Published in Mol Biosyst on September 02, 2009
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC Syst Biol (2010) 1.35
Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement. Microb Cell Fact (2010) 1.23
Using the reconstructed genome-scale human metabolic network to study physiology and pathology. J Intern Med (2012) 1.20
Responses to light intensity in a genome-scale model of rice metabolism. Plant Physiol (2013) 1.02
The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies. Microb Cell Fact (2010) 0.95
MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC Syst Biol (2011) 0.93
A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm. PLoS One (2012) 0.85
Mathematical and statistical modeling in cancer systems biology. Front Physiol (2012) 0.81
Advanced stoichiometric analysis of metabolic networks of mammalian systems. Crit Rev Biomed Eng (2011) 0.80
Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27. Microb Cell Fact (2014) 0.79
Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth. BMC Syst Biol (2012) 0.78
Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models. Metabolites (2015) 0.77
Systems biology approaches for studying the pathogenesis of non-alcoholic fatty liver disease. World J Gastroenterol (2014) 0.77
Modeling the differences in biochemical capabilities of pseudomonas species by flux balance analysis: how good are genome-scale metabolic networks at predicting the differences? ScientificWorldJournal (2014) 0.76
Gene duplication and phenotypic changes in the evolution of mammalian metabolic networks. PLoS One (2014) 0.75
Metabolic processes of Methanococcus maripaludis and potential applications. Microb Cell Fact (2016) 0.75
Cooperative metabolism in a three-partner insect-bacterial symbiosis revealed by metabolic modeling. J Bacteriol (2017) 0.75
Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl Environ Microbiol (2005) 2.13
Systems biotechnology for strain improvement. Trends Biotechnol (2005) 1.98
Metabolite essentiality elucidates robustness of Escherichia coli metabolism. Proc Natl Acad Sci U S A (2007) 1.26
Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement. Microb Cell Fact (2010) 1.23
WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model. Bioinformatics (2009) 1.17
Combined in silico modeling and metabolomics analysis to characterize fed-batch CHO cell culture. Biotechnol Bioeng (2012) 1.17
BioSilico: an integrated metabolic database system. Bioinformatics (2004) 1.12
Software applications for flux balance analysis. Brief Bioinform (2012) 1.06
Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells. PLoS One (2011) 0.99
Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis. Biotechnol Bioeng (2010) 0.95
Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network. BMC Syst Biol (2009) 0.94
Flux-based analysis of sulfur metabolism in desulfurizing strains of Rhodococcus erythropolis. FEMS Microbiol Lett (2010) 0.94
Exploring the effects of carbon sources on the metabolic capacity for shikimic acid production in Escherichia coli using in silico metabolic predictions. J Microbiol Biotechnol (2008) 0.92
Centralized modularity of N-linked glycosylation pathways in mammalian cells. PLoS One (2009) 0.92
Elucidating rice cell metabolism under flooding and drought stresses using flux-based modeling and analysis. Plant Physiol (2013) 0.88
LC-MS-based metabolic characterization of high monoclonal antibody-producing Chinese hamster ovary cells. Biotechnol Bioeng (2012) 0.87
Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis. Biotechnol Prog (2009) 0.87
Multiobjective flux balancing using the NISE method for metabolic network analysis. Biotechnol Prog (2009) 0.86
MetaFluxNet, a program package for metabolic pathway construction and analysis, and its use in large-scale metabolic flux analysis of Escherichia coli. Genome Inform (2003) 0.86
Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants. J Biotechnol (2007) 0.85
Computational codon optimization of synthetic gene for protein expression. BMC Syst Biol (2012) 0.85
Integrated transcriptome and binding sites analysis implicates E2F in the regulation of self-renewal in human pluripotent stem cells. PLoS One (2011) 0.85
Modeling and optimization of a multi-product biosynthesis factory for multiple objectives. Metab Eng (2010) 0.84
Characterizing Escherichia coli DH5alpha growth and metabolism in a complex medium using genome-scale flux analysis. Biotechnol Bioeng (2009) 0.84
Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: overexpression of malate dehydrogenase II. J Biotechnol (2010) 0.83
Web-based applications for building, managing and analysing kinetic models of biological systems. Brief Bioinform (2008) 0.82
Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice. Gene (2012) 0.82
Identifying essential genes/reactions of the rice photorespiration by in silico model-based analysis. Rice (N Y) (2013) 0.82
Elucidation of metabolism in hybridoma cells grown in fed-batch culture by genome-scale modeling. Biotechnol Bioeng (2009) 0.81
How necessary is a fast testkit for mitigation of pandemic flu? J R Soc Interface (2009) 0.80
An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins. Bioprocess Biosyst Eng (2008) 0.79
Enhanced production of neuroprogenitors, dopaminergic neurons, and identification of target genes by overexpression of sonic hedgehog in human embryonic stem cells. Stem Cells Dev (2011) 0.79
Overexpression of microRNAs enhances recombinant protein production in Chinese hamster ovary cells. Biotechnol J (2014) 0.79
Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27. Microb Cell Fact (2014) 0.79
MFAML: a standard data structure for representing and exchanging metabolic flux models. Bioinformatics (2005) 0.79
Combined data preprocessing and multivariate statistical analysis characterizes fed-batch culture of mouse hybridoma cells for rational medium design. J Biotechnol (2010) 0.79
Enhanced expression of codon optimized interferon gamma in CHO cells. J Biotechnol (2013) 0.79
Translatome analysis of CHO cells to identify key growth genes. J Biotechnol (2013) 0.79
Cofactor modification analysis: a computational framework to identify cofactor specificity engineering targets for strain improvement. J Bioinform Comput Biol (2013) 0.78
In silico analyses for the discovery of tuberculosis drug targets. J Antimicrob Chemother (2013) 0.78
Mathematical modeling and sensitivity analysis of the integrated TNFα-mediated apoptotic pathway for identifying key regulators. Comput Biol Med (2011) 0.78
NADPH-dependent pgi-gene knockout Escherichia coli metabolism producing shikimate on different carbon sources. FEMS Microbiol Lett (2011) 0.78
Metabolomics-based identification of apoptosis-inducing metabolites in recombinant fed-batch CHO culture media. J Biotechnol (2010) 0.77
Metabolic reconstruction and flux analysis of industrial Pichia yeasts. Appl Microbiol Biotechnol (2013) 0.77
Strain improvement and process development for biobutanol production. Recent Pat Biotechnol (2009) 0.76
Integrative analysis workflow for the structural and functional classification of C-type lectins. BMC Bioinformatics (2011) 0.75