COBRApy: COnstraints-Based Reconstruction and Analysis for Python

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Computational tools for the synthetic design of biochemical pathways

(2012) Marnix H. Medema et al.   NATURE REVIEWS MICROBIOLOGY

JSBML: a flexible Java library for working with SBML

(2011) Andreas Dräger et al.   BIOINFORMATICS

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

An application programming interface for CellNetAnalyzer

(2011) Steffen Klamt et al.   BIOSYSTEMS

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

A systems-level approach for metabolic engineering of yeast cell factories

(2011) Il-Kwon Kim et al.   FEMS YEAST RESEARCH

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

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

(2011) Jan Schellenberger et al.   Nature Protocols

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System

(2009) Erwin P. Gianchandani et al.   PLoS Computational Biology

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

LibSBML: an API Library for SBML

(2008) B. J. Bornstein et al.   BIOINFORMATICS

The Systems Biology Research Tool: evolvable open-source software

(2008) Jeremiah Wright et al.   BMC Systems Biology

Impact of the solvent capacity constraint on E. coli metabolism

(2008) Alexei Vazquez et al.   BMC Systems Biology

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

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH