Genome-scale strain designs based on regulatory minimal cut sets

Characterizing metabolic pathway diversification in the context of perturbation size

(2015) Laurence Yang et al.   METABOLIC ENGINEERING

Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go

(2014) Jeffrey C. Way et al.   CELL

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

(2014) I. Farasat et al.   Molecular Systems Biology

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks

(2014) Axel von Kamp et al.   PLoS Computational Biology

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

(2014) Anupam Chowdhury et al.   PLoS Computational Biology

Fast thermodynamically constrained flux variability analysis

(2013) Arne C. Müller et al.   BIOINFORMATICS

Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering

(2013) Cameron Cotten et al.   Biotechnology Journal

SMET: Systematic multiple enzyme targeting - a method to rationally design optimal strains for target chemical overproduction

(2013) David Flowers et al.   Biotechnology Journal

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

Elucidating and reprogramming Escherichia coli metabolisms for obligate anaerobic n-butanol and isobutanol production

(2012) Cong T. Trinh   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Flux variability scanning based on enforced objective flux for identifying gene amplification targets

(2012) Jong Park et al.   BMC Systems Biology

Synthetic biology and the development of tools for metabolic engineering

(2012) Jay D. Keasling   METABOLIC ENGINEERING

An integrated computational and experimental study for overproducing fatty acids in Escherichia coli

(2012) Sridhar Ranganathan et al.   METABOLIC ENGINEERING

Mathematical optimization applications in metabolic networks

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

Synthetic Biology and Metabolic Engineering

(2012) Gregory Stephanopoulos   ACS Synthetic Biology

Redesigning Escherichia coli Metabolism for Anaerobic Production of Isobutanol

(2011) Cong T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Minimal cut sets in a metabolic network are elementary modes in a dual network

(2011) Kathrin Ballerstein et al.   BIOINFORMATICS

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA

(2011) Peng Xu et al.   METABOLIC ENGINEERING

EMILiO: A fast algorithm for genome-scale strain design

(2011) Laurence Yang et al.   METABOLIC ENGINEERING

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

(2011) Harry Yim et al.   Nature Chemical Biology

Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression

(2011) J. M. Carothers et al.   SCIENCE

Deletion of Genes Encoding Cytochrome Oxidases and Quinol Monooxygenase Blocks the Aerobic-Anaerobic Shift in Escherichia coli K-12 MG1655

(2010) V. A. Portnoy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Modeling of uncertainties in biochemical reactions

(2010) Ljubiša Mišković et al.   BIOTECHNOLOGY AND BIOENGINEERING

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

(2010) Joonhoon Kim et al.   BMC Systems Biology

CASOP: A Computational Approach for Strain Optimization aiming at high Productivity

(2010) Oliver Hädicke et al.   JOURNAL OF BIOTECHNOLOGY

Computing complex metabolic intervention strategies using constrained minimal cut sets

(2010) Oliver Hädicke et al.   METABOLIC ENGINEERING

Improved vanillin production in baker's yeast through in silico design

(2010) Ana Brochado et al.   Microbial Cell Factories

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties

(2009) Guido Melzer et al.   BMC Systems Biology

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses

(2008) C. T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

(2008) Cong T. Trinh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Ensemble Modeling of Metabolic Networks

(2008) Linh M. Tran et al.   BIOPHYSICAL JOURNAL