MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models

Construction and completion of flux balance models from pathway databases

(2012) Mario Latendresse et al.   BIOINFORMATICS

Computational tools for the synthetic design of biochemical pathways

(2012) Marnix H. Medema et al.   NATURE REVIEWS MICROBIOLOGY

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

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

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

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

(2011) Mohammad Tauqeer Alam et al.   FEBS LETTERS

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

(2011) Jan Schellenberger et al.   Nature Protocols

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

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

Development of a Genetic System for Combinatorial Biosynthesis of Lipopeptides in Streptomyces fradiae and Heterologous Expression of the A54145 Biosynthesis Gene Cluster

(2010) D. C. Alexander et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Heterologous Expression of the Oxytetracycline Biosynthetic Pathway in Myxococcus xanthus

(2010) D. C. Stevens et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

S-Adenosylmethionine (SAM) and antibiotic biosynthesis: effect of external addition of SAM and of overexpression of SAM biosynthesis genes on novobiocin production in Streptomyces

(2010) Xin Qing Zhao et al.   ARCHIVES OF MICROBIOLOGY

SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

(2010) A. Gevorgyan et al.   BIOINFORMATICS

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

(2010) Mohammad T Alam et al.   BMC GENOMICS

The dynamic architecture of the metabolic switch in Streptomyces coelicolor

(2010) Kay Nieselt et al.   BMC GENOMICS

The biomass objective function

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

Metabolic Network Analysis of Pseudomonas aeruginosa during Chronic Cystic Fibrosis Lung Infection

(2010) M. A. Oberhardt et al.   JOURNAL OF BACTERIOLOGY

Soft constraints-based multiobjective framework for flux balance analysis

(2010) Deepak Nagrath et al.   METABOLIC ENGINEERING

Modeling and optimization of a multi-product biosynthesis factory for multiple objectives

(2010) Fook Choon Lee et al.   METABOLIC ENGINEERING

Comparative Analysis of Metabolic Networks Provides Insight into the Evolution of Plant Pathogenic and Nonpathogenic Lifestyles in Pseudomonas

(2010) A. Mithani et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms

(2010) Marnix H. Medema et al.   NATURE REVIEWS MICROBIOLOGY

Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus

(2010) Marnix H. Medema et al.   Microbial Biotechnology

Mycobacterium versus Streptomyces—we are different, we are the same

(2009) Nicole Scherr et al.   CURRENT OPINION IN MICROBIOLOGY

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

(2009) Adam M. Feist et al.   METABOLIC ENGINEERING

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Antibiotics for Emerging Pathogens

(2009) M. A. Fischbach et al.   SCIENCE

Redirection of flux through the FPP branch-point inSaccharomyces cerevisiaeby down-regulating squalene synthase

(2008) Eric M. Paradise et al.   BIOTECHNOLOGY AND BIOENGINEERING

Reconstruction of biochemical networks in microorganisms

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

New surveyor tools for charting microbial metabolic maps

(2007) Rainer Breitling et al.   NATURE REVIEWS MICROBIOLOGY