{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T00:59:21Z","timestamp":1783040361148,"version":"3.54.6"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,11,21]],"date-time":"2018-11-21T00:00:00Z","timestamp":1542758400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Luxembourg National Research Fund"},{"DOI":"10.13039\/100007869","name":"FNR","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007869","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ATTRACT","award":["FNR\/A12\/01"],"award-info":[{"award-number":["FNR\/A12\/01"]}]},{"name":"OPEN","award":["FNR\/O16\/11402054"],"award-info":[{"award-number":["FNR\/O16\/11402054"]}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"ERC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020","award":["757922"],"award-info":[{"award-number":["757922"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To address this gap, we created a comprehensive toolbox to model (i) microbe\u2013microbe and host\u2013microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The Microbiome Modeling Toolbox and the tutorials at https:\/\/git.io\/microbiomeModelingToolbox.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty941","type":"journal-article","created":{"date-parts":[[2018,11,19]],"date-time":"2018-11-19T10:58:35Z","timestamp":1542625115000},"page":"2332-2334","source":"Crossref","is-referenced-by-count":129,"title":["The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities"],"prefix":"10.1093","volume":"35","author":[{"given":"Federico","family":"Baldini","sequence":"first","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Almut","family":"Heinken","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurent","family":"Heirendt","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefania","family":"Magnusdottir","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronan M T","family":"Fleming","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg"},{"name":"Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, CC Leiden, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ines","family":"Thiele","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,11,21]]},"reference":[{"key":"2023051612121622100_bty941-B1","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nbt.4072","article-title":"Recon3d enables a three-dimensional view of gene variation in human metabolism","volume":"36","author":"Brunk","year":"2018","journal-title":"Nat. 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