top of page

In silico Reconstructions

Top
Please visit the Virtual Metabolic Human database for all our reconstructions of human and gut microbial metabolism.
​

  • AGORA2 - link

  • Organ-resolved, sex-specific whole-body metabolic reconstructions (Harvey and Harvetta).

    • Please cite: Thiele, I., Sahoo, S., Heinken, A., Hertel, J., Heirendt, L., Aurich, M.K., Fleming, R.M.T., "Personalized whole-body models integrate metabolism, physiology, and the gut microbiome", Molecular Systems Biology, 16:e8982 (2020).

  • Code for the Physiologically and Stoichiometrically Constrained modelling - PSCM - Toolbox.

    • Please cite: Thiele, I., Sahoo, S., Heinken, A., Hertel, J., Heirendt, L., Aurich, M.K., Fleming, R.M.T., "Personalized whole-body models integrate metabolism, physiology, and the gut microbiome", Molecular Systems Biology, 16:e8982 (2020).

​

​

Below you can find further reconstructions and models generated by the lab:

Microbial metabolic reconstructions

  • Heinken et al., "A systematic interrogation of the distinct metabolic potential in gut microbiomes of inflammatory bowel disease patients with dysbiosis",  Systems Biology & Applications (2020). InputFiles. ComputedFluxes. ConstrainedMicrobiomeModels_Set1. ConstrainedMicrobiomeModels_Set2.

  • 818 curated gut microbial metabolic reconstructions​

    • The reconstruction content can be queried here: https://vmh.life

    • The latest version can also be downloaded from github: Link

    • Please cite:  Magnusdottir, S., Heinken, A., Kutt, L., Ravcheev, D.A., Bauer, E., Noronha, A., Greenhalgh, K., Jaeger, C., Baginska, J., Wilmes, P., Fleming, R.M.T., Thiele, I., ''Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota'', Nature Biotechnology, 35(1):81-89 (2017)​

  • Bacteroides thetaiotaomicron.

    • Please cite: Heinken et al., "Systems-level characterization of the host-microbe metabolic symbiosis in the mammalian gut", Gut Microbes, 4(1):1-13 (2013)

  • Collection of 11 human gut microbe reconstructions in SBML format.

    • Please cite the original references listed in the included readme file.

  • Faecalibacterium prausnitzii.

    • Please cite “Heinken, A. et al. A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. J Bacteriol, 196(18):3289-302 (2014).

  • Pseudomonas aeruginosa.

    • Please cite: Sigurdsson, G. et al.,"A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm", PLoS One, 7(4): e34337 (2012).

  • Synechocystis sp. PCC6803.

    • Please cite: Nogales, J.et al., "Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.", PNAS, 109(7):2678-83 (2012).

  • Thermotoga maritima. 

    • Please cite: Nogales et al., "An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production", Int J Hydrogen Energ, 37(17), 12205–12218 (2012).

  • Draft metabolic reconstructions for 301 gastro-intestinal microbe models. 

    • Please cite Bauer et al., "Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires". Microbiome, 3(1):1-13, 2015.

Microbes

Eukaryotic biochemical models

Human

Host-microbe biochemical models

Host-Microbe

Multi-scale biochemical models

  • Expression matrix (E-Matrix) for E. coli. 

    • Please cite: Thiele, I., et la., "Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: A knowledge base, its mathematical formulation, and its functional characterization.", PLoS Comp Biol, 5(3):e1000312 (2009).

  • Hybrid model of levodopa gastrointestinal absorption.

    • Please cite Ben Guebila and Thiele, “Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients.”, NPJ Syst Biol Appl, doi:10.1038/npjsba.2016.13

  • Metabolism & Expression matrix (ME-Matrix) for E. coli: minimal medium glucose, aerobic conditions, wildtype.

    • Please cite: Thiele et al., "Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage", PLoS One, 7(9):e45635 (2012).

  • Toll-like receptor signalling model. 

    • Please cite: Aurich and Thiele, "Contextualization procedure and modeling of monocyte specific TLR signaling", PLoS ONE 7(12): e49978 (2012).

Multiscale
bottom of page