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

Publications

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

Auteurs: 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
Publié dans: BMC Biology, 2020, ISSN 1741-7007
Éditeur: BioMed Central
DOI: 10.1186/s12915-020-00775-7

Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics

Auteurs: Arianna Basile, Almut Heinken, Johannes Hertel, Larry Smarr, Weizhong Li, Laura Treu, Giorgio Valle, Stefano Campanaro & Ines Thiele
Publié dans: Gut Microbes, 2023, ISSN 0000-0000
Éditeur: Taylor and Francis Online
DOI: 10.1080/19490976.2023.2226921

Advances in constraint-based modelling of microbial communities

Auteurs: Almut Heinken, Arianna Basile, Ines Thiele
Publié dans: Current Opinion in Systems Biology, 2021, ISSN 2452-3100
Éditeur: Elsevier
DOI: 10.1016/j.coisb.2021.05.007

Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of Fusobacterium spp. on community butyrate production

Auteurs: Johannes Hertel, Almut Heinken, Filippo Martinelli & Ines Thiele
Publié dans: Gut Microbes, 2021, ISSN 0000-0000
Éditeur: Taylor and Francis Online
DOI: 10.1080/19490976.2021.1915673

Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism

Auteurs: Yurong Cheng, Pascal Schlosser, Johannes Hertel, Peggy Sekula, Peter J. Oefner, Ute Spiekerkoetter, Johanna Mielke, Daniel F. Freitag, Miriam Schmidts, GCKD Investigators, Florian Kronenberg, Kai-Uwe Eckardt, Ines Thiele, Yong Li & Anna Köttgen
Publié dans: Nature Communications, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-20877-8

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

Auteurs: Dmitry A. Ravcheev, Lubin Moussu, Semra Smajic, Ines Thiele
Publié dans: Frontiers in Genetics, Numéro 10, 2019, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2019.00636

Cardinality optimization in constraint-based modelling: application to human metabolism

Auteurs: Ronan M T Fleming, Hulda S Haraldsdottir, Le Hoai Minh, Phan Tu Vuong, Thomas Hankemeier, Ines Thiele
Publié dans: Bioinformatics, 2023, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btad450

DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

Auteurs: Almut Heinken, Stefanía Magnúsdóttir, Ronan M T Fleming, Ines Thiele
Publié dans: Bioinformatics, 2021, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btab622

The Effects of Hospitalisation on the Serum Metabolome in COVID-19 Patients

Auteurs: Tim Hensen, Daniel Fässler, Liam O’Mahony, Werner C. Albrich, Beatrice Barda, Christian Garzoni, Gian-Reto Kleger, Urs Pietsch, Noémie Suh, Johannes Hertel and Ines Thiele
Publié dans: Metabolites, 2023, ISSN 2218-1989
Éditeur: MDPI
DOI: 10.3390/metabo13080951

Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism

Auteurs: Leo Zhu, William Pei, Ines Thiele, Radhakrishnan Mahadevan
Publié dans: PLOS Computational Biology, 2021, ISSN 1553-7358
Éditeur: PLOS
DOI: 10.1371/journal.pcbi.1009110

Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis

Auteurs: Almut Heinken, Johannes Hertel & Ines Thiele
Publié dans: Systems Biology and Applications, 2021, ISSN 2056-7189
Éditeur: Nature Publishing Group
DOI: 10.1038/s41540-021-00178-6

MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions

Auteurs: Ines Thiele, German Preciat, Ronan M T Fleming
Publié dans: Bioinformatics, 2022, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btac596

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

Auteurs: Almut Heinken, Johannes Hertel, Geeta Acharya, Dmitry A. Ravcheev, Malgorzata Nyga, Onyedika Emmanuel Okpala, Marcus Hogan, Stefanía Magnúsdóttir, Filippo Martinelli, Bram Nap, German Preciat, Janaka N. Edirisinghe, Christopher S. Henry, Ronan M. T. Fleming & Ines Thiele
Publié dans: Nature Biotechnology, 2023, ISSN 1087-0156
Éditeur: Nature Publishing Group
DOI: 10.1038/s41587-022-01628-0

Methanogenic granule growth and development is a continual process characterized by distinct morphological features

Auteurs: Simon Mills, Anna Christine Trego, John Ward, Juan Castilla-Archilla, Johannes Hertel, Ines Thiele, Piet N.L. Lens, Umer Zeeshan Ijaz, Gavin Collins
Publié dans: Journal of Environmental Management, 2021, ISSN 1095-8630
Éditeur: Elsevier Ltd
DOI: 10.1016/j.jenvman.2021.112229

Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication

Auteurs: Ines Thiele, Ronan M.T. Fleming
Publié dans: Computational and Structural Biotechnology Journal, 2022, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2022.07.019

NMR Metabolomics Reveal Urine Markers of Microbiome Diversity and Identify Benzoate Metabolism as a Mediator between High Microbial Alpha Diversity and Metabolic Health

Auteurs: Johannes Hertel, Daniel Fässler, Almut Heinken, Frank U. Weiß, Malte Rühlemann, Corinna Bang, Andre Franke, Kathrin Budde, Ann-Kristin Henning, Astrid Petersmann, Uwe Völker, Henry Völzke, Ines Thiele, Hans-Jörgen Grabe, Markus M. Lerch, Matthias Nauck, Nele Friedrich and Fabian Frost
Publié dans: Metabolites, 2022, ISSN 2218-1989
Éditeur: MDPI
DOI: 10.3390/metabo12040308

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

Auteurs: 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
Publié dans: Cell Reports, Numéro 29/7, 2019, Page(s) 1767-1777.e8, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2019.10.035

Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses

Auteurs: Johannes Hertel, Almut Heinken, Daniel Fässler, Ines Thiele
Publié dans: Cell Reports Methods, 2023, ISSN 2667-2375
Éditeur: Cell press
DOI: 10.1016/j.crmeth.2023.100615

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

Auteurs: Federico Baldini, Almut Heinken, Laurent Heirendt, Stefania Magnusdottir, Ronan M T Fleming, Ines Thiele
Publié dans: Bioinformatics, 2018, ISSN 1367-4803
Éditeur: 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

Auteurs: 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
Publié dans: Cell Reports, Numéro 27/5, 2019, Page(s) 1621-1632.e9, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2019.04.001

Predicting gastrointestinal drug effects using contextualized metabolic models

Auteurs: Marouen Ben Guebila, Ines Thiele
Publié dans: PLOS Computational Biology, Numéro 15/6, 2019, Page(s) e1007100, ISSN 1553-7358
Éditeur: 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

Auteurs: Almut Heinken, Dmitry A. Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M. T. Fleming, Ines Thiele
Publié dans: Microbiome, Numéro 7/1, 2019, Page(s) 75, ISSN 2049-2618
Éditeur: Springer Nature
DOI: 10.1186/s40168-019-0689-3

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

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 47(D1), 2019, Page(s) D614-D624, ISSN 0305-1048
Éditeur: Oxford University Press

Dynamic flux balance analysis of whole-body metabolism for type 1 diabetes

Auteurs: Marouen Ben Guebila & Ines Thiele
Publié dans: Nature Computational Science, 2021, ISSN 2662-8457
Éditeur: Nature Computational Science
DOI: 10.1038/s43588-021-00074-3

The gut microbial metabolite formate exacerbates colorectal cancer progression

Auteurs: Dominik Ternes, Mina Tsenkova, Vitaly Igorevich Pozdeev, Marianne Meyers, Eric Koncina, Sura Atatri, Martine Schmitz, Jessica Karta, Maryse Schmoetten, Almut Heinken, Fabien Rodriguez, Catherine Delbrouck, Anthoula Gaigneaux, Aurelien Ginolhac, Tam Thuy Dan Nguyen, Lea Grandmougin, Audrey Frachet-Bour, Camille Martin-Gallausiaux, Maria Pacheco, Lorie Neuberger-Castillo, Paulo Miranda, Nikolaus Zue
Publié dans: Nature Metabolism, 2022, ISSN 2522-5812
Éditeur: Nature Metabolism
DOI: 10.1038/s42255-022-00558-0

A nutrition algorithm to optimize feed and medium composition using genome-scale metabolic models

Auteurs: Bronson R. Weston, Ines Thiele
Publié dans: Metabolic Engineering, 2023, ISSN 1096-7176
Éditeur: Academic Press
DOI: 10.1016/j.ymben.2023.01.010

Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine

Auteurs: Almut Heinken, Arianna Basile, Johannes Hertel, Cyrille Thinnes, Ines Thiele
Publié dans: Annual Review of Microbiology, 2021, ISSN 0066-4227
Éditeur: Annual Reviews, Inc.

Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta

Auteurs: Cecilia Noecker, Juan Sanchez, Jordan E. Bisanz, Veronica Escalante, Margaret Alexander, Kai Trepka, Almut Heinken, Yuanyuan Liu, Dylan Dodd, Ines Thiele, Brian C. DeFelice, Peter J. Turnbaugh
Publié dans: PLOS Biology, 2023, ISSN 1544-9173
Éditeur: Public Library of Science
DOI: 10.1371/journal.pbio.3002125

Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome

Auteurs: William F. Kindschuh, Federico Baldini, Martin C. Liu, Jingqiu Liao, Yoli Meydan, Harry H. Lee, Almut Heinken, Ines Thiele, Christoph A. Thaiss, Maayan Levy & Tal Korem
Publié dans: Nature Microbiology, 2023, ISSN 2058-5276
Éditeur: Nature Microbiology
DOI: 10.1038/s41564-022-01293-8

Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities

Auteurs: Almut Heinken, Ines Thiele
Publié dans: Bioinformatics, 2022, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btac082

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

Auteurs: Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike K Aurich, Ronan MT Fleming
Publié dans: Molecular Systems Biology, Numéro 16/5, 2020, ISSN 1744-4292
Éditeur: Nature Publishing Group
DOI: 10.15252/msb.20198982

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