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

Publikacje

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

Autorzy: 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
Opublikowane w: BMC Biology, 2020, ISSN 1741-7007
Wydawca: BioMed Central
DOI: 10.1186/s12915-020-00775-7

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

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

Advances in constraint-based modelling of microbial communities

Autorzy: Almut Heinken, Arianna Basile, Ines Thiele
Opublikowane w: Current Opinion in Systems Biology, 2021, ISSN 2452-3100
Wydawca: 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

Autorzy: Johannes Hertel, Almut Heinken, Filippo Martinelli & Ines Thiele
Opublikowane w: Gut Microbes, 2021, ISSN 0000-0000
Wydawca: 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

Autorzy: 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
Opublikowane w: Nature Communications, 2021, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-20877-8

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

Autorzy: Dmitry A. Ravcheev, Lubin Moussu, Semra Smajic, Ines Thiele
Opublikowane w: Frontiers in Genetics, Numer 10, 2019, ISSN 1664-8021
Wydawca: Frontiers Media
DOI: 10.3389/fgene.2019.00636

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

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

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

Autorzy: Almut Heinken, Stefanía Magnúsdóttir, Ronan M T Fleming, Ines Thiele
Opublikowane w: Bioinformatics, 2021, ISSN 1367-4811
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btab622

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

Autorzy: 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
Opublikowane w: Metabolites, 2023, ISSN 2218-1989
Wydawca: 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

Autorzy: Leo Zhu, William Pei, Ines Thiele, Radhakrishnan Mahadevan
Opublikowane w: PLOS Computational Biology, 2021, ISSN 1553-7358
Wydawca: PLOS
DOI: 10.1371/journal.pcbi.1009110

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

Autorzy: Almut Heinken, Johannes Hertel & Ines Thiele
Opublikowane w: Systems Biology and Applications, 2021, ISSN 2056-7189
Wydawca: Nature Publishing Group
DOI: 10.1038/s41540-021-00178-6

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

Autorzy: Ines Thiele, German Preciat, Ronan M T Fleming
Opublikowane w: Bioinformatics, 2022, ISSN 1367-4811
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btac596

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

Autorzy: 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
Opublikowane w: Nature Biotechnology, 2023, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-022-01628-0

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

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

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

Autorzy: Ines Thiele, Ronan M.T. Fleming
Opublikowane w: Computational and Structural Biotechnology Journal, 2022, ISSN 2001-0370
Wydawca: 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

Autorzy: 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
Opublikowane w: Metabolites, 2022, ISSN 2218-1989
Wydawca: MDPI
DOI: 10.3390/metabo12040308

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

Autorzy: 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
Opublikowane w: Cell Reports, Numer 29/7, 2019, Strona(/y) 1767-1777.e8, ISSN 2211-1247
Wydawca: 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

Autorzy: Johannes Hertel, Almut Heinken, Daniel Fässler, Ines Thiele
Opublikowane w: Cell Reports Methods, 2023, ISSN 2667-2375
Wydawca: Cell press
DOI: 10.1016/j.crmeth.2023.100615

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

Autorzy: Federico Baldini, Almut Heinken, Laurent Heirendt, Stefania Magnusdottir, Ronan M T Fleming, Ines Thiele
Opublikowane w: Bioinformatics, 2018, ISSN 1367-4803
Wydawca: 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

Autorzy: 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
Opublikowane w: Cell Reports, Numer 27/5, 2019, Strona(/y) 1621-1632.e9, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2019.04.001

Predicting gastrointestinal drug effects using contextualized metabolic models

Autorzy: Marouen Ben Guebila, Ines Thiele
Opublikowane w: PLOS Computational Biology, Numer 15/6, 2019, Strona(/y) e1007100, ISSN 1553-7358
Wydawca: 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

Autorzy: Almut Heinken, Dmitry A. Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M. T. Fleming, Ines Thiele
Opublikowane w: Microbiome, Numer 7/1, 2019, Strona(/y) 75, ISSN 2049-2618
Wydawca: Springer Nature
DOI: 10.1186/s40168-019-0689-3

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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 47(D1), 2019, Strona(/y) D614-D624, ISSN 0305-1048
Wydawca: Oxford University Press

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

Autorzy: Marouen Ben Guebila & Ines Thiele
Opublikowane w: Nature Computational Science, 2021, ISSN 2662-8457
Wydawca: Nature Computational Science
DOI: 10.1038/s43588-021-00074-3

The gut microbial metabolite formate exacerbates colorectal cancer progression

Autorzy: 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
Opublikowane w: Nature Metabolism, 2022, ISSN 2522-5812
Wydawca: Nature Metabolism
DOI: 10.1038/s42255-022-00558-0

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

Autorzy: Bronson R. Weston, Ines Thiele
Opublikowane w: Metabolic Engineering, 2023, ISSN 1096-7176
Wydawca: Academic Press
DOI: 10.1016/j.ymben.2023.01.010

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

Autorzy: Almut Heinken, Arianna Basile, Johannes Hertel, Cyrille Thinnes, Ines Thiele
Opublikowane w: Annual Review of Microbiology, 2021, ISSN 0066-4227
Wydawca: Annual Reviews, Inc.

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

Autorzy: 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
Opublikowane w: PLOS Biology, 2023, ISSN 1544-9173
Wydawca: Public Library of Science
DOI: 10.1371/journal.pbio.3002125

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

Autorzy: 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
Opublikowane w: Nature Microbiology, 2023, ISSN 2058-5276
Wydawca: Nature Microbiology
DOI: 10.1038/s41564-022-01293-8

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

Autorzy: Almut Heinken, Ines Thiele
Opublikowane w: Bioinformatics, 2022, ISSN 1367-4811
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btac082

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

Autorzy: Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike K Aurich, Ronan MT Fleming
Opublikowane w: Molecular Systems Biology, Numer 16/5, 2020, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.15252/msb.20198982

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