93 citations · 117 across the 11 of their papers we have counts for
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Variational kinetics: elementary reaction kinetics via conic optimisation
Ronan M. T. Fleming, Ines Thiele
Genome-scale modelling methods primarily predict reaction fluxes, whereas established high throughput experimental technologies primarily measure molecular species concentrations.…
From metagenomic data to personalized computational microbiotas: Predicting dietary supplements for Crohn's disease
Eugen Bauer, Ines Thiele
Crohn's disease (CD) is associated with an ecological imbalance of the intestinal microbiota, consisting of hundreds of species. The underlying complexity as well as individual dif…
MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models
Maike K. Aurich, Ronan M. T. Fleming, Ines Thiele
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of ana…
Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
Ding Ma, Laurence Yang, Ronan M. T. Fleming +3
Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-s…
ReconMap: An interactive visualisation of human metabolism
Alberto Noronha, Anna Dröfn Danielsdóttir, Freyr Jóhannsson +8
A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation re…
Conditions for duality between fluxes and concentrations in biochemical networks
Ronan M. T. Fleming, Nikos Vlassis, Ines Thiele +1
Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. Wh…
Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration
Ronan M. T. Fleming, Ines Thiele
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equil…