solveME: fast and reliable solution of nonlinear ME models

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

(2016) Edward J. O’Brien et al.   PLoS Computational Biology

Genome-scale strain designs based on regulatory minimal cut sets

(2015) Radhakrishnan Mahadevan et al.   BIOINFORMATICS

An algorithm for the reduction of genome-scale metabolic network models to meaningful core models

(2015) Philipp Erdrich et al.   BMC Systems Biology

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Next-generation genome-scale models for metabolic engineering

(2015) Zachary A King et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computing the functional proteome: recent progress and future prospects for genome-scale models

(2015) Edward J O’Brien et al.   CURRENT OPINION IN BIOTECHNOLOGY

Engineering of oleaginous organisms for lipid production

(2015) Jennifer Levering et al.   CURRENT OPINION IN BIOTECHNOLOGY

Characterizing metabolic pathway diversification in the context of perturbation size

(2015) Laurence Yang et al.   METABOLIC ENGINEERING

On the feasibility of growth-coupled product synthesis in microbial strains

(2015) Steffen Klamt et al.   METABOLIC ENGINEERING

Multi-scale exploration of the technical, economic, and environmental dimensions of bio-based chemical production

(2015) Kai H. Zhuang et al.   METABOLIC ENGINEERING

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

(2015) Laurence Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

(2014) Joanne K Liu et al.   BMC Systems Biology

Predicting microbial growth

(2014) J. Monk et al.   SCIENCE

Robust flux balance analysis of multiscale biochemical reaction networks

(2013) Yuekai Sun et al.   BMC BIOINFORMATICS

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

(2012) Ines Thiele et al.   PLoS One

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

EMILiO: A fast algorithm for genome-scale strain design

(2011) Laurence Yang et al.   METABOLIC ENGINEERING

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY