{"id":"https://openalex.org/W3087723605","doi":"https://doi.org/10.1109/tcbb.2021.3100893","title":"Identification of Functional Microbial Modules Through Network-Based Analysis of Meta-Microbial Features Using Matrix Factorization","display_name":"Identification of Functional Microbial Modules Through Network-Based Analysis of Meta-Microbial Features Using Matrix Factorization","publication_year":2021,"publication_date":"2021-07-30","ids":{"openalex":"https://openalex.org/W3087723605","doi":"https://doi.org/10.1109/tcbb.2021.3100893","mag":"3087723605","pmid":"https://pubmed.ncbi.nlm.nih.gov/34329170"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3100893","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3100893","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010476074","display_name":"Young\u2010Joon Ko","orcid":"https://orcid.org/0000-0002-2386-6355"},"institutions":[{"id":"https://openalex.org/I141371507","display_name":"Soongsil University","ror":"https://ror.org/017xnm587","country_code":"KR","type":"education","lineage":["https://openalex.org/I141371507"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Young-Joon Ko","raw_affiliation_strings":["Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea","Department of Bioinformatics and Life Science, Soongsil University, Seoul, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0002-2386-6355","affiliations":[{"raw_affiliation_string":"Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea","institution_ids":[]},{"raw_affiliation_string":"Department of Bioinformatics and Life Science, Soongsil University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I141371507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100780589","display_name":"Sangsoo Kim","orcid":"https://orcid.org/0000-0001-9836-9823"},"institutions":[{"id":"https://openalex.org/I141371507","display_name":"Soongsil University","ror":"https://ror.org/017xnm587","country_code":"KR","type":"education","lineage":["https://openalex.org/I141371507"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Sangsoo Kim","raw_affiliation_strings":["Department of Bioinformatics and Life Science, Soongsil University, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Life Science, Soongsil University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I141371507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088665841","display_name":"Cheol\u2010Ho Pan","orcid":"https://orcid.org/0000-0002-0322-8030"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cheol-Ho Pan","raw_affiliation_strings":["Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006597552","display_name":"Keunwan Park","orcid":"https://orcid.org/0000-0002-8783-9495"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Keunwan Park","raw_affiliation_strings":["Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0002-8783-9495","affiliations":[{"raw_affiliation_string":"Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2221,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.46765451,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"19","issue":"5","first_page":"2851","last_page":"2862"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.998199999332428,"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":0.998199999332428,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9980999827384949,"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":0.9812999963760376,"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/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.7534406185150146},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.7504793405532837},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5851706266403198},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5630279183387756},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5398966073989868},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5015952587127686},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.47204291820526123},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.4587569236755371},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.42888569831848145},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39395707845687866},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37884658575057983},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30335116386413574},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21813443303108215},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.17685773968696594},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10167285799980164},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09424498677253723}],"concepts":[{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.7534406185150146},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.7504793405532837},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5851706266403198},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5630279183387756},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5398966073989868},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5015952587127686},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.47204291820526123},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.4587569236755371},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.42888569831848145},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39395707845687866},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37884658575057983},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30335116386413574},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21813443303108215},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.17685773968696594},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10167285799980164},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09424498677253723},{"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/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2021.3100893","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3100893","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34329170","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34329170","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","score":0.7300000190734863,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G7664825163","display_name":null,"funder_award_id":"NRF-2016M3A9D3915857","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1484745993","https://openalex.org/W1864161604","https://openalex.org/W1902027874","https://openalex.org/W1903888485","https://openalex.org/W1934236512","https://openalex.org/W1966623514","https://openalex.org/W1971061059","https://openalex.org/W2018672567","https://openalex.org/W2025589766","https://openalex.org/W2026006003","https://openalex.org/W2028157318","https://openalex.org/W2029082728","https://openalex.org/W2032112360","https://openalex.org/W2057411492","https://openalex.org/W2058362335","https://openalex.org/W2059745395","https://openalex.org/W2079698171","https://openalex.org/W2085056743","https://openalex.org/W2085818382","https://openalex.org/W2093250796","https://openalex.org/W2104890139","https://openalex.org/W2113787438","https://openalex.org/W2113977541","https://openalex.org/W2121417797","https://openalex.org/W2123072153","https://openalex.org/W2134928825","https://openalex.org/W2136787567","https://openalex.org/W2136850043","https://openalex.org/W2141225828","https://openalex.org/W2144656637","https://openalex.org/W2146913572","https://openalex.org/W2151277589","https://openalex.org/W2152320972","https://openalex.org/W2156130706","https://openalex.org/W2159675211","https://openalex.org/W2171571559","https://openalex.org/W2179438025","https://openalex.org/W2235417813","https://openalex.org/W2256476336","https://openalex.org/W2273054668","https://openalex.org/W2325084313","https://openalex.org/W2477852950","https://openalex.org/W2513533432","https://openalex.org/W2522581443","https://openalex.org/W2525068948","https://openalex.org/W2551645148","https://openalex.org/W2560134402","https://openalex.org/W2569284525","https://openalex.org/W2743544008","https://openalex.org/W2765314233","https://openalex.org/W2766355490","https://openalex.org/W2766903152","https://openalex.org/W2791768957","https://openalex.org/W2800577687","https://openalex.org/W2804776817","https://openalex.org/W2895270801","https://openalex.org/W2897776677","https://openalex.org/W2901778940","https://openalex.org/W2937419365","https://openalex.org/W2949773212","https://openalex.org/W2951517287","https://openalex.org/W2952335621","https://openalex.org/W2955669984","https://openalex.org/W2969399776","https://openalex.org/W2977433364","https://openalex.org/W2980273606","https://openalex.org/W2984894304","https://openalex.org/W2990100110","https://openalex.org/W2995190362","https://openalex.org/W2995649573","https://openalex.org/W3006717925","https://openalex.org/W3007584245","https://openalex.org/W4242212377"],"related_works":["https://openalex.org/W2127243424","https://openalex.org/W2037504162","https://openalex.org/W2792706544","https://openalex.org/W1568451138","https://openalex.org/W2539013788","https://openalex.org/W2156699640","https://openalex.org/W2045265907","https://openalex.org/W2075222291","https://openalex.org/W2146544734","https://openalex.org/W4287022770"],"abstract_inverted_index":{"As":[0,83],"the":[1,138,159],"microbiome":[2,15,81,89,166,173],"is":[3,12],"composed":[4],"of":[5,8,40,78,85,137],"a":[6,19,25,55,71,128,190],"variety":[7],"microbial":[9,20,47,130,145,178,191],"interactions,":[10],"it":[11],"imperative":[13],"in":[14],"research":[16],"to":[17,35,63,98,113,149,163],"identify":[18,64,99,114],"sub-community":[21],"that":[22],"collectively":[23],"conducts":[24],"specific":[26,75],"function.":[27],"However,":[28],"current":[29],"methodologies":[30],"have":[31],"been":[32],"highly":[33,115],"limited":[34],"analyzing":[36],"conditional":[37],"abundance":[38],"changes":[39],"individual":[41],"microorganisms":[42],"without":[43],"considering":[44],"group-wise":[45],"collective":[46],"features.":[48],"To":[49],"overcome":[50],"this":[51],"limitation,":[52],"we":[53,126],"developed":[54,169],"network-based":[56],"method":[57,160,170],"using":[58,80],"nonnegative":[59],"matrix":[60],"factorization":[61],"(NMF)":[62],"functional":[65,177],"meta-microbial":[66],"features":[67],"(MMFs)":[68],"that,":[69],"as":[70],"group,":[72],"better":[73],"discriminate":[74],"environmental":[76],"conditions":[77],"samples":[79],"data.":[82,167],"proof":[84],"concept,":[86],"large-scale":[87],"human":[88],"data":[90,174],"collected":[91],"from":[92],"different":[93],"body":[94,100],"sites":[95],"were":[96,155],"used":[97],"site-specific":[101],"MMFs":[102,110,117,123],"by":[103,134,175],"applying":[104],"NMF.":[105],"The":[106,168],"statistical":[107],"test":[108],"for":[109],"led":[111],"us":[112],"discriminative":[116],"on":[118,180],"sample":[119,151,181],"classes,":[120],"called":[121],"synergistic":[122],"(SYMMFs).":[124],"Finally,":[125],"constructed":[127],"SYMMF-based":[129],"interaction":[131],"network":[132],"(SYMMF-net)":[133],"integrating":[135],"all":[136],"SYMMF":[139],"information.":[140],"Network":[141],"analysis":[142],"revealed":[143],"core":[144],"modules":[146,179],"closely":[147],"related":[148],"critical":[150],"properties.":[152],"Similar":[153],"results":[154],"also":[156],"found":[157],"when":[158],"was":[161],"applied":[162],"various":[164],"disease-associated":[165],"interprets":[171],"high-dimensional":[172],"identifying":[176],"properties":[182],"and":[183],"intuitively":[184],"representing":[185],"their":[186],"systematic":[187],"relationships":[188],"via":[189],"network.":[192]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-08-04T08:18:43.703281","created_date":"2025-10-10T00:00:00"}
