Automated generation of genome-scale metabolic draft reconstructions based on KEGG

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

(2017) Joana C. Xavier et al.   METABOLIC ENGINEERING

Robust Analysis of Fluxes in Genome-Scale Metabolic Pathways

(2017) Michael MacGillivray et al.   Scientific Reports

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model

(2016) Daniel A. Cuevas et al.   Frontiers in Microbiology

From the Lab to the Farm: An Industrial Perspective of Plant Beneficial Microorganisms

(2016) J. Jacob Parnell et al.   Frontiers in Plant Science

Reconstructing genome-scale metabolic models with merlin

(2015) Oscar Dias et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Esa Pitkänen et al.   PLoS Computational Biology

Software platforms to facilitate reconstructing genome-scale metabolic networks

(2013) Joshua J. Hamilton et al.   ENVIRONMENTAL MICROBIOLOGY

Dietary soybean protein concentrate-induced intestinal disorder in marine farmed Atlantic salmon, Salmo salar is associated with alterations in gut microbiota

(2013) Timothy J. Green et al.   VETERINARY MICROBIOLOGY

Consistent Estimation of Gibbs Energy Using Component Contributions

(2013) Elad Noor 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

Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction

(2012) H.S. Haraldsdóttir et al.   BIOPHYSICAL JOURNAL

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

(2012) Xueyang Feng et al.   BMC Systems Biology

FAME, the Flux Analysis and Modeling Environment

(2012) Joost Boele et al.   BMC Systems Biology

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Modeling microbial communities: Current, developing, and future technologies for predicting microbial community interaction

(2012) Peter Larsen et al.   JOURNAL OF BIOTECHNOLOGY

MEMOSys: Bioinformatics platform for genome-scale metabolic models

(2011) Stephan Pabinger et al.   BMC Systems Biology

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

(2011) J. D. Orth 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

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

(2011) Matthew A. Oberhardt et al.   PLoS Computational Biology

The biomass objective function

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

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

Reconstruction of biochemical networks in microorganisms

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