Critical assessment of genome-scale metabolic networks: the need for a unified standard

iOD907, the first genome-scale metabolic model for the milk yeastKluyveromyces lactis

(2014) Oscar Dias et al.   Biotechnology Journal

Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production inStreptomyces coelicolorA3(2)

(2014) Minsuk Kim et al.   Biotechnology Journal

Enhancement of acetoin production in Candida glabrata by in silico-aided metabolic engineering

(2014) Shubo Li et al.   Microbial Cell Factories

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

A Data Integration and Visualization Resource for the Metabolic Network of Synechocystis sp. PCC 6803

(2014) T. R. Maarleveld et al.   PLANT PHYSIOLOGY

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

(2014) Hulda S Haraldsdóttir et al.   Journal of Cheminformatics

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

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

Improving the reuse of computational models through version control

(2013) D. Waltemath et al.   BIOINFORMATICS

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks

(2013) M. Ganter et al.   BIOINFORMATICS

Path2Models: large-scale generation of computational models from biochemical pathway maps

(2013) Finja Büchel et al.   BMC Systems Biology

Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling

(2013) Sven EF Borgos et al.   BMC Systems Biology

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

(2013) Tobias Österlund et al.   BMC Systems Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Genome-scale reconstruction and in silico analysis of Aspergillus terreus metabolism

(2013) Jie Liu et al.   Molecular BioSystems

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

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

(2013) Henning Knoop et al.   PLoS Computational Biology

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks

(2012) Abdelhalim Larhlimi et al.   BIOINFORMATICS

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

(2012) Akhil Kumar et al.   BMC BIOINFORMATICS

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

(2012) Xueyang Feng et al.   BMC Systems Biology

iAK692: A genome-scale metabolic model of Spirulina platensis C1

(2012) Amornpan Klanchui et al.   BMC Systems Biology

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

(2012) Benjamin D Heavner et al.   BMC Systems Biology

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in-silico evaluation of their potentials

(2012) Luis Caspeta et al.   BMC Systems Biology

FAME, the Flux Analysis and Modeling Environment

(2012) Joost Boele et al.   BMC Systems Biology

Software applications for flux balance analysis

(2012) M. Lakshmanan et al.   BRIEFINGS IN BIOINFORMATICS

Software applications toward quantitative metabolic flux analysis and modeling

(2012) T. Dandekar et al.   BRIEFINGS IN BIOINFORMATICS

Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis

(2012) Balaji Balagurunathan et al.   Microbial Cell Factories

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

A Systems Biology Approach to Drug Targets in Pseudomonas aeruginosa Biofilm

(2012) Gunnar Sigurdsson et al.   PLoS One

Shrinking the Metabolic Solution Space Using Experimental Datasets

(2012) Jennifer L. Reed   PLoS Computational Biology

MetaMerge: scaling up genome-scale metabolic reconstructions, with application to Mycobacterium tuberculosis

(2012) Leonid Chindelevitch et al.   GENOME BIOLOGY

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks

(2011) S. G. Thorleifsson et al.   BIOINFORMATICS

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

(2011) Clemens Wrzodek et al.   BIOINFORMATICS

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

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

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

(2011) H. U. Kim et al.   Molecular Systems Biology

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

(2011) Jan Schellenberger et al.   Nature Protocols

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera

(2011) Tom A Mendum et al.   GENOME BIOLOGY

In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production

(2010) H. S. Choi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis

(2010) Hanifah Widiastuti et al.   BIOTECHNOLOGY AND BIOENGINEERING

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

The biomass objective function

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

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in E. coli

(2010) Xuewen Chen et al.   METABOLIC ENGINEERING

Reconstruction annotation jamborees: a community approach to systems biology

(2010) Ines Thiele et al.   Molecular Systems Biology

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

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

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

(2010) Roger L. Chang et al.   PLoS Computational Biology

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

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

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

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

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

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

(2009) Tae Yong Kim et al.   METABOLIC ENGINEERING

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Caroline Colijn et al.   PLoS Computational Biology

Detection of stoichiometric inconsistencies in biomolecular models

(2008) A. Gevorgyan et al.   BIOINFORMATICS

In silico genome-scale reconstruction and validation of theCorynebacterium glutamicummetabolic network

(2008) Kjeld Raunkjaer Kjeldsen et al.   BIOTECHNOLOGY AND BIOENGINEERING

Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

(2008) Maxime Durot et al.   BMC Systems Biology

Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

(2008) M. A. Oberhardt et al.   JOURNAL OF BACTERIOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

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

(2008) Jacek Puchałka et al.   PLoS Computational Biology