{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:50Z","timestamp":1772138090101,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T00:00:00Z","timestamp":1531958400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"German Federal Ministry of Education and Research","award":["01ZX1313C"],"award-info":[{"award-number":["01ZX1313C"]}]},{"name":"European Union\u2019s Seventh Framework Program","award":["305280"],"award-info":[{"award-number":["305280"]}]},{"name":"National Institute of Aging","award":["1RF1AG057452-01"],"award-info":[{"award-number":["1RF1AG057452-01"]}]},{"DOI":"10.13039\/100008982","name":"Qatar National Research Fund","doi-asserted-by":"publisher","award":["NPRP8-061-3-011"],"award-info":[{"award-number":["NPRP8-061-3-011"]}],"id":[{"id":"10.13039\/100008982","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019460","name":"Weill Cornell Medical College in Qatar","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100019460","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Associations of metabolomics data with phenotypic outcomes are expected to span functional modules, which are defined as sets of correlating metabolites that are coordinately regulated. Moreover, these associations occur at different scales, from entire pathways to only a few metabolites; an aspect that has not been addressed by previous methods. Here, we present MoDentify, a free R package to identify regulated modules in metabolomics networks at different layers of resolution. Importantly, MoDentify shows higher statistical power than classical association analysis. Moreover, the package offers direct interactive visualization of the results in Cytoscape. We present an application example using complex, multifluid metabolomics data. Due to its generic character, the method is widely applicable to other types of data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/krumsieklab\/MoDentify (vignette includes detailed workflow).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty650","type":"journal-article","created":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T06:12:44Z","timestamp":1531980764000},"page":"532-534","source":"Crossref","is-referenced-by-count":17,"title":["<i>MoDentify<\/i>\n                    : phenotype-driven module identification in metabolomics networks at different resolutions"],"prefix":"10.1093","volume":"35","author":[{"given":"Kieu Trinh","family":"Do","sequence":"first","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}]},{"given":"Livia Dahlia","family":"Rasp","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}]},{"given":"Gabi","family":"Kastenm\u00fcller","sequence":"additional","affiliation":[{"name":"German Center for Diabetes Research (DZD), Neuherberg, Germany"},{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum, Neuherberg, Germany"}]},{"given":"Karsten","family":"Suhre","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biophysics, Weill Cornell Medical College\u2014Qatar Education City, Doha, Qatar"}]},{"given":"Jan","family":"Krumsiek","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"},{"name":"German Center for Diabetes Research (DZD), Neuherberg, Germany"},{"name":"Department of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,7,19]]},"reference":[{"key":"2025072403065386700_bty650-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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