Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal

Recon 2.2: from reconstruction to model of human metabolism

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Phenotypic innovation through recombination in genome-scale metabolic networks

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Adaptive evolution of complex innovations through stepwise metabolic niche expansion

(2016) Balázs Szappanos et al.   Nature Communications

Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets

(2016) Daniel Hartleb et al.   PLoS Computational Biology

CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions

(2015) A. A. Desouki et al.   BIOINFORMATICS

Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity

(2015) Gautham Sridharan et al.   BMC Systems Biology

Using Genome-scale Models to Predict Biological Capabilities

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

Reducing Recon 2 for steady-state flux analysis of HEK cell culture

(2014) Lake-Ee Quek et al.   JOURNAL OF BIOTECHNOLOGY

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

(2013) M. Ganter et al.   BIOINFORMATICS

Fast thermodynamically constrained flux variability analysis

(2013) Arne C. Müller et al.   BIOINFORMATICS

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(2013) Gabriel Gelius-Dietrich et al.   BMC Systems Biology

A latent capacity for evolutionary innovation through exaptation in metabolic systems

(2013) Aditya Barve et al.   NATURE

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

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

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

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

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

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

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

Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks

(2009) João F. Matias Rodrigues et al.   PLoS Computational Biology