{"id":"https://openalex.org/W2173503307","doi":"https://doi.org/10.1371/journal.pcbi.1004573","title":"Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes","display_name":"Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes","publication_year":2015,"publication_date":"2015-11-13","ids":{"openalex":"https://openalex.org/W2173503307","doi":"https://doi.org/10.1371/journal.pcbi.1004573","mag":"2173503307","pmid":"https://pubmed.ncbi.nlm.nih.gov/26565399"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004573","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004573","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004573&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.1004573&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056935885","display_name":"Stephen Nayfach","orcid":"https://orcid.org/0000-0003-4625-4164"},"institutions":[{"id":"https://openalex.org/I1321430492","display_name":"Gladstone Institutes","ror":"https://ror.org/038321296","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321430492"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen Nayfach","raw_affiliation_strings":["Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I1321430492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062044906","display_name":"Patrick H. Bradley","orcid":"https://orcid.org/0000-0002-9231-8344"},"institutions":[{"id":"https://openalex.org/I1321430492","display_name":"Gladstone Institutes","ror":"https://ror.org/038321296","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321430492"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick H. Bradley","raw_affiliation_strings":["Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I1321430492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034519888","display_name":"Stacia K. Wyman","orcid":"https://orcid.org/0000-0002-8937-8397"},"institutions":[{"id":"https://openalex.org/I1321430492","display_name":"Gladstone Institutes","ror":"https://ror.org/038321296","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321430492"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stacia K. Wyman","raw_affiliation_strings":["Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I1321430492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103430755","display_name":"Timothy Laurent","orcid":null},"institutions":[{"id":"https://openalex.org/I1321430492","display_name":"Gladstone Institutes","ror":"https://ror.org/038321296","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321430492"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy J. Laurent","raw_affiliation_strings":["Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I1321430492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102503389","display_name":"Alex Williams","orcid":null},"institutions":[{"id":"https://openalex.org/I1321430492","display_name":"Gladstone Institutes","ror":"https://ror.org/038321296","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321430492"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex Williams","raw_affiliation_strings":["Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I1321430492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059066311","display_name":"Jonathan A. Eisen","orcid":"https://orcid.org/0000-0002-0159-2197"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan A. Eisen","raw_affiliation_strings":["Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, UC Davis Genome Center, University of California, Davis, Davis, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, UC Davis Genome Center, University of California, Davis, Davis, California, United States of America","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005062415","display_name":"Katherine S. Pollard","orcid":"https://orcid.org/0000-0002-9870-6196"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I1321430492","display_name":"Gladstone Institutes","ror":"https://ror.org/038321296","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321430492"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Katherine S. Pollard","raw_affiliation_strings":["Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America","Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I1321430492"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076795528","display_name":"Thomas J. Sharpton","orcid":"https://orcid.org/0000-0002-5996-7764"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]},{"id":"https://openalex.org/I1321430492","display_name":"Gladstone Institutes","ror":"https://ror.org/038321296","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321430492"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Thomas J. Sharpton","raw_affiliation_strings":["Department of Microbiology, Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America","Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America","institution_ids":["https://openalex.org/I131249849"]},{"raw_affiliation_string":"Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I1321430492"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5005062415","https://openalex.org/A5076795528"],"corresponding_institution_ids":["https://openalex.org/I131249849","https://openalex.org/I1321430492","https://openalex.org/I180670191"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.8672,"has_fulltext":true,"cited_by_count":66,"citation_normalized_percentile":{"value":0.912836,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"11","issue":"11","first_page":"e1004573","last_page":"e1004573"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9836999773979187,"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":0.9726999998092651,"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/metagenomics","display_name":"Metagenomics","score":0.899695634841919},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7714946269989014},{"id":"https://openalex.org/keywords/shotgun","display_name":"Shotgun","score":0.7033708095550537},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.6719189286231995},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6400891542434692},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.5943312644958496},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5800802707672119},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.4264209568500519},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4226107597351074},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.37145835161209106},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3388059139251709},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.3132082223892212},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2666279673576355},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23667198419570923}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.899695634841919},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7714946269989014},{"id":"https://openalex.org/C2781434637","wikidata":"https://www.wikidata.org/wiki/Q486396","display_name":"Shotgun","level":3,"score":0.7033708095550537},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.6719189286231995},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6400891542434692},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.5943312644958496},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5800802707672119},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.4264209568500519},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4226107597351074},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37145835161209106},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3388059139251709},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3132082223892212},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2666279673576355},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23667198419570923},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D003424","descriptor_name":"Crohn Disease","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D003424","descriptor_name":"Crohn Disease","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D003424","descriptor_name":"Crohn Disease","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005819","descriptor_name":"Genetic Markers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005819","descriptor_name":"Genetic Markers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005819","descriptor_name":"Genetic Markers","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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.1004573","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004573","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004573&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:26565399","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26565399","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:ark:/13030/qt34k164bz","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:bad24c999a3b4c6f9ba4015f1ddb5e8d","is_oa":true,"landing_page_url":"https://doaj.org/article/bad24c999a3b4c6f9ba4015f1ddb5e8d","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 11, Iss 11, p e1004573 (2015)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt34k164bz","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/34k164bz","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS computational biology, vol 11, iss 11","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3621475","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4643905","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/1602281","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Automated_and_Accurate_Estimation_of_Gene_Family_Abundance_from_Shotgun_Metagenomes_/1602281","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:qt34k164bz","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/34k164bz","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nayfach, S; Bradley, PH; Wyman, SK; Laurent, TJ; Williams, A; Eisen, JA; \u00c2\u00a0et al.(2015). Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PLoS Computational Biology, 11(11). doi: 10.1371/journal.pcbi.1004573. UC Davis: Retrieved from: http://www.escholarship.org/uc/item/34k164bz","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004573","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004573","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004573&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":[{"display_name":"Life below water","score":0.8600000143051147,"id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G3747166797","display_name":"Exploring the Niche Space of Human Microbiome Functions through Convex Geometry and Evolutionary Genomics","funder_award_id":"1069303","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5533717888","display_name":null,"funder_award_id":"DMS-1069303","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310168","display_name":"Gladstone Institutes","ror":"https://ror.org/038321296"},{"id":"https://openalex.org/F4320311401","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2173503307.pdf","grobid_xml":"https://content.openalex.org/works/W2173503307.grobid-xml"},"referenced_works_count":83,"referenced_works":["https://openalex.org/W1551460710","https://openalex.org/W1841471854","https://openalex.org/W1964895626","https://openalex.org/W1966689073","https://openalex.org/W1970807272","https://openalex.org/W1974102906","https://openalex.org/W1974662412","https://openalex.org/W1975970608","https://openalex.org/W1986090258","https://openalex.org/W1987927808","https://openalex.org/W1989348205","https://openalex.org/W1996423252","https://openalex.org/W1998990856","https://openalex.org/W2000259070","https://openalex.org/W2000589358","https://openalex.org/W2001561488","https://openalex.org/W2001714428","https://openalex.org/W2007715568","https://openalex.org/W2014097763","https://openalex.org/W2015151182","https://openalex.org/W2016098250","https://openalex.org/W2020809151","https://openalex.org/W2022655651","https://openalex.org/W2025653612","https://openalex.org/W2030421888","https://openalex.org/W2031893281","https://openalex.org/W2034873817","https://openalex.org/W2036682827","https://openalex.org/W2038036959","https://openalex.org/W2038802458","https://openalex.org/W2041561663","https://openalex.org/W2042507296","https://openalex.org/W2046668733","https://openalex.org/W2047059509","https://openalex.org/W2048673910","https://openalex.org/W2048981133","https://openalex.org/W2055043387","https://openalex.org/W2057759034","https://openalex.org/W2058947330","https://openalex.org/W2062602663","https://openalex.org/W2062835892","https://openalex.org/W2067773009","https://openalex.org/W2069689025","https://openalex.org/W2075536793","https://openalex.org/W2085284704","https://openalex.org/W2087992157","https://openalex.org/W2088192427","https://openalex.org/W2094116491","https://openalex.org/W2095200684","https://openalex.org/W2097804645","https://openalex.org/W2098506435","https://openalex.org/W2100649505","https://openalex.org/W2100947345","https://openalex.org/W2101911260","https://openalex.org/W2113883363","https://openalex.org/W2116439669","https://openalex.org/W2116895571","https://openalex.org/W2120655738","https://openalex.org/W2122089920","https://openalex.org/W2122210493","https://openalex.org/W2123009189","https://openalex.org/W2124715997","https://openalex.org/W2125826054","https://openalex.org/W2128769815","https://openalex.org/W2131415145","https://openalex.org/W2132415967","https://openalex.org/W2135277010","https://openalex.org/W2136231029","https://openalex.org/W2138122982","https://openalex.org/W2141200343","https://openalex.org/W2143777796","https://openalex.org/W2151372451","https://openalex.org/W2155208388","https://openalex.org/W2156145269","https://openalex.org/W2159406441","https://openalex.org/W2165335121","https://openalex.org/W2166727051","https://openalex.org/W2167639526","https://openalex.org/W2168330474","https://openalex.org/W2169230701","https://openalex.org/W2170089054","https://openalex.org/W4238394506","https://openalex.org/W4249805893"],"related_works":["https://openalex.org/W4210312276","https://openalex.org/W3043668926","https://openalex.org/W4389452281","https://openalex.org/W3036436206","https://openalex.org/W3194449900","https://openalex.org/W3111832393","https://openalex.org/W4321764688","https://openalex.org/W4226340145","https://openalex.org/W2769345399","https://openalex.org/W2798082096"],"abstract_inverted_index":{"Shotgun":[0,106],"metagenomic":[1],"DNA":[2],"sequencing":[3],"is":[4,49,112],"a":[5,125,129,164],"widely":[6],"applicable":[7],"tool":[8],"for":[9],"characterizing":[10],"the":[11,35,39,58,61,81,102,105,143],"functions":[12],"that":[13,119,175,208],"are":[14,183],"encoded":[15],"by":[16],"microbial":[17],"communities.":[18],"Several":[19],"bioinformatic":[20],"tools":[21],"can":[22,120],"be":[23,121],"used":[24],"to":[25,31,42,68,72,100,136,160,205],"functionally":[26,184],"annotate":[27],"metagenomes,":[28],"allowing":[29],"researchers":[30],"draw":[32],"inferences":[33],"about":[34,51],"functional":[36,45,151],"potential":[37],"of":[38,60,80,104,145,168,201,214],"community":[40],"and":[41,76,87,97,149],"identify":[43,91],"putative":[44,212],"biomarkers.":[46],"However,":[47],"little":[48],"known":[50],"how":[52,71,138,146],"decisions":[53],"made":[54],"during":[55],"annotation":[56,74,96,117,140],"affect":[57],"reliability":[59],"results.":[62],"Here,":[63],"we":[64],"use":[65,98,134],"statistical":[66],"simulations":[67],"rigorously":[69],"assess":[70,137],"optimize":[73],"accuracy":[75],"speed,":[77],"given":[78],"parameters":[79],"input":[82],"data":[83,161],"like":[84],"read":[85],"length":[86],"library":[88],"size.":[89],"We":[90,133,156],"best":[92],"practices":[93],"in":[94],"metagenome":[95,148],"them":[99],"guide":[101],"development":[103],"Metagenome":[107],"Annotation":[108],"Pipeline":[109],"(ShotMAP).":[110],"ShotMAP":[111,135,159],"an":[113],"analytically":[114],"flexible,":[115],"end-to-end":[116],"pipeline":[118],"implemented":[122],"either":[123,191],"on":[124],"local":[126],"computer":[127],"or":[128,195],"cloud":[130],"compute":[131],"cluster.":[132],"different":[139],"databases":[141],"impact":[142],"interpretation":[144],"marine":[147],"metatranscriptome":[150],"capacity":[152],"changes":[153],"across":[154],"seasons.":[155],"also":[157],"apply":[158],"obtained":[162],"from":[163,179,186,190],"clinical":[165],"microbiome":[166],"investigation":[167],"inflammatory":[169],"bowel":[170],"disease.":[171,215],"This":[172],"analysis":[173],"finds":[174],"gut":[176,187],"microbiota":[177,188],"collected":[178,189],"Crohn's":[180],"disease":[181],"patients":[182,194],"distinct":[185],"ulcerative":[192],"colitis":[193],"healthy":[196],"controls,":[197],"with":[198],"differential":[199],"abundance":[200],"metabolic":[202],"pathways":[203],"related":[204],"host-microbiome":[206],"interactions":[207],"may":[209],"serve":[210],"as":[211],"biomarkers":[213]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
