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Almut Heinken
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Gut microbiota functions: metabolism of nutrients and other food components
I Rowland, G Gibson, A Heinken, K Scott, J Swann, I Thiele, K Tuohy
European journal of nutrition 57, 1-24, 2018
23932018
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0
L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ...
Nature protocols 14 (3), 639-702, 2019
10372019
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
S Magnúsdóttir, A Heinken, L Kutt, DA Ravcheev, E Bauer, A Noronha, ...
Nature biotechnology 35 (1), 81-89, 2017
7292017
Recon3D enables a three-dimensional view of gene variation in human metabolism
E Brunk, S Sahoo, DC Zielinski, A Altunkaya, A Dräger, N Mih, F Gatto, ...
Nature biotechnology 36 (3), 272-281, 2018
6392018
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease
A Noronha, J Modamio, Y Jarosz, E Guerard, N Sompairac, G Preciat, ...
Nucleic acids research 47 (D1), D614-D624, 2019
3242019
Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
A Heinken, DA Ravcheev, F Baldini, L Heirendt, RMT Fleming, I Thiele
Microbiome 7, 1-18, 2019
2512019
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
A Heinken, S Sahoo, RMT Fleming, I Thiele
Gut microbes 4 (1), 28-40, 2013
2492013
Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe
A Heinken, MT Khan, G Paglia, DA Rodionov, HJM Harmsen, I Thiele
Journal of bacteriology 196 (18), 3289-3302, 2014
2262014
Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome
I Thiele, S Sahoo, A Heinken, J Hertel, L Heirendt, MK Aurich, ...
Molecular systems biology 16 (5), e8982, 2020
1612020
The gut microbial metabolite formate exacerbates colorectal cancer progression
D Ternes, M Tsenkova, VI Pozdeev, M Meyers, E Koncina, S Atatri, ...
Nature metabolism 4 (4), 458-475, 2022
1392022
Metabolic network analysis reveals altered bile acid synthesis and metabolism in Alzheimer’s disease
P Baloni, CC Funk, J Yan, JT Yurkovich, A Kueider-Paisley, K Nho, ...
Cell Reports Medicine 1 (8), 2020
1352020
The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases
F Hosseinkhani, A Heinken, I Thiele, PW Lindenburg, AC Harms, ...
Gut microbes 13 (1), 1882927, 2021
1322021
The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities
F Baldini, A Heinken, L Heirendt, S Magnusdottir, RMT Fleming, I Thiele
Bioinformatics 35 (13), 2332-2334, 2019
1322019
Integrated analyses of microbiome and longitudinal metabolome data reveal microbial-host interactions on sulfur metabolism in Parkinson’s disease
J Hertel, AC Harms, A Heinken, F Baldini, CC Thinnes, E Glaab, ...
Cell reports 29 (7), 1767-1777. e8, 2019
1312019
A systems biology approach to studying the role of microbes in human health
I Thiele, A Heinken, RMT Fleming
Current opinion in biotechnology 24 (1), 4-12, 2013
1202013
Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico
A Heinken, I Thiele
Applied and environmental microbiology 81 (12), 4049-4061, 2015
1162015
Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework
A Heinken, I Thiele
Gut microbes 6 (2), 120-130, 2015
1052015
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
A Heinken, J Hertel, G Acharya, DA Ravcheev, M Nyga, OE Okpala, ...
Nature Biotechnology 41 (9), 1320-1331, 2023
972023
Systems biology of host–microbe metabolomics
A Heinken, I Thiele
Wiley Interdisciplinary Reviews: Systems Biology and Medicine 7 (4), 195-219, 2015
942015
Integrated in vitro and in silico modeling delineates the molecular effects of a synbiotic regimen on colorectal-cancer-derived cells
K Greenhalgh, J Ramiro-Garcia, A Heinken, P Ullmann, T Bintener, ...
Cell reports 27 (5), 1621-1632. e9, 2019
702019
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Articles 1–20