e1006534","last_page":"e1006534"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10195","display_name":"Antimicrobial Resistance in Staphylococcus","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10195","display_name":"Antimicrobial Resistance in Staphylococcus","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.998199999332428,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9940000176429749,"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/approximate-bayesian-computation","display_name":"Approximate Bayesian computation","score":0.828143835067749},{"id":"https://openalex.org/keywords/colonization","display_name":"Colonization","score":0.6952289342880249},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.6911174058914185},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5967136025428772},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5653195977210999},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.5489792823791504},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.5457415580749512},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5379894375801086},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5342764854431152},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42716288566589355},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3586629629135132},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2755556106567383},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18571504950523376},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.13402312994003296},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.10925883054733276}],"concepts":[{"id":"https://openalex.org/C2779377595","wikidata":"https://www.wikidata.org/wiki/Q21045424","display_name":"Approximate Bayesian computation","level":3,"score":0.828143835067749},{"id":"https://openalex.org/C2776927270","wikidata":"https://www.wikidata.org/wiki/Q815962","display_name":"Colonization","level":2,"score":0.6952289342880249},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.6911174058914185},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5967136025428772},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5653195977210999},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.5489792823791504},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.5457415580749512},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5379894375801086},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5342764854431152},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42716288566589355},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3586629629135132},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2755556106567383},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18571504950523376},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.13402312994003296},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10925883054733276},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"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":"D000465","descriptor_name":"Algorithms","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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002353","descriptor_name":"Carrier State","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D002353","descriptor_name":"Carrier State","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D002353","descriptor_name":"Carrier State","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D002353","descriptor_name":"Carrier State","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D002353","descriptor_name":"Carrier State","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009296","descriptor_name":"Nasal Cavity","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009296","descriptor_name":"Nasal Cavity","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009296","descriptor_name":"Nasal Cavity","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009296","descriptor_name":"Nasal Cavity","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009296","descriptor_name":"Nasal Cavity","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D013203","descriptor_name":"Staphylococcal Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D013203","descriptor_name":"Staphylococcal Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D013203","descriptor_name":"Staphylococcal Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D013203","descriptor_name":"Staphylococcal Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D013203","descriptor_name":"Staphylococcal Infections","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"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":false},{"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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D055624","descriptor_name":"Methicillin-Resistant Staphylococcus aureus","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":true},{"descriptor_ui":"D055624","descriptor_name":"Methicillin-Resistant Staphylococcus aureus","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":true},{"descriptor_ui":"D055624","descriptor_name":"Methicillin-Resistant Staphylococcus aureus","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":true},{"descriptor_ui":"D055624","descriptor_name":"Methicillin-Resistant Staphylococcus aureus","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":true},{"descriptor_ui":"D055624","descriptor_name":"Methicillin-Resistant Staphylococcus aureus","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":true},{"descriptor_ui":"D055624","descriptor_name":"Methicillin-Resistant Staphylococcus aureus","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D055624","descriptor_name":"Methicillin-Resistant Staphylococcus aureus","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D055624","descriptor_name":"Methicillin-Resistant Staphylococcus aureus","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D055624","descriptor_name":"Methicillin-Resistant Staphylococcus aureus","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D055624","descriptor_name":"Methicillin-Resistant Staphylococcus aureus","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1006534","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006534","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006534&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:31009452","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31009452","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:RePEc:plo:pcbi00:1006534","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006534","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:aaltodoc.aalto.fi:123456789/38356","is_oa":true,"landing_page_url":"https://research.aalto.fi/en/publications/b9847cd7-2b49-4723-809b-abc0acbaa43d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401663","display_name":"Aaltodoc (Aalto University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9927081","host_organization_name":"Aalto University","host_organization_lineage":["https://openalex.org/I9927081"],"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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:066995ba28c84377a85b62dd2a33fb37","is_oa":true,"landing_page_url":"https://doaj.org/article/066995ba28c84377a85b62dd2a33fb37","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"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 15, Iss 4, p e1006534 (2019)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt9nv505mk","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/9nv505mk","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 15, iss 4","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5494293","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6497309","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":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/8021300","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/A_Bayesian_model_of_acquisition_and_clearance_of_bacterial_colonization_incorporating_within-host_variation/8021300","pdf_url":null,"source":{"id":"https://openalex.org/S4306400572","display_name":"OPAL (Open@LaTrobe) (La Trobe University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I196829312","host_organization_name":"La Trobe University","host_organization_lineage":["https://openalex.org/I196829312"],"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":null},{"id":"pmh:qt9nv505mk","is_oa":true,"landing_page_url":"http://www.escholarship.org/uc/item/9nv505mk","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":"J\u00e4rvenp\u00e4\u00e4, Marko; Sater, Mohamad R Abdul; Lagoudas, Georgia K; Blainey, Paul C; Miller, Loren G; McKinnell, James A; \u00a0et al.(2019). A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation.. PLoS computational biology, 15(4), e1006534. doi: 10.1371/journal.pcbi.1006534. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/9nv505mk","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006534","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006534","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006534&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":[],"awards":[{"id":"https://openalex.org/G21708494","display_name":"NSF Student Travel Grant for 2020 Conferences on  File and Storage Technologies (FAST) and Networked Design and Implementation (NSDI)","funder_award_id":"2016092","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2373499510","display_name":null,"funder_award_id":"R21 AI121932","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3264944329","display_name":null,"funder_award_id":"R01 HS019388","funder_id":"https://openalex.org/F4320332177","funder_display_name":"Agency for Healthcare Research and Quality"},{"id":"https://openalex.org/G3960214123","display_name":"PROJECT CLEAR - CHANGING LIVES BY ERADICATING ANTIBIOTIC RESISTANCE","funder_award_id":"R01HS019388","funder_id":"https://openalex.org/F4320332177","funder_display_name":"Agency for Healthcare Research and Quality"},{"id":"https://openalex.org/G68902159","display_name":null,"funder_award_id":"UL1 TR000153","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G7060621449","display_name":null,"funder_award_id":"UL1 TR000153","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G711945402","display_name":null,"funder_award_id":"UL1 TR000153","funder_id":"https://openalex.org/F4320332688","funder_display_name":"University of California, Irvine"},{"id":"https://openalex.org/G8414295574","display_name":null,"funder_award_id":"TR000153","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332177","display_name":"Agency for Healthcare Research and Quality","ror":"https://ror.org/03jmfdf59"},{"id":"https://openalex.org/F4320332688","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"},{"id":"https://openalex.org/F4320337963","display_name":"Institute for Clinical and Translational Science, University of California, Irvine","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2894351956.pdf","grobid_xml":"https://content.openalex.org/works/W2894351956.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W84515509","https://openalex.org/W1506806321","https://openalex.org/W1528471431","https://openalex.org/W1584328577","https://openalex.org/W1903655767","https://openalex.org/W1972145956","https://openalex.org/W1982855075","https://openalex.org/W1985093013","https://openalex.org/W1989125010","https://openalex.org/W1995606284","https://openalex.org/W2025021478","https://openalex.org/W2034677156","https://openalex.org/W2040322059","https://openalex.org/W2045656233","https://openalex.org/W2088077322","https://openalex.org/W2091321829","https://openalex.org/W2098159900","https://openalex.org/W2103441770","https://openalex.org/W2115328541","https://openalex.org/W2116416291","https://openalex.org/W2123864627","https://openalex.org/W2136133754","https://openalex.org/W2139812092","https://openalex.org/W2142108063","https://openalex.org/W2224150270","https://openalex.org/W2273624252","https://openalex.org/W2330229417","https://openalex.org/W2492038761","https://openalex.org/W2534708821","https://openalex.org/W2550737095","https://openalex.org/W2588835098","https://openalex.org/W2591806215","https://openalex.org/W2610253859","https://openalex.org/W2765855012","https://openalex.org/W2779599349","https://openalex.org/W2800970122","https://openalex.org/W2884099873","https://openalex.org/W2949213260","https://openalex.org/W2951384372","https://openalex.org/W2953324318","https://openalex.org/W2964089699","https://openalex.org/W4248681815","https://openalex.org/W4292691288"],"related_works":["https://openalex.org/W2109606780","https://openalex.org/W1480082381","https://openalex.org/W4299976848","https://openalex.org/W308423894","https://openalex.org/W1436597729","https://openalex.org/W3087071515","https://openalex.org/W2226294016","https://openalex.org/W4283077537","https://openalex.org/W2999603699","https://openalex.org/W2464065341"],"abstract_inverted_index":{"Bacterial":[0],"populations":[1],"that":[2,18,145],"colonize":[3],"a":[4,16,57,77,90,141,187,217,227],"host":[5,11],"can":[6],"play":[7],"important":[8],"roles":[9],"in":[10,131,213],"health,":[12],"including":[13],"serving":[14],"as":[15],"reservoir":[17],"transmits":[19],"to":[20,71,80,88,100,111,159],"other":[21],"hosts":[22],"and":[23,38,83,128,135,163,181,194,209],"from":[24,165,226],"which":[25,96],"invasive":[26],"strains":[27,151],"emerge,":[28],"thus":[29],"emphasizing":[30],"the":[31,65,102,114,117,122,129,132,155,174,182,202,238],"importance":[32],"of":[33,36,40,44,52,67,116,148,189,219,237],"understanding":[34],"rates":[35,85],"acquisition":[37,82,134,164],"clearance":[39,84,136,162],"colonizing":[41],"populations.":[42],"Studies":[43],"colonization":[45,62],"dynamics":[46],"have":[47],"been":[48,87],"based":[49],"on":[50],"assessment":[51],"whether":[53,149],"serial":[54],"samples":[55],"represent":[56,101],"single":[58],"population":[59,178],"or":[60],"distinct":[61],"events.":[63],"With":[64],"use":[66,212],"whole":[68],"genome":[69],"sequencing":[70],"determine":[72,160],"genetic":[73,92,179],"distance":[74,93],"between":[75,125],"isolates,":[76],"common":[78],"solution":[79],"estimate":[81],"has":[86],"assume":[89],"fixed":[91],"threshold":[94],"below":[95],"isolates":[97,225],"are":[98],"considered":[99,154],"same":[103],"strain.":[104],"However,":[105],"this":[106],"approach":[107],"is":[108,184,240],"often":[109],"inadequate":[110],"account":[112],"for":[113],"diversity":[115],"underlying":[118],"within-host":[119,175],"evolving":[120],"population,":[121],"time":[123],"intervals":[124],"consecutive":[126],"measurements,":[127],"uncertainty":[130],"estimated":[133],"rates.":[137],"Here,":[138],"we":[139],"present":[140],"fully":[142],"Bayesian":[143,191],"model":[144],"provides":[146],"probabilities":[147],"two":[150],"should":[152],"be":[153],"same,":[156],"allowing":[157],"us":[158],"bacterial":[161],"genomes":[166],"sampled":[167],"over":[168],"time.":[169],"Our":[170],"method":[171,203,239],"explicitly":[172],"models":[173],"variation":[176],"using":[177,186],"simulation,":[180],"inference":[183],"done":[185],"combination":[188],"Approximate":[190],"Computation":[192],"(ABC)":[193],"Markov":[195],"Chain":[196],"Monte":[197],"Carlo":[198],"(MCMC).":[199],"We":[200],"validate":[201],"with":[204],"multiple":[205],"carefully":[206],"conducted":[207],"simulations":[208],"demonstrate":[210],"its":[211],"practice":[214],"by":[215],"analyzing":[216],"collection":[218],"methicillin":[220],"resistant":[221],"Staphylococcus":[222],"aureus":[223],"(MRSA)":[224],"large":[228],"recently":[229],"completed":[230],"longitudinal":[231],"clinical":[232],"study.":[233],"An":[234],"R-code":[235],"implementation":[236],"freely":[241],"available":[242],"at:":[243],"https://github.com/mjarvenpaa/bacterial-colonization-model.":[244]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-06T08:01:05.025921","created_date":"2025-10-10T00:00:00"}