Identification of Functional Differences in Metabolic Networks Using Comparative Genomics and Constraint-Based Models

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

(2011) Colin T Archer et al.   BMC GENOMICS

Constraint-based modeling analysis of the metabolism of two Pelobacter species

(2011) Jun Sun et al.   BMC Systems Biology

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans

(2011) Vinay Satish Kumar et al.   BMC Systems Biology

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

Photosynthesis driven conversion of carbon dioxide to fatty alcohols and hydrocarbons in cyanobacteria

(2011) Xiaoming Tan et al.   METABOLIC ENGINEERING

EMILiO: A fast algorithm for genome-scale strain design

(2011) Laurence Yang et al.   METABOLIC ENGINEERING

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

(2011) H. U. Kim et al.   Molecular Systems Biology

Large-Scale Bi-Level Strain Design Approaches and Mixed-Integer Programming Solution Techniques

(2011) Joonhoon Kim et al.   PLoS One

Fatty acid production in genetically modified cyanobacteria

(2011) X. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

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

Characterization of Nicotinamidases: Steady State Kinetic Parameters, Classwide Inhibition by Nicotinaldehydes, and Catalytic Mechanism

(2010) Jarrod B. French et al.   BIOCHEMISTRY

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

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

(2010) Arnau Montagud et al.   BMC Systems Biology

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

(2010) Joonhoon Kim et al.   BMC Systems Biology

Manipulating redox and ATP balancing for improved production of succinate in E. coli

(2010) Amarjeet Singh et al.   METABOLIC ENGINEERING

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

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

The Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth

(2010) Henning Knoop et al.   PLANT PHYSIOLOGY

Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation

(2010) Grigoriy E. Pinchuk et al.   PLoS Computational Biology

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

(2009) N. Tepper et al.   BIOINFORMATICS

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

(2009) Anu Raghunathan et al.   BMC Systems Biology

Genome-scale constraint-based modeling of Geobacter metallireducens

(2009) Jun Sun et al.   BMC Systems Biology

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Engineering a platform for photosynthetic isoprene production in cyanobacteria, using Synechocystis as the model organism

(2009) Pia Lindberg et al.   METABOLIC ENGINEERING

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

Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde

(2009) Shota Atsumi et al.   NATURE BIOTECHNOLOGY

Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis

(2009) Pooja Arora et al.   Nature Chemical Biology

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

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Has nature already identified all useful antibacterial targets?

(2008) Dirk Bumann   CURRENT OPINION IN MICROBIOLOGY

Genome-scale modeling ofSynechocystissp. PCC 6803 and prediction of pathway insertion

(2008) Pengcheng Fu   JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY

Inhibition of Siderophore Biosynthesis inMycobacterium tuberculosiswith Nucleoside Bisubstrate Analogues: Structure−Activity Relationships of the Nucleobase Domain of 5′-O-[N-(Salicyl)sulfamoyl]adenosine

(2008) João Neres et al.   JOURNAL OF MEDICINAL CHEMISTRY

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY