PSAMM: A Portable System for the Analysis of Metabolic Models

INCA: a computational platform for isotopically non-stationary metabolic flux analysis

(2014) J. D. Young   BIOINFORMATICS

An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

(2014) Leonid Chindelevitch et al.   Nature Communications

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens

(2014) Adam M. Feist et al.   PLoS Computational Biology

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

(2014) Esa Pitkänen et al.   PLoS Computational Biology

Improving the reuse of computational models through version control

(2013) D. Waltemath et al.   BIOINFORMATICS

Fast thermodynamically constrained flux variability analysis

(2013) Arne C. Müller et al.   BIOINFORMATICS

Genomically and biochemically accurate metabolic reconstruction ofMethanosarcina barkeriFusaro, iMG746

(2013) Matthew C. Gonnerman et al.   Biotechnology Journal

MC3: a steady-state model and constraint consistency checker for biochemical networks

(2013) Mona Yousofshahi et al.   BMC Systems Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models

(2013) J. P. Faria et al.   BRIEFINGS IN BIOINFORMATICS

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

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

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

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

Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

(2012) Rajib Saha et al.   PLoS One

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

(2012) J. Nogales et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

(2011) Colin T Archer et al.   BMC GENOMICS

Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

(2011) Kechi Fang et al.   BMC Systems Biology

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

iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

(2011) Saheed Imam et al.   BMC Systems Biology

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism

(2011) R. L. Chang et al.   Molecular Systems Biology

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

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

(2010) Martin I Sigurdsson et al.   BMC Systems Biology

Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

(2010) Xin Fang et al.   BMC Systems Biology

Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

(2010) Seth B Roberts et al.   BMC Systems Biology

Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network

(2010) Germán Plata et al.   Molecular Systems Biology

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model

(2010) M. Ahsanul Islam et al.   PLoS Computational Biology

An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models

(2010) Dipak Barua et al.   PLoS Computational Biology

E. coli cardiolipin synthase: Function of N-terminal conserved residues

(2009) Bernard R. Quigley et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

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

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Genome Scale Reconstruction of a Salmonella Metabolic Model

(2009) Manal AbuOun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks

(2009) Tae Yong Kim et al.   METABOLIC ENGINEERING

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

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

Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE

(2009) Hyun Uk Kim et al.   Molecular BioSystems

Predicting metabolic biomarkers of human inborn errors of metabolism

(2009) Tomer Shlomi et al.   Molecular Systems Biology

Applications of genome-scale metabolic reconstructions

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

Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

(2009) Y. Zhang et al.   SCIENCE

LibSBML: an API Library for SBML

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

Modes and cuts in metabolic networks: Complexity and algorithms

(2008) Vicente Acuña et al.   BIOSYSTEMS

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

(2008) Juan Nogales et al.   BMC Systems Biology

Metabolic engineering of microorganisms: general strategies and drug production

(2008) Sang Yup Lee et al.   DRUG DISCOVERY TODAY

Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

(2008) Mikael Rørdam Andersen 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

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

(2008) Jacek Puchałka et al.   PLoS Computational Biology

Context-Specific Metabolic Networks Are Consistent with Experiments

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