Almut Heinken
Cited by
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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), 1-24, 2018
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
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
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
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
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
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
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), 1-18, 2019
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
Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework
A Heinken, I Thiele
Gut microbes 6 (2), 120-130, 2015
Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico
A Heinken, I Thiele
Applied and environmental microbiology 81 (12), 4049-4061, 2015
Systems biology of host–microbe metabolomics
A Heinken, I Thiele
Wiley Interdisciplinary Reviews: Systems Biology and Medicine 7 (4), 195-219, 2015
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
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
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
A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm
G Sigurdsson, RMT Fleming, A Heinken, I Thiele
PLoS One 7 (4), e34337, 2012
Quantitative systems pharmacology and the personalized drug–microbiota–diet axis
I Thiele, CM Clancy, A Heinken, RMT Fleming
Current Opinion in Systems Biology 4, 43-52, 2017
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
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), 100138, 2020
Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals
A Heinken, DA Ravcheev, F Baldini, L Heirendt, RMT Fleming, I Thiele
BioRxiv, 229138, 2017
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