{"id":"https://openalex.org/W3163924330","doi":"https://doi.org/10.1371/journal.pcbi.1009021","title":"MiMeNet: Exploring microbiome-metabolome relationships using neural networks","display_name":"MiMeNet: Exploring microbiome-metabolome relationships using neural networks","publication_year":2021,"publication_date":"2021-05-17","ids":{"openalex":"https://openalex.org/W3163924330","doi":"https://doi.org/10.1371/journal.pcbi.1009021","mag":"3163924330","pmid":"https://pubmed.ncbi.nlm.nih.gov/33999922"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009021","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009021","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009021&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.1009021&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076460126","display_name":"Derek Reiman","orcid":"https://orcid.org/0000-0002-7955-3980"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Derek Reiman","raw_affiliation_strings":["Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7955-3980","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I39422238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020254328","display_name":"Brian T. Layden","orcid":"https://orcid.org/0000-0003-2176-5654"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]},{"id":"https://openalex.org/I4210135737","display_name":"Jesse Brown VA Medical Center","ror":"https://ror.org/049qtwc86","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210115976","https://openalex.org/I4210135737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian T. Layden","raw_affiliation_strings":["Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, Illinois, United States of America","Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I39422238"]},{"raw_affiliation_string":"Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I4210135737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025440962","display_name":"Yang Dai","orcid":"https://orcid.org/0000-0002-7638-849X"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yang Dai","raw_affiliation_strings":["Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7638-849X","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I39422238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5025440962"],"corresponding_institution_ids":["https://openalex.org/I39422238"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":4.3685,"has_fulltext":true,"cited_by_count":78,"citation_normalized_percentile":{"value":0.96016798,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"17","issue":"5","first_page":"e1009021","last_page":"e1009021"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9995999932289124,"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":0.9988999962806702,"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/metabolome","display_name":"Metabolome","score":0.9867494106292725},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.8938400149345398},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.8218833208084106},{"id":"https://openalex.org/keywords/metabolite","display_name":"Metabolite","score":0.8114579916000366},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6688084602355957},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6587007641792297},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3706684410572052},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1578715741634369}],"concepts":[{"id":"https://openalex.org/C135870905","wikidata":"https://www.wikidata.org/wiki/Q903667","display_name":"Metabolome","level":3,"score":0.9867494106292725},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.8938400149345398},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.8218833208084106},{"id":"https://openalex.org/C2777477808","wikidata":"https://www.wikidata.org/wiki/Q407595","display_name":"Metabolite","level":2,"score":0.8114579916000366},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6688084602355957},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6587007641792297},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3706684410572052},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1578715741634369}],"mesh":[{"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":"D015212","descriptor_name":"Inflammatory Bowel Diseases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015212","descriptor_name":"Inflammatory Bowel Diseases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015212","descriptor_name":"Inflammatory Bowel Diseases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015212","descriptor_name":"Inflammatory Bowel Diseases","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D015212","descriptor_name":"Inflammatory Bowel Diseases","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D015212","descriptor_name":"Inflammatory Bowel Diseases","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1009021","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009021","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009021&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:33999922","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33999922","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:doaj.org/article:686100387158412f8ba63e45a3c1897e","is_oa":true,"landing_page_url":"https://doaj.org/article/686100387158412f8ba63e45a3c1897e","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":"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 17, Iss 5, p e1009021 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8158931","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8158931","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.1009021","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009021","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009021&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":[],"awards":[{"id":"https://openalex.org/G110457350","display_name":null,"funder_award_id":"P30\u2010DK\u2010020595","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1575963820","display_name":null,"funder_award_id":"R01-Dk104927","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1612467417","display_name":null,"funder_award_id":"I01 BX003382","funder_id":"https://openalex.org/F4320306127","funder_display_name":"U.S. Department of Veterans Affairs"},{"id":"https://openalex.org/G18062229","display_name":null,"funder_award_id":"P30DK020595","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G382530363","display_name":null,"funder_award_id":"R01 DK104927","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"}],"funders":[{"id":"https://openalex.org/F4320306127","display_name":"U.S. Department of Veterans Affairs","ror":"https://ror.org/05rsv9s98"},{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3163924330.pdf","grobid_xml":"https://content.openalex.org/works/W3163924330.grobid-xml"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W1510318546","https://openalex.org/W1548779692","https://openalex.org/W1778175015","https://openalex.org/W1903478710","https://openalex.org/W1921848483","https://openalex.org/W1934481644","https://openalex.org/W1966327575","https://openalex.org/W1979308600","https://openalex.org/W1979966476","https://openalex.org/W1986386190","https://openalex.org/W2009170813","https://openalex.org/W2020398205","https://openalex.org/W2031821244","https://openalex.org/W2060915038","https://openalex.org/W2072875396","https://openalex.org/W2135785255","https://openalex.org/W2143777796","https://openalex.org/W2159675211","https://openalex.org/W2160166285","https://openalex.org/W2164027931","https://openalex.org/W2169053895","https://openalex.org/W2170657181","https://openalex.org/W2175951661","https://openalex.org/W2182088010","https://openalex.org/W2232186956","https://openalex.org/W2284521682","https://openalex.org/W2318393934","https://openalex.org/W2396111360","https://openalex.org/W2404920363","https://openalex.org/W2463312000","https://openalex.org/W2539807368","https://openalex.org/W2549976854","https://openalex.org/W2550084345","https://openalex.org/W2551372307","https://openalex.org/W2597526148","https://openalex.org/W2624871570","https://openalex.org/W2755486443","https://openalex.org/W2770707670","https://openalex.org/W2770933704","https://openalex.org/W2777466035","https://openalex.org/W2782327081","https://openalex.org/W2783006976","https://openalex.org/W2790046972","https://openalex.org/W2804621837","https://openalex.org/W2885492105","https://openalex.org/W2885531798","https://openalex.org/W2893922683","https://openalex.org/W2899158256","https://openalex.org/W2903406988","https://openalex.org/W2909878330","https://openalex.org/W2921335902","https://openalex.org/W2921966151","https://openalex.org/W2923496707","https://openalex.org/W2937419365","https://openalex.org/W2944986981","https://openalex.org/W2954821544","https://openalex.org/W2958564218","https://openalex.org/W2966227815","https://openalex.org/W2977421651","https://openalex.org/W2977433364","https://openalex.org/W2985101369","https://openalex.org/W2987653794","https://openalex.org/W2988641875","https://openalex.org/W3000322545","https://openalex.org/W3011166092","https://openalex.org/W3014126386","https://openalex.org/W3020949534","https://openalex.org/W3023514173","https://openalex.org/W3044813747","https://openalex.org/W6749018555"],"related_works":["https://openalex.org/W1996644818","https://openalex.org/W1965468642","https://openalex.org/W2093500216","https://openalex.org/W2053588008","https://openalex.org/W2916376502","https://openalex.org/W3101161779","https://openalex.org/W423371831","https://openalex.org/W2777729175","https://openalex.org/W2260452057","https://openalex.org/W4295779760"],"abstract_inverted_index":{"The":[0],"advance":[1],"in":[2,19,97,179],"microbiome":[3,190],"and":[4,87,91,110,131,137,191],"metabolome":[5],"studies":[6],"has":[7],"generated":[8],"rich":[9],"omics":[10],"data":[11],"revealing":[12],"the":[13,16,33,98,141,145,174,186,189],"involvement":[14],"of":[15,58,100,144,176,188],"microbial":[17],"community":[18],"host":[20,27],"disease":[21],"pathogenesis":[22],"through":[23,157],"interactions":[24],"with":[25,133],"their":[26],"at":[28,185],"a":[29,47,167],"metabolic":[30,177],"level.":[31],"However,":[32],"computational":[34],"tools":[35],"to":[36,82,85,89,105,108,112,115,139,170],"uncover":[37],"these":[38],"relationships":[39],"are":[40],"just":[41],"emerging.":[42],"Here,":[43],"we":[44,66,124],"present":[45],"MiMeNet,":[46],"neural":[48],"network":[49],"framework":[50],"for":[51,119],"modeling":[52],"microbe-metabolite":[53,146],"relationships.":[54],"Using":[55],"ten":[56],"iterations":[57],"10-fold":[59],"cross-validation":[60],"on":[61,154],"three":[62],"paired":[63],"microbiome-metabolome":[64],"datasets,":[65],"show":[67],"that":[68,126,164],"MiMeNet":[69,127,165],"more":[70,93],"accurately":[71],"predicts":[72],"metabolite":[73,121],"abundances":[74],"(mean":[75],"Spearman":[76],"correlation":[77],"coefficients":[78],"increase":[79],"from":[80,103],"0.108":[81],"0.309,":[83],"0.276":[84],"0.457,":[86],"-0.272":[88],"0.264)":[90],"identifies":[92],"well-predicted":[94,101],"metabolites":[95,102,132,156],"(increase":[96],"number":[99],"198":[104],"366,":[106],"104":[107],"143,":[109],"4":[111],"29)":[113],"compared":[114],"state-of-art":[116],"linear":[117],"models":[118],"individual":[120],"predictions.":[122],"Additionally,":[123],"demonstrate":[125],"can":[128],"group":[129],"microbes":[130],"similar":[134],"interaction":[135,147],"patterns":[136],"functions":[138],"illuminate":[140],"underlying":[142],"structure":[143],"network,":[148],"which":[149],"could":[150],"potentially":[151],"shed":[152],"light":[153],"uncharacterized":[155],"\"Guilt":[158],"by":[159],"Association\".":[160],"Our":[161],"results":[162],"demonstrated":[163],"is":[166],"powerful":[168],"tool":[169],"provide":[171],"insights":[172],"into":[173],"causes":[175],"dysregulation":[178],"disease,":[180],"facilitating":[181],"future":[182],"hypothesis":[183],"generation":[184],"interface":[187],"metabolomics.":[192]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":5}],"updated_date":"2026-08-02T14:50:37.381335","created_date":"2025-10-10T00:00:00"}