{"id":"https://openalex.org/W2473355215","doi":"https://doi.org/10.1371/journal.pcbi.1004977","title":"Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights","display_name":"Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights","publication_year":2016,"publication_date":"2016-07-11","ids":{"openalex":"https://openalex.org/W2473355215","doi":"https://doi.org/10.1371/journal.pcbi.1004977","mag":"2473355215","pmid":"https://pubmed.ncbi.nlm.nih.gov/27400279"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004977","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004977","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004977&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.1004977&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075665406","display_name":"Edoardo Pasolli","orcid":"https://orcid.org/0000-0003-0799-3490"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Edoardo Pasolli","raw_affiliation_strings":["Centre for Integrative Biology, University of Trento, Trento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Integrative Biology, University of Trento, Trento, Italy","institution_ids":["https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019607564","display_name":"Duy Tin Truong","orcid":"https://orcid.org/0000-0002-4169-7727"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Duy Tin Truong","raw_affiliation_strings":["Centre for Integrative Biology, University of Trento, Trento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Integrative Biology, University of Trento, Trento, Italy","institution_ids":["https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045473392","display_name":"Faizan Malik","orcid":"https://orcid.org/0000-0001-8597-5074"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Faizan Malik","raw_affiliation_strings":["Graduate School of Public Health and Health Policy, City University of New York, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Public Health and Health Policy, City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052283192","display_name":"Levi Waldron","orcid":"https://orcid.org/0000-0003-2725-0694"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Levi Waldron","raw_affiliation_strings":["Graduate School of Public Health and Health Policy, City University of New York, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Public Health and Health Policy, City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I174216632"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068576885","display_name":"Nicola Segata","orcid":"https://orcid.org/0000-0002-1583-5794"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Nicola Segata","raw_affiliation_strings":["Centre for Integrative Biology, University of Trento, Trento, Italy"],"raw_orcid":"https://orcid.org/0000-0002-1583-5794","affiliations":[{"raw_affiliation_string":"Centre for Integrative Biology, University of Trento, Trento, Italy","institution_ids":["https://openalex.org/I193223587"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5068576885"],"corresponding_institution_ids":["https://openalex.org/I193223587"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":20.8942,"has_fulltext":true,"cited_by_count":672,"citation_normalized_percentile":{"value":0.99590441,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"12","issue":"7","first_page":"e1004977","last_page":"e1004977"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9995999932289124,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9995999932289124,"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/T10066","display_name":"Gut microbiota and health","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/T10885","display_name":"Gene expression and cancer classification","score":0.9757000207901001,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.8718887567520142},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5058709979057312},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4439542293548584},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.425202876329422},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33982914686203003},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3270752429962158},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32506197690963745},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32420071959495544}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8718887567520142},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5058709979057312},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4439542293548584},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.425202876329422},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33982914686203003},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3270752429962158},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32506197690963745},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32420071959495544},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D009765","descriptor_name":"Obesity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009765","descriptor_name":"Obesity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009765","descriptor_name":"Obesity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015212","descriptor_name":"Inflammatory Bowel Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015212","descriptor_name":"Inflammatory Bowel Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015212","descriptor_name":"Inflammatory Bowel Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1004977","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004977","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004977&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:27400279","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27400279","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:RePEc:plo:pcbi00:1004977","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004977","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:878ed84a65bf4861b0625ddaba2cc5e9","is_oa":false,"landing_page_url":"https://doaj.org/article/878ed84a65bf4861b0625ddaba2cc5e9","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 12, Iss 7, p e1004977 (2016)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/3902712","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Machine_Learning_Meta-analysis_of_Large_Metagenomic_Datasets_Tools_and_Biological_Insights/3902712","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:iris.unitn.it:11572/147871","is_oa":true,"landing_page_url":"http://hdl.handle.net/11572/147871","pdf_url":null,"source":{"id":"https://openalex.org/S4306401913","display_name":"Institutional Research Information System (Universit\u00e0 degli Studi di Trento)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193223587","host_organization_name":"University of Trento","host_organization_lineage":["https://openalex.org/I193223587"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4939962","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4939962","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004977","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004977","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004977&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":[{"score":0.4300000071525574,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1208640691","display_name":null,"funder_award_id":"2013.0239","funder_id":"https://openalex.org/F4320325935","funder_display_name":"Fondazione Cassa Di Risparmio Di Trento E Rovereto"},{"id":"https://openalex.org/G1863591755","display_name":null,"funder_award_id":"CNS-0855217","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2351007112","display_name":null,"funder_award_id":"CNS-958379","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2408204019","display_name":null,"funder_award_id":"1R21AI121784-01","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3809907919","display_name":null,"funder_award_id":"FIR RBFR13EWWI","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G4854971850","display_name":null,"funder_award_id":"1126113","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5008888910","display_name":null,"funder_award_id":"RBFR13EWWI","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G796344792","display_name":null,"funder_award_id":"Rif.Int.2013.0239","funder_id":"https://openalex.org/F4320325935","funder_display_name":"Fondazione Cassa Di Risparmio Di Trento E Rovereto"},{"id":"https://openalex.org/G8181399231","display_name":null,"funder_award_id":"ACI-1126113","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8722295751","display_name":"Computational shotgun metagenomics to detail mother-to-infant vertical microbiome transmission and microbiome-pathogen interaction in Cystic Fibrosis","funder_award_id":"618833","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8724749099","display_name":"II-EN: City University of New York - Computing Research Infrastructure","funder_award_id":"0855217","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/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320325935","display_name":"Fondazione Cassa Di Risparmio Di Trento E Rovereto","ror":"https://ror.org/02pgnjz11"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2473355215.pdf","grobid_xml":"https://content.openalex.org/works/W2473355215.grobid-xml"},"referenced_works_count":75,"referenced_works":["https://openalex.org/W34176136","https://openalex.org/W1480376833","https://openalex.org/W1510526001","https://openalex.org/W1618905105","https://openalex.org/W1679625911","https://openalex.org/W1703384511","https://openalex.org/W1860189396","https://openalex.org/W1964027278","https://openalex.org/W1971415551","https://openalex.org/W1995393174","https://openalex.org/W2002011878","https://openalex.org/W2004549986","https://openalex.org/W2004690636","https://openalex.org/W2023615726","https://openalex.org/W2027951608","https://openalex.org/W2028582941","https://openalex.org/W2031893281","https://openalex.org/W2032230795","https://openalex.org/W2033002674","https://openalex.org/W2038802458","https://openalex.org/W2045449780","https://openalex.org/W2051322058","https://openalex.org/W2071841602","https://openalex.org/W2073332363","https://openalex.org/W2081319466","https://openalex.org/W2085284704","https://openalex.org/W2096561439","https://openalex.org/W2097875133","https://openalex.org/W2100080086","https://openalex.org/W2100616135","https://openalex.org/W2101120467","https://openalex.org/W2101234009","https://openalex.org/W2103568877","https://openalex.org/W2104422209","https://openalex.org/W2108728387","https://openalex.org/W2115057945","https://openalex.org/W2115358726","https://openalex.org/W2119821739","https://openalex.org/W2122825543","https://openalex.org/W2124201592","https://openalex.org/W2124776405","https://openalex.org/W2124927293","https://openalex.org/W2125826054","https://openalex.org/W2127807352","https://openalex.org/W2128769815","https://openalex.org/W2130725058","https://openalex.org/W2131026689","https://openalex.org/W2133856765","https://openalex.org/W2134809046","https://openalex.org/W2135046866","https://openalex.org/W2136609875","https://openalex.org/W2146281049","https://openalex.org/W2147637673","https://openalex.org/W2148603752","https://openalex.org/W2153201655","https://openalex.org/W2156145269","https://openalex.org/W2157159562","https://openalex.org/W2159175617","https://openalex.org/W2166183437","https://openalex.org/W2170245265","https://openalex.org/W2170951896","https://openalex.org/W2188930066","https://openalex.org/W2194591433","https://openalex.org/W2307206101","https://openalex.org/W2319405466","https://openalex.org/W2328023807","https://openalex.org/W2414212485","https://openalex.org/W2911964244","https://openalex.org/W2925318921","https://openalex.org/W3085162807","https://openalex.org/W4206713405","https://openalex.org/W4239510810","https://openalex.org/W6675354045","https://openalex.org/W6678851513","https://openalex.org/W6687492581"],"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/W3195915274","https://openalex.org/W4285082713","https://openalex.org/W2344981695"],"abstract_inverted_index":{"Shotgun":[0],"metagenomic":[1,133],"analysis":[2],"of":[3,12,23,32,66,86,89,111,129,154,158,184,211,226,250],"the":[4,21,30,62,87,182,212,227],"human":[5,24],"associated":[6],"microbiome":[7,103,213,229,244],"provides":[8],"a":[9,95,127,218,233],"rich":[10],"set":[11],"microbial":[13,35,199,239],"features":[14,36,225],"for":[15,44,83,98,248],"prediction":[16,80,99,196],"and":[17,26,40,64,82,109,152,246],"biomarker":[18],"discovery":[19],"in":[20,56,126,146,170,223],"context":[22],"diseases":[25],"health":[27],"conditions.":[28],"However,":[29],"use":[31,153],"such":[33],"high-resolution":[34],"presents":[37],"new":[38],"challenges,":[39],"validated":[41,55],"computational":[42,96],"tools":[43],"learning":[45],"tasks":[46,81,100],"are":[47,252],"lacking.":[48],"Moreover,":[49],"classification":[50],"rules":[51],"have":[52],"scarcely":[53],"been":[54],"independent":[57],"studies,":[58],"posing":[59],"questions":[60],"about":[61],"generality":[63],"generalization":[65,121],"disease-predictive":[67],"models":[68,165,176],"across":[69,122],"cohorts.":[70],"In":[71,162],"this":[72],"paper,":[73],"we":[74],"comprehensively":[75],"assess":[76],"approaches":[77],"to":[78,191,206],"metagenomics-based":[79],"quantitative":[84,102],"assessment":[85],"strength":[88],"potential":[90],"microbiome-phenotype":[91],"associations.":[92],"We":[93],"develop":[94],"framework":[97],"using":[101],"profiles,":[104,245],"including":[105],"species-level":[106,159],"relative":[107],"abundances":[108],"presence":[110],"strain-specific":[112,155],"markers.":[113],"A":[114],"comprehensive":[115],"meta-analysis,":[116],"with":[117,217],"particular":[118],"emphasis":[119],"on":[120],"cohorts,":[123],"was":[124],"performed":[125],"collection":[128],"2424":[130],"publicly":[131,253],"available":[132,254],"samples":[134,187,251],"from":[135,188],"eight":[136],"large-scale":[137],"studies.":[138],"Cross-validation":[139],"revealed":[140],"good":[141],"disease-prediction":[142],"capabilities,":[143],"which":[144],"were":[145,169],"general":[147,208,238],"improved":[148,194],"by":[149,178],"feature":[150],"selection":[151],"markers":[156],"instead":[157],"taxonomic":[160],"abundance.":[161],"cross-study":[163],"analysis,":[164],"transferred":[166],"between":[167],"studies":[168,190],"some":[171],"cases":[172],"less":[173],"accurate":[174],"than":[175,215],"tested":[177],"within-study":[179],"cross-validation.":[180],"Interestingly,":[181],"addition":[183],"healthy":[185],"(control)":[186],"other":[189],"training":[192],"sets":[193],"disease":[195],"capabilities.":[197],"Some":[198],"species":[200],"(most":[201],"notably":[202],"Streptococcus":[203],"anginosus)":[204],"seem":[205],"characterize":[207],"dysbiotic":[209],"states":[210],"rather":[214],"connections":[216],"specific":[219],"disease.":[220],"Our":[221],"results":[222],"modelling":[224],"\"healthy\"":[228],"can":[230],"be":[231],"considered":[232],"first":[234],"step":[235],"toward":[236],"defining":[237],"dysbiosis.":[240],"The":[241],"software":[242],"framework,":[243],"metadata":[247],"thousands":[249],"at":[255],"http://segatalab.cibio.unitn.it/tools/metaml.":[256]},"counts_by_year":[{"year":2026,"cited_by_count":34},{"year":2025,"cited_by_count":68},{"year":2024,"cited_by_count":91},{"year":2023,"cited_by_count":78},{"year":2022,"cited_by_count":93},{"year":2021,"cited_by_count":93},{"year":2020,"cited_by_count":95},{"year":2019,"cited_by_count":47},{"year":2018,"cited_by_count":42},{"year":2017,"cited_by_count":29},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-17T08:01:34.144755","created_date":"2025-10-10T00:00:00"}
