In Silico Models

1. Bacterial biochemical models

  • 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, 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.

2. Eukaryotic biochemical models

3. Host-microbe biochemical models

4. 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
  • Metabolims & 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 inE. coli and its application to the evolution of codon usage", PLoS One, 7(9):e45635 (2012).
  • Toll-like receptor signaling model. Please cite: Aurich and Thiele, "Contextualization procedure and modeling of monocyte specific TLR signaling", PLoS ONE 7(12): e49978 (2012).