{"id":"https://openalex.org/W308769260","doi":"https://doi.org/10.1371/journal.pcbi.1004344","title":"Inferring the Clonal Structure of Viral Populations from Time Series Sequencing","display_name":"Inferring the Clonal Structure of Viral Populations from Time Series Sequencing","publication_year":2015,"publication_date":"2015-11-16","ids":{"openalex":"https://openalex.org/W308769260","doi":"https://doi.org/10.1371/journal.pcbi.1004344","mag":"308769260","pmid":"https://pubmed.ncbi.nlm.nih.gov/26571026"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004344","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004344","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004344&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.1004344&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067833239","display_name":"Donatien Fotso Chedom","orcid":null},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I4210100714","display_name":"Earlham Institute","ror":"https://ror.org/018cxtf62","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799693246","https://openalex.org/I4210087105","https://openalex.org/I4210100714"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Donatien F. Chedom","raw_affiliation_strings":["The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I4210100714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086188845","display_name":"Pablo R. Murcia","orcid":"https://orcid.org/0000-0002-4352-394X"},"institutions":[{"id":"https://openalex.org/I4210146449","display_name":"MRC University of Glasgow Centre for Virus Research","ror":"https://ror.org/03vaer060","country_code":"GB","type":"government","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4210146449","https://openalex.org/I7882870","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Pablo R. Murcia","raw_affiliation_strings":["MRC-University of Glasgow Centre for Virus Research, United Kingdom","MRC \u2014 University of Glasgow Centre for Virus Research, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MRC-University of Glasgow Centre for Virus Research, United Kingdom","institution_ids":["https://openalex.org/I4210146449"]},{"raw_affiliation_string":"MRC \u2014 University of Glasgow Centre for Virus Research, United Kingdom","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010958185","display_name":"Chris Greenman","orcid":"https://orcid.org/0000-0002-4338-8012"},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]},{"id":"https://openalex.org/I4210100714","display_name":"Earlham Institute","ror":"https://ror.org/018cxtf62","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799693246","https://openalex.org/I4210087105","https://openalex.org/I4210100714"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Chris D. Greenman","raw_affiliation_strings":["School of Computing Sciences, University of East Anglia, Norwich, United Kingdom","The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Sciences, University of East Anglia, Norwich, United Kingdom","institution_ids":["https://openalex.org/I1118541"]},{"raw_affiliation_string":"The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I4210100714"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010958185"],"corresponding_institution_ids":["https://openalex.org/I1118541","https://openalex.org/I2799300731","https://openalex.org/I4210100714"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00300978,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"11","issue":"11","first_page":"e1004344","last_page":"e1004344"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9991000294685364,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9991000294685364,"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":0.9987000226974487,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987000226974487,"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/reassortment","display_name":"Reassortment","score":0.7685620784759521},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7402350902557373},{"id":"https://openalex.org/keywords/viral-phylodynamics","display_name":"Viral phylodynamics","score":0.5883069038391113},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5737985372543335},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.550900399684906},{"id":"https://openalex.org/keywords/clone","display_name":"clone (Java method)","score":0.537603497505188},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5216753482818604},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.509194552898407},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4694516062736511},{"id":"https://openalex.org/keywords/viral-quasispecies","display_name":"Viral quasispecies","score":0.4561341404914856},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.44890445470809937},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.44455793499946594},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4370434284210205},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.34356623888015747},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2527769207954407},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.19667083024978638},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.07366356253623962}],"concepts":[{"id":"https://openalex.org/C16154277","wikidata":"https://www.wikidata.org/wiki/Q2004399","display_name":"Reassortment","level":5,"score":0.7685620784759521},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7402350902557373},{"id":"https://openalex.org/C21833749","wikidata":"https://www.wikidata.org/wiki/Q7189431","display_name":"Viral phylodynamics","level":4,"score":0.5883069038391113},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5737985372543335},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.550900399684906},{"id":"https://openalex.org/C81089528","wikidata":"https://www.wikidata.org/wiki/Q5134986","display_name":"clone (Java method)","level":3,"score":0.537603497505188},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5216753482818604},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.509194552898407},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4694516062736511},{"id":"https://openalex.org/C14500911","wikidata":"https://www.wikidata.org/wiki/Q3413375","display_name":"Viral quasispecies","level":4,"score":0.4561341404914856},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.44890445470809937},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.44455793499946594},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4370434284210205},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.34356623888015747},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2527769207954407},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.19667083024978638},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.07366356253623962},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"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":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1004344","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004344","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004344&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:26571026","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26571026","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:eprints.gla.ac.uk:111271","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":false,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Articles"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.767.1237","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.767.1237","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arxiv.org/pdf/1407.7997.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:089e93c351964aaca7a8ddf8b122f21a","is_oa":true,"landing_page_url":"https://doaj.org/article/089e93c351964aaca7a8ddf8b122f21a","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 11, Iss 11, p e1004344 (2015)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3627760","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4646700","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/1603771","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Inferring_the_Clonal_Structure_of_Viral_Populations_from_Time_Series_Sequencing_/1603771","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004344","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004344","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004344&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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W308769260.pdf","grobid_xml":"https://content.openalex.org/works/W308769260.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W84515509","https://openalex.org/W1487612538","https://openalex.org/W1565354039","https://openalex.org/W1967178396","https://openalex.org/W1968225289","https://openalex.org/W1982172875","https://openalex.org/W1986146966","https://openalex.org/W1987021091","https://openalex.org/W1992442812","https://openalex.org/W1993210385","https://openalex.org/W1993577356","https://openalex.org/W2006046315","https://openalex.org/W2010884070","https://openalex.org/W2012069101","https://openalex.org/W2020939898","https://openalex.org/W2026152438","https://openalex.org/W2026721694","https://openalex.org/W2031861067","https://openalex.org/W2037809979","https://openalex.org/W2048818637","https://openalex.org/W2057467440","https://openalex.org/W2064030256","https://openalex.org/W2065256070","https://openalex.org/W2083925087","https://openalex.org/W2106007739","https://openalex.org/W2108451182","https://openalex.org/W2112400707","https://openalex.org/W2118395479","https://openalex.org/W2129386317","https://openalex.org/W2145605402","https://openalex.org/W2148336751","https://openalex.org/W2151265018","https://openalex.org/W2157890018","https://openalex.org/W2158073495","https://openalex.org/W2159021003","https://openalex.org/W2163326395","https://openalex.org/W2170551349","https://openalex.org/W2170765088","https://openalex.org/W2178838370","https://openalex.org/W2337526125","https://openalex.org/W2340149117","https://openalex.org/W2478170177","https://openalex.org/W2498775860","https://openalex.org/W2616697817","https://openalex.org/W2914081640","https://openalex.org/W4210729409","https://openalex.org/W4212955684","https://openalex.org/W4236872582","https://openalex.org/W4388212639","https://openalex.org/W6641964592","https://openalex.org/W6647013262","https://openalex.org/W6685184340","https://openalex.org/W6738002306"],"related_works":["https://openalex.org/W1023129440","https://openalex.org/W1971669591","https://openalex.org/W2994069192","https://openalex.org/W4200124146","https://openalex.org/W2270733519","https://openalex.org/W2964755683","https://openalex.org/W2564146941","https://openalex.org/W3160626125","https://openalex.org/W2145454219","https://openalex.org/W1972828598"],"abstract_inverted_index":{"RNA":[0],"virus":[1],"populations":[2],"will":[3],"undergo":[4],"processes":[5],"of":[6,15,21,30,47,86,94,107,110],"mutation":[7,57],"and":[8,56,66,104],"selection":[9],"resulting":[10],"in":[11],"a":[12,22,27,92],"mixed":[13,28],"population":[14,24],"viral":[16,23],"particles.":[17],"High":[18],"throughput":[19],"sequencing":[20,116],"subsequently":[25],"contains":[26],"signal":[29],"the":[31,39,76,108],"underlying":[32,40],"clones.":[33],"We":[34,43,59],"would":[35],"like":[36],"to":[37,49,91,118],"identify":[38],"evolutionary":[41,70,100],"structures.":[42],"utilize":[44],"two":[45],"sources":[46],"information":[48],"attempt":[50],"this;":[51],"within":[52],"segment":[53],"linkage":[54],"information,":[55],"prevalence.":[58],"demonstrate":[60,105],"that":[61,112],"clone":[62],"haplotypes,":[63],"their":[64],"prevalence,":[65],"maximum":[67],"parsimony":[68],"reticulate":[69],"structures":[71],"can":[72],"be":[73,80],"identified,":[74],"although":[75],"solutions":[77],"may":[78],"not":[79],"unique,":[81],"even":[82],"for":[83],"complete":[84],"sets":[85],"information.":[87],"This":[88],"is":[89],"applied":[90],"chain":[93],"influenza":[95],"infection,":[96],"where":[97],"we":[98],"infer":[99],"structures,":[101],"including":[102],"reassortment,":[103],"some":[106],"difficulties":[109],"interpretation":[111],"arise":[113],"from":[114],"deep":[115],"due":[117],"artifacts":[119],"such":[120],"as":[121],"template":[122],"switching":[123],"during":[124],"PCR":[125],"amplification.":[126]},"counts_by_year":[],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
