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

targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

(2012) Karthik Raman et al.   BMC Systems Biology

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models

(2010) R. M. T. Fleming et al.   BIOINFORMATICS

Functional Characterization of Alternate Optimal Solutions of Escherichia coli's Transcriptional and Translational Machinery

(2010) Ines Thiele et al.   BIOPHYSICAL JOURNAL

Systematizing the generation of missing metabolic knowledge

(2010) Jeffrey D. Orth et al.   BIOTECHNOLOGY AND BIOENGINEERING

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular 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

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

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Towards genome-scale signalling-network reconstructions

(2010) Daniel R. Hyduke et al.   NATURE REVIEWS GENETICS

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli

(2009) R.M.T. Fleming et al.   BIOPHYSICAL CHEMISTRY

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

(2009) Anu Raghunathan et al.   BMC Systems Biology

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

Metabolic systems biology

(2009) Bernhard Palsson   FEBS LETTERS

Flux balance analysis: A geometric perspective

(2009) Kieran Smallbone et al.   JOURNAL OF THEORETICAL BIOLOGY

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

(2009) Adam M. Feist et al.   METABOLIC ENGINEERING

Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis

(2009) Karthik Raman et al.   Molecular BioSystems

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

Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling

(2009) Fan Li et al.   PLoS Computational Biology

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

Overexpression of Apoptotic Cell Removal Receptor MERTK in Alveolar Macrophages of Cigarette Smokers

(2008) Angeliki Kazeros et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

LibSBML: an API Library for SBML

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

Impact of the solvent capacity constraint on E. coli metabolism

(2008) Alexei Vazquez et al.   BMC Systems Biology

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

(2008) Juan Nogales et al.   BMC Systems Biology

The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

(2008) Intawat Nookaew et al.   BMC Systems Biology

Use of Randomized Sampling for Analysis of Metabolic Networks

(2008) Jan Schellenberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

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

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Co-Regulation of Metabolic Genes Is Better Explained by Flux Coupling Than by Network Distance

(2008) Richard A. Notebaart et al.   PLoS Computational Biology

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology

Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism

(2007) Orland Gonzalez et al.   Molecular BioSystems