{"id":"https://openalex.org/W2990771615","doi":"https://doi.org/10.1371/journal.pcbi.1006863","title":"Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity","display_name":"Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity","publication_year":2019,"publication_date":"2019-11-22","ids":{"openalex":"https://openalex.org/W2990771615","doi":"https://doi.org/10.1371/journal.pcbi.1006863","mag":"2990771615","pmid":"https://pubmed.ncbi.nlm.nih.gov/31756192"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006863","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006863","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006863&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.1006863&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054621218","display_name":"George S. Watts","orcid":"https://orcid.org/0000-0001-8216-0144"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]},{"id":"https://openalex.org/I4390039223","display_name":"University of Arizona Cancer Center","ror":"https://ror.org/04tvx8690","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4390039223"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"George S. Watts","raw_affiliation_strings":["University of Arizona Cancer Center and Department of Pharmacology, University of Arizona, Tucson, Arizona, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Arizona Cancer Center and Department of Pharmacology, University of Arizona, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243","https://openalex.org/I4390039223"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043734013","display_name":"James E. Thornton","orcid":"https://orcid.org/0000-0001-6691-9114"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James E. Thornton","raw_affiliation_strings":["Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053141061","display_name":"Ken Youens\u2010Clark","orcid":"https://orcid.org/0000-0001-9961-144X"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ken Youens-Clark","raw_affiliation_strings":["Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009706037","display_name":"Alise J. Ponsero","orcid":"https://orcid.org/0000-0002-4125-7561"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alise J. Ponsero","raw_affiliation_strings":["Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070730048","display_name":"Marvin J. Slepian","orcid":"https://orcid.org/0000-0002-7864-6691"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marvin J. Slepian","raw_affiliation_strings":["Arizona Center for Accelerated Biomedical Innovation, University of Arizona, Tucson, Arizona, United States of America","Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, United States of America","Department of Medicine, University of Arizona, Tucson, Arizona, United States of America"],"affiliations":[{"raw_affiliation_string":"Arizona Center for Accelerated Biomedical Innovation, University of Arizona, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"Department of Medicine, University of Arizona, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004483382","display_name":"Emmanuel Menashi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210130412","display_name":"HonorHealth","ror":"https://ror.org/03szbwj17","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210130412"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emmanuel Menashi","raw_affiliation_strings":["Honor Health Hospital, Scottsdale, Arizona, United States of America"],"affiliations":[{"raw_affiliation_string":"Honor Health Hospital, Scottsdale, Arizona, United States of America","institution_ids":["https://openalex.org/I4210130412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111627121","display_name":"Charles Hu","orcid":null},"institutions":[{"id":"https://openalex.org/I2802827176","display_name":"Dignity Health","ror":"https://ror.org/05c9r4685","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2802827176"]},{"id":"https://openalex.org/I4210137555","display_name":"Regional Medical Center","ror":"https://ror.org/03t2egq54","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles Hu","raw_affiliation_strings":["Dignity Health Chandler Regional Medical Center, Chandler, Arizona, United States of America"],"affiliations":[{"raw_affiliation_string":"Dignity Health Chandler Regional Medical Center, Chandler, Arizona, United States of America","institution_ids":["https://openalex.org/I2802827176","https://openalex.org/I4210137555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108824421","display_name":"Wuquan Deng","orcid":"https://orcid.org/0009-0004-4172-4571"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wuquan Deng","raw_affiliation_strings":["Department of Endocrinology, Multidisciplinary Diabetic Foot Medical Center, Affiliated Central Hospital of Chongqing University, Chongqing, China"],"affiliations":[{"raw_affiliation_string":"Department of Endocrinology, Multidisciplinary Diabetic Foot Medical Center, Affiliated Central Hospital of Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034035627","display_name":"David G. Armstrong","orcid":"https://orcid.org/0000-0003-1887-9175"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David G. Armstrong","raw_affiliation_strings":["Southwestern Academic Limb Salvage Alliance (SALSA), Department of Surgery, Keck School of Medicine of University of Southern California, Los Angeles, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Southwestern Academic Limb Salvage Alliance (SALSA), Department of Surgery, Keck School of Medicine of University of Southern California, Los Angeles, California, United States of America","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015360936","display_name":"Spenser Reed","orcid":null},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Spenser Reed","raw_affiliation_strings":["University of Arizona Department of Family and Community Medicine, Tucson, Arizona, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Arizona Department of Family and Community Medicine, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058943490","display_name":"Lee D. Cranmer","orcid":"https://orcid.org/0000-0002-7789-5442"},"institutions":[{"id":"https://openalex.org/I1332479046","display_name":"Seattle Cancer Care Alliance","ror":"https://ror.org/03jq88n71","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1332479046"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]},{"id":"https://openalex.org/I4210127473","display_name":"Cancer Research Center","ror":"https://ror.org/03fbwjm33","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210127473"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lee D. Cranmer","raw_affiliation_strings":["Department of Medicine, University of Washington and Fred Hutchinson Cancer Research Center, and Seattle Cancer Care Alliance, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Washington and Fred Hutchinson Cancer Research Center, and Seattle Cancer Care Alliance, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I1332479046","https://openalex.org/I4210089486","https://openalex.org/I4210127473","https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068732878","display_name":"Bonnie L. Hurwitz","orcid":"https://orcid.org/0000-0001-8699-957X"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bonnie L. Hurwitz","raw_affiliation_strings":["BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America","Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America"],"affiliations":[{"raw_affiliation_string":"BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"Department of Biosystems Engineering, University of Arizona, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5068732878"],"corresponding_institution_ids":["https://openalex.org/I138006243"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.1165,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.78024935,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"15","issue":"11","first_page":"e1006863","last_page":"e1006863"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/T11316","display_name":"Mycobacterium research and diagnosis","score":0.9958000183105469,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.9027743935585022},{"id":"https://openalex.org/keywords/centrifuge","display_name":"Centrifuge","score":0.8513370752334595},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6225106716156006},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5699772238731384},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.5283573269844055},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5192390084266663},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3366495966911316},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28010109066963196},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14774984121322632},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12909919023513794},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08485046029090881}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9027743935585022},{"id":"https://openalex.org/C2780657338","wikidata":"https://www.wikidata.org/wiki/Q191134","display_name":"Centrifuge","level":2,"score":0.8513370752334595},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6225106716156006},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5699772238731384},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.5283573269844055},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5192390084266663},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3366495966911316},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28010109066963196},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14774984121322632},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12909919023513794},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08485046029090881},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C185544564","wikidata":"https://www.wikidata.org/wiki/Q81197","display_name":"Nuclear physics","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":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1006863","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006863","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006863&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:31756192","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31756192","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:doaj.org/article:a45dc5c6d5854b179b7341d782e0bba9","is_oa":true,"landing_page_url":"https://doaj.org/article/a45dc5c6d5854b179b7341d782e0bba9","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 15, Iss 11, p e1006863 (2019)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/10819868","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Identification_and_quantitation_of_clinically_relevant_microbes_in_patient_samples_Comparison_of_three_k-mer_based_classifiers_for_speed_accuracy_and_sensitivity/10819868","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:6897419","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6897419","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006863","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006863","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006863&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/G2579644219","display_name":null,"funder_award_id":"NIEHS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5203703131","display_name":null,"funder_award_id":"ES06694","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7412009865","display_name":null,"funder_award_id":"ES06694","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G7609969090","display_name":null,"funder_award_id":"CA23074","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7809553560","display_name":null,"funder_award_id":"Leukemia","funder_id":"https://openalex.org/F4320308295","funder_display_name":"Leukemia and Lymphoma Society"},{"id":"https://openalex.org/G8435383300","display_name":null,"funder_award_id":"CA23074","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8802334385","display_name":null,"funder_award_id":"2097","funder_id":"https://openalex.org/F4320306335","funder_display_name":"Flinn Foundation"}],"funders":[{"id":"https://openalex.org/F4320306335","display_name":"Flinn Foundation","ror":"https://ror.org/058qtek75"},{"id":"https://openalex.org/F4320308295","display_name":"Leukemia and Lymphoma Society","ror":"https://ror.org/04m0xav37"},{"id":"https://openalex.org/F4320309707","display_name":"University of Arizona Cancer Center","ror":"https://ror.org/03m2x1q45"},{"id":"https://openalex.org/F4320310160","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2990771615.pdf","grobid_xml":"https://content.openalex.org/works/W2990771615.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1968634605","https://openalex.org/W1978818199","https://openalex.org/W1988056820","https://openalex.org/W2003347102","https://openalex.org/W2010502385","https://openalex.org/W2058653685","https://openalex.org/W2080450388","https://openalex.org/W2096279745","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2105486091","https://openalex.org/W2106780559","https://openalex.org/W2108234281","https://openalex.org/W2117654562","https://openalex.org/W2122467784","https://openalex.org/W2127750623","https://openalex.org/W2131452956","https://openalex.org/W2133371096","https://openalex.org/W2137662380","https://openalex.org/W2143420371","https://openalex.org/W2144709865","https://openalex.org/W2149527175","https://openalex.org/W2158322625","https://openalex.org/W2159008215","https://openalex.org/W2159954944","https://openalex.org/W2161488606","https://openalex.org/W2164852757","https://openalex.org/W2169643748","https://openalex.org/W2170486072","https://openalex.org/W2170551349","https://openalex.org/W2259815689","https://openalex.org/W2272721999","https://openalex.org/W2336665242","https://openalex.org/W2339602899","https://openalex.org/W2586669928","https://openalex.org/W2592810481","https://openalex.org/W2595100206","https://openalex.org/W2728203316","https://openalex.org/W2756224199","https://openalex.org/W2762071667","https://openalex.org/W2801729932","https://openalex.org/W2886730163","https://openalex.org/W2898474558","https://openalex.org/W2899356484","https://openalex.org/W2907815526","https://openalex.org/W2943113312","https://openalex.org/W2945390479","https://openalex.org/W2947712017","https://openalex.org/W2950150251","https://openalex.org/W2950964375","https://openalex.org/W2951160681","https://openalex.org/W2952152744","https://openalex.org/W2953017819","https://openalex.org/W2956864158","https://openalex.org/W2966125063","https://openalex.org/W4238252746"],"related_works":["https://openalex.org/W2210738511","https://openalex.org/W2487541429","https://openalex.org/W1910109602","https://openalex.org/W2080583581","https://openalex.org/W4297131566","https://openalex.org/W2017364432","https://openalex.org/W2329606903","https://openalex.org/W3156493549","https://openalex.org/W3195915274","https://openalex.org/W3158976456"],"abstract_inverted_index":{"Infections":[0],"are":[1,56],"a":[2,131,184],"serious":[3],"health":[4],"concern":[5],"worldwide,":[6],"particularly":[7],"in":[8,19,126,189],"vulnerable":[9],"populations":[10],"such":[11],"as":[12],"the":[13,28,54,70,109,123],"immunocompromised,":[14],"elderly,":[15],"and":[16,24,58,63,66,73,90,115,153,168,175,219],"young.":[17],"Advances":[18],"metagenomic":[20,44,79,195],"sequencing":[21,196],"availability,":[22],"speed,":[23],"decreased":[25],"cost":[26],"offer":[27],"opportunity":[29],"to":[30,103],"supplement":[31],"or":[32,183],"even":[33],"replace":[34],"culture-based":[35],"identification":[36],"of":[37,53,76,94,113,135,159,164,214],"pathogens":[38,198],"with":[39],"DNA":[40],"sequence-based":[41],"diagnostics.":[42],"Adopting":[43],"analysis":[45,62,158],"for":[46,155],"clinical":[47,185],"use":[48,83],"requires":[49],"that":[50,82,178,206],"all":[51,97],"aspects":[52],"workflow":[55],"optimized":[57],"tested,":[59],"including":[60],"data":[61],"computational":[64,151],"time":[65,154],"resources.":[67],"We":[68],"tested":[69],"accuracy,":[71],"sensitivity,":[72],"resource":[74],"requirements":[75],"three":[77,98,120],"top":[78],"taxonomic":[80],"classifiers":[81,121],"fast":[84],"k-mer":[85],"based":[86],"algorithms:":[87],"Centrifuge,":[88],"CLARK,":[89],"KrakenUniq.":[91],"Binary":[92],"mixtures":[93],"bacteria":[95,174],"showed":[96,170],"reliably":[99],"identified":[100,122,172,197],"organisms":[101,124],"down":[102],"1%":[104],"relative":[105,110],"abundance,":[106],"while":[107],"only":[108,139],"abundance":[111],"estimates":[112],"Centrifuge":[114,140,147,157,171,207],"CLARK":[116],"were":[117,179,209],"accurate.":[118],"All":[119],"present":[125],"their":[127],"default":[128],"databases":[129],"from":[130,162],"mock":[132],"bacterial":[133],"community":[134],"20":[136],"organisms,":[137],"but":[138],"had":[141],"no":[142],"false":[143],"positives.":[144],"In":[145],"addition,":[146],"required":[148],"far":[149],"less":[150],"resources":[152],"analysis.":[156],"metagenomes":[160],"obtained":[161],"samples":[163],"VAP,":[165],"infected":[166],"DFUs,":[167],"FN":[169],"pathogenic":[173],"one":[176],"virus":[177],"corroborated":[180],"by":[181,212],"culture":[182],"PCR":[186],"assay.":[187],"Importantly,":[188],"both":[190],"diabetic":[191],"foot":[192],"ulcer":[193],"patients,":[194],"4-6":[199],"weeks":[200],"before":[201],"culture.":[202],"Finally,":[203],"we":[204],"show":[205],"results":[208],"minimally":[210],"affected":[211],"elimination":[213],"time-consuming":[215],"read":[216],"quality":[217],"control":[218],"host":[220],"screening":[221],"steps.":[222]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}