93 citations · 117 across the 11 of their papers we have counts for
13 papers
gpuGEM: GPU-based linear optimisation of genome-scale metabolic models
Farid Zare†, Timothy Hulshof†, Ines Thiele +1
Summary: Genome-scale metabolic models increasingly challenge CPU linear-programming solvers in repeated-optimisation workflows. We present gpuGEM, an open-source Python library fo…
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.…
DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations
Almut Heinken, Stefanía Magnúsdóttir, Ronan M. T. Fleming +1
Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manuall…
ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software
Laurent Heirendt, Sylvain Arreckx, Christophe Trefois +6
Motivation: Automatically testing changes to code is an essential feature of continuous integration. For open-source code, without licensed dependencies, a variety of continuous in…
Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0
Laurent Heirendt, Sylvain Arreckx, Thomas Pfau +52
COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physico…
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…
Comparative genomic analysis of the human gut microbiome reveals a broad distribution of metabolic pathways for the degradation of host-synthetized mucin glycans
Dmitry A. Ravcheev, Ines Thiele
The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily glycosylated proteins. Colonic m…
DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia
Laurent Heirendt, Ronan M. T. Fleming, Ines Thiele
Motivation: Flux balance analysis, and its variants, are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high di…
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…