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

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Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions

Author(s): Federico Baldini, Johannes Hertel, Estelle Sandt, Cyrille C. Thinnes, Lorieza Neuberger-Castillo, Lukas Pavelka, Fay Betsou, Rejko Krüger, Ines Thiele & on behalf of the NCER-PD Consortium
Published in: BMC Biology, 2020, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-020-00775-7

Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome

Author(s): Dmitry A. Ravcheev, Lubin Moussu, Semra Smajic, Ines Thiele
Published in: Frontiers in Genetics, 10, 2019, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2019.00636

Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease

Author(s): Johannes Hertel, Amy C. Harms, Almut Heinken, Federico Baldini, Cyrille C. Thinnes, Enrico Glaab, Daniel A. Vasco, Maik Pietzner, Isobel D. Stewart, Nicholas J. Wareham, Claudia Langenberg, Claudia Trenkwalder, Rejko Krüger, Thomas Hankemeier, Ronan M.T. Fleming, Brit Mollenhauer, Ines Thiele
Published in: Cell Reports, 29/7, 2019, Page(s) 1767-1777.e8, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2019.10.035

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
Publisher: Oxford University Press
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, 27/5, 2019, Page(s) 1621-1632.e9, ISSN 2211-1247
Publisher: Cell Press
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, 15/6, 2019, Page(s) e1007100, ISSN 1553-7358
Publisher: Public Library of Science
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, 7/1, 2019, Page(s) 75, ISSN 2049-2618
Publisher: Springer Nature
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, 47(D1), 2019, Page(s) D614-D624, ISSN 0305-1048
Publisher: Oxford University Press

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome

Author(s): Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike K Aurich, Ronan MT Fleming
Published in: Molecular Systems Biology, 16/5, 2020, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20198982