{"id":"https://openalex.org/W2567082498","doi":"https://doi.org/10.1371/journal.pcbi.1005252","title":"Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota","display_name":"Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota","publication_year":2016,"publication_date":"2016-12-16","ids":{"openalex":"https://openalex.org/W2567082498","doi":"https://doi.org/10.1371/journal.pcbi.1005252","mag":"2567082498","pmid":"https://pubmed.ncbi.nlm.nih.gov/27984592"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005252","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005252","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005252&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.1005252&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068581426","display_name":"S\u00e9bastien Raguideau","orcid":"https://orcid.org/0000-0001-8727-2604"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I3017594750","display_name":"Microbiologie de l\u2019alimentation au service de la sant\u00e9","ror":"https://ror.org/0471cyx86","country_code":"FR","type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I3017594750","https://openalex.org/I4210088668","https://openalex.org/I4210099460"]},{"id":"https://openalex.org/I22248866","display_name":"AgroParisTech","ror":"https://ror.org/02kbmgc12","country_code":"FR","type":"education","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210099460","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"S\u00e9bastien Raguideau","raw_affiliation_strings":["Institut Micalis, INRA, AgroParisTech, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","MaIAGE, INRA, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","MICALIS - MICrobiologie de l'ALImentation au Service de la Sant\u00e9 (F-78350 JOUY-EN-JOSAS - France)"],"affiliations":[{"raw_affiliation_string":"Institut Micalis, INRA, AgroParisTech, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I3017594750","https://openalex.org/I22248866","https://openalex.org/I277688954"]},{"raw_affiliation_string":"MaIAGE, INRA, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481","https://openalex.org/I277688954"]},{"raw_affiliation_string":"MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"MICALIS - MICrobiologie de l'ALImentation au Service de la Sant\u00e9 (F-78350 JOUY-EN-JOSAS - France)","institution_ids":["https://openalex.org/I3017594750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059378069","display_name":"Sandra Plancade","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210099460","https://openalex.org/I4210159481"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sandra Plancade","raw_affiliation_strings":["MaIAGE, INRA, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)"],"affiliations":[{"raw_affiliation_string":"MaIAGE, INRA, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481","https://openalex.org/I277688954"]},{"raw_affiliation_string":"MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","institution_ids":["https://openalex.org/I4210159481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079424364","display_name":"Nicolas Pons","orcid":"https://orcid.org/0000-0003-1926-8077"},"institutions":[{"id":"https://openalex.org/I4210139571","display_name":"Laboratoire d'Analyses G\u00e9n\u00e9tiques pour les Esp\u00e8ces Animales","ror":"https://ror.org/03t2hta05","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210139571"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Nicolas Pons","raw_affiliation_strings":["MGP, INRA, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","MetaGenoPolis ( Centre de recherche - 78352 Jouy-en-Josas - France)"],"affiliations":[{"raw_affiliation_string":"MGP, INRA, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","institution_ids":[]},{"raw_affiliation_string":"MetaGenoPolis ( Centre de recherche - 78352 Jouy-en-Josas - France)","institution_ids":["https://openalex.org/I4210139571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022945722","display_name":"Marion Leclerc","orcid":"https://orcid.org/0000-0001-8684-2847"},"institutions":[{"id":"https://openalex.org/I22248866","display_name":"AgroParisTech","ror":"https://ror.org/02kbmgc12","country_code":"FR","type":"education","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954"]},{"id":"https://openalex.org/I3017594750","display_name":"Microbiologie de l\u2019alimentation au service de la sant\u00e9","ror":"https://ror.org/0471cyx86","country_code":"FR","type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I3017594750","https://openalex.org/I4210088668","https://openalex.org/I4210099460"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Marion Leclerc","raw_affiliation_strings":["Institut Micalis, INRA, AgroParisTech, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","MICALIS - MICrobiologie de l'ALImentation au Service de la Sant\u00e9 (F-78350 JOUY-EN-JOSAS - France)"],"affiliations":[{"raw_affiliation_string":"Institut Micalis, INRA, AgroParisTech, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I3017594750","https://openalex.org/I22248866","https://openalex.org/I277688954"]},{"raw_affiliation_string":"MICALIS - MICrobiologie de l'ALImentation au Service de la Sant\u00e9 (F-78350 JOUY-EN-JOSAS - France)","institution_ids":["https://openalex.org/I3017594750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073557000","display_name":"B\u00e9atrice Laroche","orcid":"https://orcid.org/0000-0001-7821-332X"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210099460","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"B\u00e9atrice Laroche","raw_affiliation_strings":["MaIAGE, INRA, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)"],"affiliations":[{"raw_affiliation_string":"MaIAGE, INRA, Universit\u00e9 Paris-Saclay, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481","https://openalex.org/I277688954"]},{"raw_affiliation_string":"MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","institution_ids":["https://openalex.org/I4210159481"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5068581426"],"corresponding_institution_ids":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I3017594750","https://openalex.org/I4210159481"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.0169,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.78903923,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"12","issue":"12","first_page":"e1005252","last_page":"e1005252"},"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9901000261306763,"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/T11928","display_name":"Genetic Syndromes and Imprinting","score":0.9453999996185303,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.8561570644378662},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5800842046737671},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.5537477731704712},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5514062643051147},{"id":"https://openalex.org/keywords/community-structure","display_name":"Community structure","score":0.47528377175331116},{"id":"https://openalex.org/keywords/microbial-ecology","display_name":"Microbial ecology","score":0.4678056538105011},{"id":"https://openalex.org/keywords/functional-ecology","display_name":"Functional ecology","score":0.4541941285133362},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.43905436992645264},{"id":"https://openalex.org/keywords/ecosystem","display_name":"Ecosystem","score":0.43673843145370483},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.4289352297782898},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2506569027900696},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21435508131980896}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8561570644378662},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5800842046737671},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.5537477731704712},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5514062643051147},{"id":"https://openalex.org/C133079900","wikidata":"https://www.wikidata.org/wiki/Q5155065","display_name":"Community structure","level":2,"score":0.47528377175331116},{"id":"https://openalex.org/C69562835","wikidata":"https://www.wikidata.org/wiki/Q3054637","display_name":"Microbial ecology","level":3,"score":0.4678056538105011},{"id":"https://openalex.org/C129091987","wikidata":"https://www.wikidata.org/wiki/Q5508816","display_name":"Functional ecology","level":3,"score":0.4541941285133362},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.43905436992645264},{"id":"https://openalex.org/C110872660","wikidata":"https://www.wikidata.org/wiki/Q37813","display_name":"Ecosystem","level":2,"score":0.43673843145370483},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.4289352297782898},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2506569027900696},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21435508131980896},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","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":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004043","descriptor_name":"Dietary Fiber","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004043","descriptor_name":"Dietary Fiber","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004043","descriptor_name":"Dietary Fiber","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004043","descriptor_name":"Dietary Fiber","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1005252","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005252","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005252&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:27984592","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27984592","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:HAL:hal-01454674v1","is_oa":true,"landing_page_url":"https://hal.science/hal-01454674","pdf_url":"https://hal.science/hal-01454674v1/document","source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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, 2016, 12 (12), pp.1:29. &#x27E8;10.1371/journal.pcbi.1005252&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:be6f6f042bb241e9bdb2abd9c908c9ec","is_oa":true,"landing_page_url":"https://doaj.org/article/be6f6f042bb241e9bdb2abd9c908c9ec","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 12, Iss 12, p e1005252 (2016)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/4476959","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Inferring_Aggregated_Functional_Traits_from_Metagenomic_Data_Using_Constrained_Non-negative_Matrix_Factorization_Application_to_Fiber_Degradation_in_the_Human_Gut_Microbiota/4476959","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:5161307","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5161307","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005252","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005252","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005252&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 in Land","score":0.7699999809265137,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2567082498.pdf","grobid_xml":"https://content.openalex.org/works/W2567082498.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W8935401","https://openalex.org/W174157651","https://openalex.org/W1989784325","https://openalex.org/W1991497480","https://openalex.org/W1992715872","https://openalex.org/W2001561488","https://openalex.org/W2004549986","https://openalex.org/W2007651364","https://openalex.org/W2029943794","https://openalex.org/W2031893281","https://openalex.org/W2038802458","https://openalex.org/W2069645361","https://openalex.org/W2071841602","https://openalex.org/W2072974424","https://openalex.org/W2076566842","https://openalex.org/W2076621797","https://openalex.org/W2083501377","https://openalex.org/W2097124003","https://openalex.org/W2097804645","https://openalex.org/W2103539617","https://openalex.org/W2103901746","https://openalex.org/W2108929776","https://openalex.org/W2115057945","https://openalex.org/W2123072153","https://openalex.org/W2124927293","https://openalex.org/W2125826054","https://openalex.org/W2126809954","https://openalex.org/W2128601422","https://openalex.org/W2131415145","https://openalex.org/W2131848047","https://openalex.org/W2136787567","https://openalex.org/W2137853307","https://openalex.org/W2138636857","https://openalex.org/W2147847105","https://openalex.org/W2159482845","https://openalex.org/W2165685007","https://openalex.org/W2168024725","https://openalex.org/W2317724253","https://openalex.org/W3104577407","https://openalex.org/W4230770774","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W4390394189","https://openalex.org/W2037504162","https://openalex.org/W2539013788","https://openalex.org/W2792706544","https://openalex.org/W1568451138","https://openalex.org/W2156699640","https://openalex.org/W2045265907","https://openalex.org/W2972997031","https://openalex.org/W2146544734","https://openalex.org/W2075222291"],"abstract_inverted_index":{"Whole":[0],"Genome":[1],"Shotgun":[2],"(WGS)":[3],"metagenomics":[4],"is":[5,157,186,273],"increasingly":[6],"used":[7,83,228],"to":[8,58,84,109,163,170,247,279],"study":[9,85],"the":[10,20,35,59,74,89,147,184,204,213,223,249,268,284],"structure":[11,135],"and":[12,22,54,92,96,239,275],"functions":[13],"of":[14,25,29,39,45,61,76,112,124,136,206,215,219,231,267],"complex":[15,151],"microbial":[16,32,40,62,142],"ecosystems,":[17],"both":[18],"from":[19,52,69,234],"taxonomic":[21],"functional":[23,37,56,217,259],"point":[24],"view.":[26],"Gene":[27],"inventories":[28],"otherwise":[30],"uncultured":[31],"communities":[33,41],"make":[34],"direct":[36],"profiling":[38],"possible.":[42],"The":[43,155,175],"concept":[44],"community":[46],"aggregated":[47,65,113],"trait":[48],"has":[49],"been":[50],"adapted":[51],"environmental":[53,94],"plant":[55],"ecology":[57],"framework":[60],"ecology.":[63],"Community":[64],"traits":[66,114,218],"are":[67,139],"quantified":[68],"WGS":[70],"data":[71,254],"by":[72,150,188,222],"computing":[73],"abundance":[75],"relevant":[77,173],"marker":[78],"genes.":[79],"They":[80],"can":[81,276],"be":[82,277],"key":[86],"processes":[87,282],"at":[88,146],"ecosystem":[90,97,148],"level":[91,149],"correlate":[93],"factors":[95],"functions.":[98],"In":[99],"this":[100],"paper":[101],"we":[102],"propose":[103],"a":[104,122,133,190,199,263],"novel":[105],"model":[106,123,156],"based":[107],"approach":[108],"infer":[110],"combinations":[111],"characterizing":[115],"specific":[116],"ecosystemic":[117,216],"metabolic":[118,281],"processes.":[119],"We":[120,197,208,227],"formulate":[121],"these":[125],"Combined":[126],"Aggregated":[127],"Functional":[128],"Traits":[129],"(CAFTs)":[130],"accounting":[131],"for":[132,203],"hierarchical":[134],"genes,":[137],"which":[138],"associated":[140],"on":[141,212],"genomes,":[143],"further":[144],"linked":[145],"co-occurrences":[152],"or":[153,286],"interactions.":[154],"completed":[158],"with":[159],"constraints":[160],"specifically":[161],"designed":[162],"exploit":[164],"available":[165],"genomic":[166],"information,":[167],"in":[168,183,283,287],"order":[169],"favor":[171],"biologically":[172,257],"CAFTs.":[174,207],"CAFTs":[176,243],"structure,":[177],"as":[178,180],"well":[179],"their":[181],"intensity":[182],"ecosystem,":[185],"obtained":[187],"solving":[189],"constrained":[191],"Non-negative":[192],"Matrix":[193],"Factorization":[194],"(NMF)":[195],"problem.":[196],"developed":[198],"multicriteria":[200],"selection":[201],"procedure":[202],"number":[205],"illustrated":[209],"our":[210],"method":[211,272],"modelling":[214],"fiber":[220,250],"degradation":[221,251],"human":[224],"gut":[225,285],"microbiota.":[226],"1408":[229],"samples":[230],"gene":[232],"abundances":[233],"several":[235],"high-throughput":[236],"sequencing":[237],"projects":[238],"found":[240],"that":[241],"four":[242],"only":[244],"were":[245],"needed":[246],"represent":[248],"potential.":[252],"This":[253],"reduction":[255],"highlighted":[256],"consistent":[258],"patterns":[260],"while":[261],"providing":[262],"high":[264],"quality":[265],"preservation":[266],"original":[269],"data.":[270],"Our":[271],"generic":[274],"applied":[278],"other":[280,288],"ecosystems.":[289]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":8},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
