In silico profiling of cell growth and succinate production in Escherichia coli NZN111

[1]  Y. Jang,et al.  Production of succinic acid by metabolically engineered microorganisms. , 2016, Current opinion in biotechnology.

[2]  Qiang Hua,et al.  In silico identification of gene amplification targets based on analysis of production and growth coupling , 2016, Biosyst..

[3]  Qiang Hua,et al.  IdealKnock: A framework for efficiently identifying knockout strategies leading to targeted overproduction , 2016, Comput. Biol. Chem..

[4]  Sang Yup Lee,et al.  Flux-sum analysis identifies metabolite targets for strain improvement , 2015, BMC Systems Biology.

[5]  Meiyappan Lakshmanan,et al.  In silico model-driven cofactor engineering strategies for improving the overall NADP(H) turnover in microbial cell factories , 2015, Journal of Industrial Microbiology & Biotechnology.

[6]  Kazuyuki Shimizu,et al.  Current status and future perspectives of kinetic modeling for the cell metabolism with incorporation of the metabolic regulation mechanism , 2015, Bioresources and Bioprocessing.

[7]  Takashi Ishida,et al.  Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures , 2015, BMC Systems Biology.

[8]  B. Palsson,et al.  Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods , 2012, Nature Reviews Microbiology.

[9]  Bernhard O. Palsson,et al.  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions , 2010, BMC Bioinformatics.

[10]  Xing-Ming Zhao,et al.  APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility , 2010, BMC Bioinformatics.

[11]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[12]  P. Wei,et al.  Effect of Growth Phase Feeding Strategies on Succinate Production by Metabolically Engineered Escherichia coli , 2009, Applied and Environmental Microbiology.

[13]  Dong-Yup Lee,et al.  Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network , 2009, BMC Systems Biology.

[14]  Ryan T Gill,et al.  Genes restoring redox balance in fermentation-deficient E. coli NZN111. , 2009, Metabolic engineering.

[15]  Jan Schellenberger,et al.  Use of Randomized Sampling for Analysis of Metabolic Networks* , 2009, Journal of Biological Chemistry.

[16]  Zhimin Li,et al.  Production of succinate by a pflB ldhA double mutant of Escherichia coli overexpressing malate dehydrogenase , 2009, Bioprocess and biosystems engineering.

[17]  Holger Fröhlich,et al.  Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance , 2009, BMC Systems Biology.

[18]  Q. Ye,et al.  Improved Succinic Acid Production in the Anaerobic Culture of an Escherichia coli pflB ldhA Double Mutant as a Result of Enhanced Anaplerotic Activities in the Preceding Aerobic Culture , 2007, Applied and Environmental Microbiology.

[19]  David K. Johnson,et al.  Top Value-Added Chemicals from Biomass - Volume II—Results of Screening for Potential Candidates from Biorefinery Lignin , 2007 .

[20]  Pei Yee Ho,et al.  Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations , 2007, Science.

[21]  E. Somersalo,et al.  Statistical Analysis of Metabolic Pathways of Brain Metabolism at Steady State , 2007, Annals of Biomedical Engineering.

[22]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[23]  Neema Jamshidi,et al.  Systems biology of SNPs , 2006, Molecular systems biology.

[24]  G. Bennett,et al.  Enhancement of lactate and succinate formation in adhE or pta‐ackA mutants of NADH dehydrogenase‐deficient Escherichia coli , 2005, Journal of applied microbiology.

[25]  B. Palsson,et al.  Candidate Metabolic Network States in Human Mitochondria , 2005, Journal of Biological Chemistry.

[26]  Bernhard O Palsson,et al.  Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. , 2004, Trends in biochemical sciences.

[27]  B. Palsson,et al.  Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. , 2004, Biophysical journal.

[28]  K. Shimizu,et al.  The effect of pfl gene knockout on the metabolism for optically pure d-lactate production by Escherichia coli , 2004, Applied Microbiology and Biotechnology.

[29]  A. Barabasi,et al.  Global organization of metabolic fluxes in the bacterium Escherichia coli , 2004, Nature.

[30]  A. Burgard,et al.  Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization , 2003, Biotechnology and bioengineering.

[31]  B. Palsson,et al.  Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[32]  G. Bennett,et al.  The effect of increasing NADH availability on the redistribution of metabolic fluxes in Escherichia coli chemostat cultures. , 2002, Metabolic engineering.

[33]  Ka-Yiu San,et al.  Metabolic engineering of Escherichia coli: increase of NADH availability by overexpressing an NAD(+)-dependent formate dehydrogenase. , 2002, Metabolic engineering.

[34]  David P. Clark,et al.  Mutation of the ptsG Gene Results in Increased Production of Succinate in Fermentation of Glucose byEscherichia coli , 2001, Applied and Environmental Microbiology.

[35]  G. Bennett,et al.  Effect of inactivation of nuo and ackA-pta on redistribution of metabolic fluxes in Escherichia coli. , 1999, Biotechnology and bioengineering.

[36]  Svetlana Alexeeva,et al.  The Steady-State Internal Redox State (NADH/NAD) Reflects the External Redox State and Is Correlated with Catabolic Adaptation in Escherichia coli , 1999, Journal of bacteriology.

[37]  L. Stols,et al.  Production of succinic acid through overexpression of NAD(+)-dependent malic enzyme in an Escherichia coli mutant , 1997, Applied and environmental microbiology.

[38]  C. S. Millard,et al.  Enhanced production of succinic acid by overexpression of phosphoenolpyruvate carboxylase in Escherichia coli , 1996, Applied and environmental microbiology.

[39]  D. Clark,et al.  Mutants of Escherichia coli deficient in the fermentative lactate dehydrogenase , 1989, Journal of bacteriology.

[40]  J. Trevors,et al.  Genetic improvement of native xylose-fermenting yeasts for ethanol production , 2014, Journal of Industrial Microbiology & Biotechnology.

[41]  V. Hatzimanikatis,et al.  Manipulating redox and ATP balancing for improved production of succinate in E. coli. , 2011, Metabolic engineering.

[42]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[43]  G. Bennett,et al.  Metabolic flux analysis of Escherichia coli deficient in the acetate production pathway and expressing the Bacillus subtilis acetolactate synthase. , 1999, Metabolic engineering.

[44]  George N. Bennett,et al.  Metabolic Flux Analysis ofEscherichia coliDeficient in the Acetate Production Pathway and Expressing theBacillus subtilisAcetolactate Synthase , 1999 .

[45]  Robert L. Smith,et al.  Direction Choice for Accelerated Convergence in Hit-and-Run Sampling , 1998, Oper. Res..

[46]  D. Clark,et al.  The ldhA gene encoding the fermentative lactate dehydrogenase of Escherichia coli. , 1997, Microbiology.

[47]  David P. Clark,et al.  The IdhA Gene Encoding the Fermentative Lactate Dehydrogenase of Escherichia Coli , 1997 .