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Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
The advent of genome‐scale models of metabolism has laid the foundation for the development of computational procedures for suggesting genetic manipulations that lead to overproduction. In this work,… Expand
Flux coupling analysis of genome-scale metabolic network reconstructions.
In this paper, we introduce the Flux Coupling Finder (FCF) framework for elucidating the topological and flux connectivity features of genome-scale metabolic networks. The framework is demonstrated… Expand
An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems.
We introduce a computational framework termed OptReg that determines the optimal reaction activations/inhibitions and eliminations for targeted biochemical production. A reaction is deemed up- or… Expand
OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions
We introduce the OptForce procedure that identifies all possible engineering interventions by classifying reactions in the metabolic model depending upon whether their flux values must increase, decrease or become equal to zero to meet a pre-specified overproduction target. Expand
Optimization based automated curation of metabolic reconstructions
We identify the metabolites in the metabolic network reconstruction which cannot be produced under any uptake conditions and subsequently we identify the reactions from a customized multi-organism database that restores the connectivity of these metabolites to the parent network using four mechanisms. Expand
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
- Laurent Heirendt, Sylvain Arreckx, +52 authors R. Fleming
- Computer Science, Medicine
- Nature Protocols
- 20 February 2019
The COBRA Toolbox v.3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. Expand
Managing demand uncertainty in supply chain planning
In this work, we provide an overview of our previously published works on incorporating demand uncertainty in midterm planning of multisite supply chains. Expand
OptStrain: a computational framework for redesign of microbial production systems.
This paper introduces the hierarchical computational framework OptStrain aimed at guiding pathway modifications, through reaction additions and deletions, of microbial networks for the overproduction… Expand
Finding all solutions of nonlinearly constrained systems of equations
A new approach is proposed for finding allε-feasible solutions for certain classes of nonlinearly constrained systems of equations. Expand
GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions
We use GrowMatch to resolve inconsistencies between the predictions of the latest in silico Escherichia coli (iAF1260) model and the in vivo data available in the Keio collection in order to reconcile experimental and computational growth predictions across different mutants. Expand