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

Pubblicazioni

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

Autori: 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
Pubblicato in: BMC Biology, 2020, ISSN 1741-7007
Editore: BioMed Central
DOI: 10.1186/s12915-020-00775-7

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

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

Advances in constraint-based modelling of microbial communities

Autori: Almut Heinken, Arianna Basile, Ines Thiele
Pubblicato in: Current Opinion in Systems Biology, 2021, ISSN 2452-3100
Editore: 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

Autori: Johannes Hertel, Almut Heinken, Filippo Martinelli & Ines Thiele
Pubblicato in: Gut Microbes, 2021, ISSN 0000-0000
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-20877-8

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

Autori: Dmitry A. Ravcheev, Lubin Moussu, Semra Smajic, Ines Thiele
Pubblicato in: Frontiers in Genetics, Numero 10, 2019, ISSN 1664-8021
Editore: Frontiers Media
DOI: 10.3389/fgene.2019.00636

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

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

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

Autori: Almut Heinken, Stefanía Magnúsdóttir, Ronan M T Fleming, Ines Thiele
Pubblicato in: Bioinformatics, 2021, ISSN 1367-4811
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btab622

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

Autori: 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
Pubblicato in: Metabolites, 2023, ISSN 2218-1989
Editore: 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

Autori: Leo Zhu, William Pei, Ines Thiele, Radhakrishnan Mahadevan
Pubblicato in: PLOS Computational Biology, 2021, ISSN 1553-7358
Editore: PLOS
DOI: 10.1371/journal.pcbi.1009110

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

Autori: Almut Heinken, Johannes Hertel & Ines Thiele
Pubblicato in: Systems Biology and Applications, 2021, ISSN 2056-7189
Editore: Nature Publishing Group
DOI: 10.1038/s41540-021-00178-6

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

Autori: Ines Thiele, German Preciat, Ronan M T Fleming
Pubblicato in: Bioinformatics, 2022, ISSN 1367-4811
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btac596

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

Autori: 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
Pubblicato in: Nature Biotechnology, 2023, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.1038/s41587-022-01628-0

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

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

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

Autori: Ines Thiele, Ronan M.T. Fleming
Pubblicato in: Computational and Structural Biotechnology Journal, 2022, ISSN 2001-0370
Editore: 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

Autori: 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
Pubblicato in: Metabolites, 2022, ISSN 2218-1989
Editore: MDPI
DOI: 10.3390/metabo12040308

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

Autori: 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
Pubblicato in: Cell Reports, Numero 29/7, 2019, Pagina/e 1767-1777.e8, ISSN 2211-1247
Editore: 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

Autori: Johannes Hertel, Almut Heinken, Daniel Fässler, Ines Thiele
Pubblicato in: Cell Reports Methods, 2023, ISSN 2667-2375
Editore: Cell press
DOI: 10.1016/j.crmeth.2023.100615

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

Autori: Federico Baldini, Almut Heinken, Laurent Heirendt, Stefania Magnusdottir, Ronan M T Fleming, Ines Thiele
Pubblicato in: Bioinformatics, 2018, ISSN 1367-4803
Editore: 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

Autori: 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
Pubblicato in: Cell Reports, Numero 27/5, 2019, Pagina/e 1621-1632.e9, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2019.04.001

Predicting gastrointestinal drug effects using contextualized metabolic models

Autori: Marouen Ben Guebila, Ines Thiele
Pubblicato in: PLOS Computational Biology, Numero 15/6, 2019, Pagina/e e1007100, ISSN 1553-7358
Editore: 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

Autori: Almut Heinken, Dmitry A. Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M. T. Fleming, Ines Thiele
Pubblicato in: Microbiome, Numero 7/1, 2019, Pagina/e 75, ISSN 2049-2618
Editore: Springer Nature
DOI: 10.1186/s40168-019-0689-3

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

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 47(D1), 2019, Pagina/e D614-D624, ISSN 0305-1048
Editore: Oxford University Press

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

Autori: Marouen Ben Guebila & Ines Thiele
Pubblicato in: Nature Computational Science, 2021, ISSN 2662-8457
Editore: Nature Computational Science
DOI: 10.1038/s43588-021-00074-3

The gut microbial metabolite formate exacerbates colorectal cancer progression

Autori: 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
Pubblicato in: Nature Metabolism, 2022, ISSN 2522-5812
Editore: Nature Metabolism
DOI: 10.1038/s42255-022-00558-0

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

Autori: Bronson R. Weston, Ines Thiele
Pubblicato in: Metabolic Engineering, 2023, ISSN 1096-7176
Editore: Academic Press
DOI: 10.1016/j.ymben.2023.01.010

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

Autori: Almut Heinken, Arianna Basile, Johannes Hertel, Cyrille Thinnes, Ines Thiele
Pubblicato in: Annual Review of Microbiology, 2021, ISSN 0066-4227
Editore: Annual Reviews, Inc.

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

Autori: 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
Pubblicato in: PLOS Biology, 2023, ISSN 1544-9173
Editore: Public Library of Science
DOI: 10.1371/journal.pbio.3002125

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

Autori: 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
Pubblicato in: Nature Microbiology, 2023, ISSN 2058-5276
Editore: Nature Microbiology
DOI: 10.1038/s41564-022-01293-8

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

Autori: Almut Heinken, Ines Thiele
Pubblicato in: Bioinformatics, 2022, ISSN 1367-4811
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btac082

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

Autori: Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike K Aurich, Ronan MT Fleming
Pubblicato in: Molecular Systems Biology, Numero 16/5, 2020, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.20198982

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