FastPros: screening of reaction knockout strategies for metabolic engineering

Comparing methods for metabolic network analysis and an application to metabolic engineering

(2013) Namrata Tomar et al.   GENE

An in silico platform for the design of heterologous pathways in nonnative metabolite production

(2012) Sunisa Chatsurachai et al.   BMC BIOINFORMATICS

In silico screening of triple reaction knockout Escherichia coli strains for overproduction of useful metabolites

(2012) Satoshi Ohno et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Mathematical optimization applications in metabolic networks

(2012) Ali R. Zomorrodi et al.   METABOLIC ENGINEERING

Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803

(2011) Katsunori Yoshikawa et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

From zero to hero—Design-based systems metabolic engineering of Corynebacterium glutamicum for l-lysine production

(2011) Judith Becker et al.   METABOLIC ENGINEERING

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

Large-Scale Bi-Level Strain Design Approaches and Mixed-Integer Programming Solution Techniques

(2011) Joonhoon Kim et al.   PLoS One

Prediction of novel synthetic pathways for the production of desired chemicals

(2010) Ayoun Cho et al.   BMC Systems Biology

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

(2010) Joonhoon Kim et al.   BMC Systems Biology

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Evolution of Bacterial Phosphoglycerate Mutases: Non-Homologous Isofunctional Enzymes Undergoing Gene Losses, Gains and Lateral Transfers

(2010) Jeremy M. Foster et al.   PLoS One

Manufacturing Molecules Through Metabolic Engineering

(2010) J. D. Keasling   SCIENCE

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

(2009) N. Tepper et al.   BIOINFORMATICS

Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum

(2009) Yohei Shinfuku et al.   Microbial Cell Factories

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Large-scale identification of genetic design strategies using local search

(2009) Desmond S Lun et al.   Molecular Systems Biology

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

High-throughput, quantitative analyses of genetic interactions in E. coli

(2008) Athanasios Typas et al.   NATURE METHODS

Multi-objective steady state optimization of biochemical reaction networks using a constrained genetic algorithm

(2007) Hannes Link et al.   COMPUTERS & CHEMICAL ENGINEERING

Metabolic engineering of Escherichia coli for 1-butanol production

(2007) Shota Atsumi et al.   METABOLIC ENGINEERING