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Predicting the effects of gut microbiota and diet on an individual’s drug response and safety

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The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

Author(s): Federico Baldini, Almut Heinken, Laurent Heirendt, Stefania Magnusdottir, Ronan M T Fleming, Ines Thiele
Published in: Bioinformatics, 2018, ISSN 1367-4803
DOI: 10.1093/bioinformatics/bty941

Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells

Author(s): Kacy Greenhalgh, Javier Ramiro-Garcia, Almut Heinken, Pit Ullmann, Tamara Bintener, Maria Pires Pacheco, Joanna Baginska, Pranjul Shah, Audrey Frachet, Rashi Halder, Joëlle V. Fritz, Thomas Sauter, Ines Thiele, Serge Haan, Elisabeth Letellier, Paul Wilmes
Published in: Cell Reports, Issue 27/5, 2019, Page(s) 1621-1632.e9, ISSN 2211-1247
DOI: 10.1016/j.celrep.2019.04.001

Predicting gastrointestinal drug effects using contextualized metabolic models

Author(s): Marouen Ben Guebila, Ines Thiele
Published in: PLOS Computational Biology, Issue 15/6, 2019, Page(s) e1007100, ISSN 1553-7358
DOI: 10.1371/journal.pcbi.1007100

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

Author(s): Almut Heinken, Dmitry A. Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M. T. Fleming, Ines Thiele
Published in: Microbiome, Issue 7/1, 2019, Page(s) 75, ISSN 2049-2618
DOI: 10.1186/s40168-019-0689-3

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

Author(s): Alberto Noronha, Jennifer Modamio, Yohan Jarosz, Elisabeth Guerard, Nicolas Sompairac, German Preciat, Anna Dröfn Daníelsdóttir, Max Krecke, Diane Merten, Hulda S Haraldsdóttir, Almut Heinken, Laurent Heirendt, Stefanía Magnúsdóttir, Dmitry A Ravcheev, Swagatika Sahoo, Piotr Gawron, Lucia Friscioni, Beatriz Garcia, Mabel Prendergast, Alberto Puente, Mariana Rodrigues, Akansha Roy, Mouss Rou
Published in: Nucleic Acids Research, Issue 47(D1), 2019, Page(s) D614-D624, ISSN 0305-1048