Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance

(2013) Benjamin D. Heavner et al.   Database-The Journal of Biological Databases and Curation

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

Global probabilistic annotation of metabolic networks enables enzyme discovery

(2012) Germán Plata et al.   Nature Chemical Biology

MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks

(2012) Edward Vitkin et al.   GENOME BIOLOGY

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

(2011) Caroline B Milne et al.   BMC Systems Biology

Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A

(2011) M. N. Benedict et al.   JOURNAL OF BACTERIOLOGY

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

(2011) Jan Schellenberger et al.   Nature Protocols

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

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

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Metabolic engineering ofClostridium acetobutylicumM5 for highly selective butanol production

(2009) Jin Young Lee et al.   Biotechnology Journal

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

(2009) Caroline B. Milne et al.   Biotechnology Journal

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study

(2009) Reed Taffs et al.   BMC Systems Biology

Comparative Genome-Scale Metabolic Reconstruction and Flux Balance Analysis of Multiple Staphylococcus aureus Genomes Identify Novel Antimicrobial Drug Targets

(2009) D.-S. Lee et al.   JOURNAL OF BACTERIOLOGY

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

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

(2009) Christopher S Henry et al.   GENOME BIOLOGY

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

Large-scale transposon mutagenesis ofMycoplasma pulmonis

(2008) Christopher T. French et al.   MOLECULAR MICROBIOLOGY