{"id":"https://openalex.org/W2135515858","doi":"https://doi.org/10.1093/bioinformatics/btt389","title":"Scalable metagenomic taxonomy classification using a reference genome database","display_name":"Scalable metagenomic taxonomy classification using a reference genome database","publication_year":2013,"publication_date":"2013-07-04","ids":{"openalex":"https://openalex.org/W2135515858","doi":"https://doi.org/10.1093/bioinformatics/btt389","mag":"2135515858","pmid":"https://pubmed.ncbi.nlm.nih.gov/23828782"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt389","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt389","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/18/2253/17128159/btt389.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/18/2253/17128159/btt389.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034847086","display_name":"Sasha Ames","orcid":"https://orcid.org/0000-0001-9981-2997"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sasha K. Ames","raw_affiliation_strings":["1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078876685","display_name":"David Hysom","orcid":null},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David A. Hysom","raw_affiliation_strings":["1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112156788","display_name":"Shea N. Gardner","orcid":null},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shea N. Gardner","raw_affiliation_strings":["1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108696851","display_name":"Greg Lloyd","orcid":null},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G. Scott Lloyd","raw_affiliation_strings":["1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043476271","display_name":"Maya Gokhale","orcid":"https://orcid.org/0000-0003-4229-5735"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maya B. Gokhale","raw_affiliation_strings":["1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035849909","display_name":"Jonathan Allen","orcid":"https://orcid.org/0000-0002-4359-8263"},"institutions":[{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan E. Allen","raw_affiliation_strings":["1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Applied Scientific Computing, 2Lawrence Livermore National Laboratory and 3Global Security Directorate, P. O. Box 808, Livermore, CA 94551, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5034847086"],"corresponding_institution_ids":["https://openalex.org/I1282311441","https://openalex.org/I4210138311"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":8.2261,"has_fulltext":true,"cited_by_count":219,"citation_normalized_percentile":{"value":0.98330681,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"29","issue":"18","first_page":"2253","last_page":"2260"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8582000136375427,"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":0.8582000136375427,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.06430000066757202,"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"}},{"id":"https://openalex.org/T13220","display_name":"Plant and Fungal Interactions Research","score":0.009100000374019146,"subfield":{"id":"https://openalex.org/subfields/1310","display_name":"Endocrinology"},"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/metagenomics","display_name":"Metagenomics","score":0.9306071996688843},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7235405445098877},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6876986026763916},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.573085606098175},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5079801678657532},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4049171209335327},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4039456844329834},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38908058404922485},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28233611583709717},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.258463978767395},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0756615698337555},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07231685519218445}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9306071996688843},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7235405445098877},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6876986026763916},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.573085606098175},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5079801678657532},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4049171209335327},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4039456844329834},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38908058404922485},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28233611583709717},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.258463978767395},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0756615698337555},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07231685519218445},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":"D002965","descriptor_name":"Classification","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","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":"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":6,"locations":[{"id":"doi:10.1093/bioinformatics/btt389","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt389","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/18/2253/17128159/btt389.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23828782","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23828782","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:2745040","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3753567","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:osti.gov:1625283","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1625283","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:osti.gov:1860775","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1860775","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3753567","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3753567","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt389","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt389","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/18/2253/17128159/btt389.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4343739756","display_name":null,"funder_award_id":"Contract DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G574795485","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5816449448","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G69709960","display_name":null,"funder_award_id":"Contract DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8374966015","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G991281326","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320338286","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135515858.pdf","grobid_xml":"https://content.openalex.org/works/W2135515858.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1969882260","https://openalex.org/W1972166243","https://openalex.org/W1997512351","https://openalex.org/W2000589358","https://openalex.org/W2032107956","https://openalex.org/W2040486579","https://openalex.org/W2042056700","https://openalex.org/W2048818637","https://openalex.org/W2053462745","https://openalex.org/W2085631282","https://openalex.org/W2090819968","https://openalex.org/W2095841885","https://openalex.org/W2113256118","https://openalex.org/W2113601822","https://openalex.org/W2116895571","https://openalex.org/W2124985265","https://openalex.org/W2131026689","https://openalex.org/W2134751812","https://openalex.org/W2144550002","https://openalex.org/W2148181108","https://openalex.org/W2160945762","https://openalex.org/W2162210683","https://openalex.org/W2163830511","https://openalex.org/W4233928114"],"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/W3198631238","https://openalex.org/W4388282505","https://openalex.org/W3151146928"],"abstract_inverted_index":{"MOTIVATION:":[0],"Deep":[1],"metagenomic":[2,28,40,74,136],"sequencing":[3],"of":[4,24,92,106,138],"biological":[5,18],"samples":[6,19,96],"has":[7],"the":[8,90,107,135,139],"potential":[9],"to":[10,37,58,62,85,117],"recover":[11],"otherwise":[12],"difficult-to-detect":[13],"microorganisms":[14],"and":[15,42,82,102,130,147],"accurately":[16],"characterize":[17],"with":[20,46],"limited":[21],"prior":[22],"knowledge":[23],"sample":[25],"contents.":[26],"Existing":[27],"taxonomic":[29],"classification":[30,44,88,105],"algorithms,":[31],"however,":[32],"do":[33],"not":[34],"scale":[35],"well":[36],"analyze":[38],"large":[39,127],"datasets,":[41],"balancing":[43],"accuracy":[45],"computational":[47,60],"efficiency":[48],"presents":[49],"a":[50,68,122],"fundamental":[51],"challenge.":[52],"RESULTS:":[53],"A":[54],"method":[55],"is":[56,78,148],"presented":[57],"shift":[59],"costs":[61],"an":[63],"off-line":[64],"computation":[65],"by":[66],"creating":[67],"taxonomy/genome":[69],"index":[70],"that":[71,97],"supports":[72],"scalable":[73],"classification.":[75],"Scalable":[76],"performance":[77],"demonstrated":[79],"on":[80,95,121,134],"real":[81],"simulated":[83],"data":[84,158],"show":[86],"accurate":[87],"in":[89,145],"presence":[91],"novel":[93],"organisms":[94],"include":[98],"viruses,":[99],"prokaryotes,":[100],"fungi":[101],"protists.":[103],"Taxonomic":[104],"previously":[108],"published":[109],"150":[110],"giga-base":[111],"Tyrolean":[112],"Iceman":[113],"dataset":[114],"was":[115,143],"found":[116],"take":[118],"<20":[119],"h":[120],"single":[123],"node":[124],"40":[125],"core":[126],"memory":[128],"machine":[129],"provide":[131],"new":[132],"insights":[133],"contents":[137],"sample.":[140],"AVAILABILITY:":[141],"Software":[142],"implemented":[144],"C++":[146],"freely":[149],"available":[150,160],"at":[151,161],"http://sourceforge.net/projects/lmat":[152],"CONTACT:":[153],"allen99@llnl.gov":[154],"SUPPLEMENTARY":[155],"INFORMATION:":[156],"Supplementary":[157],"are":[159],"Bioinformatics":[162],"online.":[163]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":24},{"year":2020,"cited_by_count":22},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":24},{"year":2017,"cited_by_count":29},{"year":2016,"cited_by_count":25},{"year":2015,"cited_by_count":18},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-18T08:16:58.900851","created_date":"2025-10-10T00:00:00"}
