In silico Reconstructions

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

In an effort to make our work reproducible, we deposit our code on github either within the COBRA toolbox (link), if it is generic, or if it is paper specific (link or link).
Additionally, you can find the required data for specific papers here:

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

Microbial metabolic reconstructions

  • 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.

 

Eukaryotic biochemical models

 

Host-microbe biochemical models

 

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).