{"id":"https://openalex.org/W2949087252","doi":"https://doi.org/10.1371/journal.pcbi.1006096","title":"Using pseudoalignment and base quality to accurately quantify microbial community composition","display_name":"Using pseudoalignment and base quality to accurately quantify microbial community composition","publication_year":2018,"publication_date":"2018-04-16","ids":{"openalex":"https://openalex.org/W2949087252","doi":"https://doi.org/10.1371/journal.pcbi.1006096","mag":"2949087252","pmid":"https://pubmed.ncbi.nlm.nih.gov/29659582"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006096","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006096","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006096&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.1006096&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022552422","display_name":"Mark Reppell","orcid":"https://orcid.org/0000-0001-7992-4537"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark Reppell","raw_affiliation_strings":["Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7992-4537","affiliations":[{"raw_affiliation_string":"Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073718055","display_name":"John Novembre","orcid":"https://orcid.org/0000-0001-5345-0214"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John Novembre","raw_affiliation_strings":["Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5022552422","https://openalex.org/A5073718055"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.8352,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.73393328,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"14","issue":"4","first_page":"e1006096","last_page":"e1006096"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9972000122070312,"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"}},"topics":[{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9972000122070312,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.993399977684021,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9850999712944031,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5874270796775818},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5260648131370544},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.49416688084602356},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.449776828289032},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4309849143028259},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.4247050881385803},{"id":"https://openalex.org/keywords/trait","display_name":"Trait","score":0.4206744432449341},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.41353729367256165},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33350640535354614},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23102089762687683},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1942516565322876},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09500870108604431}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5874270796775818},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5260648131370544},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.49416688084602356},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.449776828289032},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4309849143028259},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.4247050881385803},{"id":"https://openalex.org/C106934330","wikidata":"https://www.wikidata.org/wiki/Q1971873","display_name":"Trait","level":2,"score":0.4206744432449341},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.41353729367256165},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33350640535354614},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23102089762687683},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1942516565322876},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09500870108604431},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059013","descriptor_name":"Microbial Consortia","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059013","descriptor_name":"Microbial Consortia","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059013","descriptor_name":"Microbial Consortia","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1006096","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006096","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006096&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:29659582","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29659582","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:uchicago.tind.io:6353","is_oa":true,"landing_page_url":"http://knowledge.uchicago.edu/record/6353","pdf_url":null,"source":{"id":"https://openalex.org/S4306402460","display_name":"Knowledge@UChicago (University of Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40347166","host_organization_name":"University of Chicago","host_organization_lineage":["https://openalex.org/I40347166"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://knowledge.uchicago.edu/record/6353","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1006096","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006096","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:6d8a5c04dbb04811b78eed24dabda9a5","is_oa":true,"landing_page_url":"https://doaj.org/article/6d8a5c04dbb04811b78eed24dabda9a5","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 14, Iss 4, p e1006096 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4918989","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5945057","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/6146057","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Using_pseudoalignment_and_base_quality_to_accurately_quantify_microbial_community_composition/6146057","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:5945057","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5945057","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006096","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006096","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006096&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/G507176310","display_name":null,"funder_award_id":"RO1 HG007089","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320309626","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949087252.pdf","grobid_xml":"https://content.openalex.org/works/W2949087252.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W1853921426","https://openalex.org/W1968105193","https://openalex.org/W1980168725","https://openalex.org/W1988925586","https://openalex.org/W1998601670","https://openalex.org/W2003347102","https://openalex.org/W2008528231","https://openalex.org/W2010002522","https://openalex.org/W2018686814","https://openalex.org/W2032525833","https://openalex.org/W2034285706","https://openalex.org/W2055043387","https://openalex.org/W2058662042","https://openalex.org/W2066852475","https://openalex.org/W2068187483","https://openalex.org/W2071623230","https://openalex.org/W2087232033","https://openalex.org/W2088833470","https://openalex.org/W2089423792","https://openalex.org/W2097600042","https://openalex.org/W2100947741","https://openalex.org/W2101305949","https://openalex.org/W2105329815","https://openalex.org/W2110065044","https://openalex.org/W2116895571","https://openalex.org/W2117457769","https://openalex.org/W2124351063","https://openalex.org/W2124799197","https://openalex.org/W2125230147","https://openalex.org/W2125249373","https://openalex.org/W2146379626","https://openalex.org/W2146828922","https://openalex.org/W2147628946","https://openalex.org/W2149573313","https://openalex.org/W2150337627","https://openalex.org/W2151350595","https://openalex.org/W2152885278","https://openalex.org/W2159591897","https://openalex.org/W2159954944","https://openalex.org/W2160209604","https://openalex.org/W2163903604","https://openalex.org/W2166171121","https://openalex.org/W2170506381","https://openalex.org/W2171571559","https://openalex.org/W2190487303","https://openalex.org/W2212407137","https://openalex.org/W2215907530","https://openalex.org/W2228637465","https://openalex.org/W2257287664","https://openalex.org/W2273522830","https://openalex.org/W2307206101","https://openalex.org/W2312022769","https://openalex.org/W2323326409","https://openalex.org/W2390359191","https://openalex.org/W2469762261","https://openalex.org/W2484915396","https://openalex.org/W2508929473","https://openalex.org/W2518795824","https://openalex.org/W2533383604","https://openalex.org/W2561338758","https://openalex.org/W2578210650","https://openalex.org/W2773939681","https://openalex.org/W2951176108","https://openalex.org/W2952766115","https://openalex.org/W2963629592"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W4242417330","https://openalex.org/W4388282505","https://openalex.org/W3198631238","https://openalex.org/W4255657129"],"abstract_inverted_index":{"Pooled":[0],"DNA":[1,53],"from":[2,16,134,137],"multiple":[3],"unknown":[4],"organisms":[5,135],"arises":[6],"in":[7,51,102,144,176,203],"a":[8,45,66,93,99,114,160,189],"variety":[9,115],"of":[10,25,35,61,87,96,116,163,184,192],"contexts,":[11],"for":[12,48,180,200],"example":[13],"microbial":[14,204],"samples":[15,27,130],"ecological":[17],"or":[18],"human":[19],"health":[20],"research.":[21,104],"Determining":[22],"the":[23,33,56,82,85,109,138,177],"composition":[24],"pooled":[26,52],"can":[28],"be":[29],"difficult,":[30],"especially":[31],"at":[32,124],"scale":[34],"modern":[36],"sequencing":[37],"data":[38,154],"and":[39,58,128,194],"reference":[40,94,122],"databases.":[41],"Here":[42],"we":[43,107,149],"propose":[44],"novel":[46,190],"method":[47,83,110,158,175],"taxonomic":[49],"profiling":[50],"that":[54,69,196],"combines":[55],"speed":[57,193],"low-memory":[59],"requirements":[60],"k-mer":[62,181],"based":[63,182],"pseudoalignment":[64],"with":[65,119],"likelihood":[67],"framework":[68],"uses":[70],"base":[71],"quality":[72],"information":[73],"to":[74,84,155,187],"better":[75],"resolve":[76],"multiply":[77],"mapped":[78],"reads.":[79],"We":[80,140,172],"apply":[81],"problem":[86],"classifying":[88],"16S":[89,146],"rRNA":[90],"reads":[91,132],"using":[92],"database":[95],"known":[97],"organisms,":[98],"common":[100],"challenge":[101],"microbiome":[103],"Using":[105],"simulations,":[106],"show":[108,156],"is":[111,197],"accurate":[112],"across":[113],"read":[117,185],"lengths,":[118],"different":[120,125],"length":[121],"sequences,":[123],"sample":[126],"depths,":[127],"when":[129],"contain":[131],"originating":[133],"absent":[136],"reference.":[139],"also":[141],"assess":[142],"performance":[143],"real":[145],"data,":[147],"where":[148],"reanalyze":[150],"previous":[151],"genetic":[152],"association":[153],"our":[157,174],"discovers":[159],"larger":[161],"number":[162],"quantitative":[164],"trait":[165],"associations":[166],"than":[167],"other":[168],"widely":[169],"used":[170],"methods.":[171],"implement":[173],"software":[178],"Karp,":[179],"analysis":[183],"pools,":[186],"provide":[188],"combination":[191],"accuracy":[195],"uniquely":[198],"suited":[199],"enhancing":[201],"discoveries":[202],"studies.":[205]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
