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

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

(2013) Brian J. Schmidt et al.   BIOINFORMATICS

Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites

(2013) Kyu-Sang Hwang et al.   BIOTECHNOLOGY ADVANCES

Genomically and biochemically accurate metabolic reconstruction ofMethanosarcina barkeriFusaro, iMG746

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

Engineering precursor metabolite pools for increasing production of antitumor mithramycins in Streptomyces argillaceus

(2013) Daniel Zabala et al.   METABOLIC ENGINEERING

Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement

(2013) Di Huang et al.   Microbial Cell Factories

Molecular Regulation of Antibiotic Biosynthesis in Streptomyces

(2013) G. Liu et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

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

Characterization of a new ScbR-like γ-butyrolactone binding regulator (SlbR) in Streptomyces coelicolor

(2012) Yung-Hun Yang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

In silico aided metabolic engineering of Streptomyces roseosporus for daptomycin yield improvement

(2012) Di Huang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Combined in silico modeling and metabolomics analysis to characterize fed-batch CHO cell culture

(2012) Suresh Selvarasu et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome-scale metabolic flux analysis of Streptomyces lividans growing on a complex medium

(2012) Pieter-Jan D’Huys et al.   JOURNAL OF BIOTECHNOLOGY

Fifteen years of large scale metabolic modeling of yeast: Developments and impacts

(2011) Tobias Österlund et al.   BIOTECHNOLOGY ADVANCES

Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803

(2011) Arnau Montagud et al.   Biotechnology Journal

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization

(2011) Richard A Lewis et al.   BMC GENOMICS

Recent advances in reconstruction and applications of genome-scale metabolic models

(2011) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Streptomyces coelicolor RedP and FabH enzymes, initiating undecylprodiginine and fatty acid biosynthesis, exhibit distinct acyl-CoA and malonyl-acyl carrier protein substrate specificities

(2011) Renu Singh et al.   FEMS MICROBIOLOGY LETTERS

EMILiO: A fast algorithm for genome-scale strain design

(2011) Laurence Yang et al.   METABOLIC ENGINEERING

Economics of membrane occupancy and respiro-fermentation

(2011) K. Zhuang et al.   Molecular 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

Fumarate Reductase Activity Maintains an Energized Membrane in Anaerobic Mycobacterium tuberculosis

(2011) Shinya Watanabe et al.   PLoS Pathogens

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

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

In silicogenome-scale metabolic analysis ofPseudomonas putidaKT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival

(2010) Seung Bum Sohn et al.   Biotechnology Journal

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

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

(2010) Mohammad T Alam et al.   BMC GENOMICS

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

(2010) Isabel Rocha et al.   BMC Systems Biology

Amino acid uptake profiling of wild type and recombinant Streptomyces lividans TK24 batch fermentations

(2010) Pieter-Jan D’Huys et al.   JOURNAL OF 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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

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

(2009) Christopher S Henry et al.   GENOME BIOLOGY

Antibiotic Overproduction inStreptomyces coelicolorA3(2) Mediated by Phosphofructokinase Deletion

(2008) Irina Borodina et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Branched-chain amino acid catabolism provides precursors for the Type II polyketide antibiotic, actinorhodin, via pathways that are nutrient dependent

(2008) Karen Stirrett et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Selection of objective function in genome scale flux balance analysis for process feed development in antibiotic production

(2008) Chiraphan Khannapho et al.   METABOLIC ENGINEERING

An Alternative Menaquinone Biosynthetic Pathway Operating in Microorganisms

(2008) T. Hiratsuka et al.   SCIENCE