Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

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

Biofuel production improvement with genome-scale models: The role of cell composition

(2010) Ryan S. Senger   Biotechnology Journal

Resolving the TCA cycle and pentose-phosphate pathway of Clostridium acetobutylicum ATCC 824: Isotopomer analysis, in vitro activities and expression analysis

(2010) Scott B. Crown et al.   Biotechnology Journal

Systems-Level Metabolic Flux Profiling Elucidates a Complete, Bifurcated Tricarboxylic Acid Cycle in Clostridium acetobutylicum

(2010) D. Amador-Noguez et al.   JOURNAL OF BACTERIOLOGY

Targeting multiple targets inPseudomonas aeruginosaPAO1 using flux balance analysis of a reconstructed genome-scale metabolic network

(2010) Deepak Perumal et al.   JOURNAL OF DRUG TARGETING

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

(2010) Radhakrishnan Mahadevan et al.   NATURE REVIEWS MICROBIOLOGY

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

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

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

Genome Scale Reconstruction of a Salmonella Metabolic Model

(2009) Manal AbuOun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE

(2009) Hyun Uk Kim et al.   Molecular BioSystems

NADH Availability Limits Asymmetric Biocatalytic Epoxidation in a Growing Recombinant Escherichia coli Strain

(2008) B. Buhler et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

(2008) Joungmin Lee et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

(2008) Matthew D. Jankowski et al.   BIOPHYSICAL JOURNAL

Genome-scale model forClostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems

(2008) Ryan S. Senger et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome-scale model forClostridium acetobutylicum: Part I. Metabolic network resolution and analysis

(2008) Ryan S. Senger et al.   BIOTECHNOLOGY AND BIOENGINEERING

Aldehyde-alcohol dehydrogenase and/or thiolase overexpression coupled with CoA transferase downregulation lead to higher alcohol titers and selectivity inClostridium acetobutylicumfermentations

(2008) Ryan Sillers et al.   BIOTECHNOLOGY AND BIOENGINEERING

Metabolic engineering of the non-sporulating, non-solventogenic Clostridium acetobutylicum strain M5 to produce butanol without acetone demonstrate the robustness of the acid-formation pathways and the importance of the electron balance

(2008) Ryan Sillers et al.   METABOLIC ENGINEERING

The genomic and epidemiological dynamics of human influenza A virus

(2008) Andrew Rambaut et al.   NATURE

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

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

The transcriptional program underlying the physiology of clostridial sporulation

(2008) Shawn W Jones et al.   GENOME BIOLOGY

Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism

(2007) Orland Gonzalez et al.   Molecular BioSystems