Rethinking glycolysis: on the biochemical logic of metabolic pathways, Nat Chem Biol, vol.8, pp.509-517, 2012. ,
Metabolic footprinting of mutant libraries to map metabolite utilization to genotype, ACS Chem Biol, vol.8, pp.189-199, 2013. ,
13 C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation, PLoS Pathog, vol.7, p.1002091, 2011. ,
Alternative Methods of Regression, 1993. ,
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast, Sci Signal, vol.3, p.4, 2010. ,
Dynamics of glycolytic regulation during adaptation of Saccharomyces cerevisiae to fermentative metabolism, Appl Environ Microbiol, vol.74, pp.5710-5723, 2008. ,
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism, Science, vol.335, pp.1099-1103, 2012. ,
Ultrahigh performance liquid chromatography À tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites, Anal Chem, vol.82, pp.4403-4412, 2010. ,
Regulatory architecture determines optimal regulation of gene expression in metabolic pathways, Proc Natl Acad Sci, vol.109, pp.5127-5132, 2012. ,
The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels, Proc Natl Acad Sci, vol.104, pp.15753-15758, 2007. ,
Bacillus subtilis metabolism and energetics in carbon-limited and excess-carbon chemostat culture, J Bacteriol, vol.183, pp.7308-7317, 2001. ,
Regulation of the central glycolytic genes in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate, Mol Microbiol, vol.47, pp.1709-1721, 2003. ,
Transcriptional, translational and metabolic regulation of glycolysis in Lactococcus lactis subsp. cremoris MG 1363 grown in continuous acidic cultures, Microbiology, vol.149, pp.1935-1944, 2003. ,
Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis, J Bacteriol, vol.184, pp.2500-2520, 2002. ,
Physiological control of metabolic flux: the requirement for multisite modulation, Biochem J, vol.311, pp.35-39, 1995. ,
Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast, Mol Syst Biol, vol.6, p.432, 2010. ,
Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS, Eur J Biochem, vol.270, pp.880-891, 2003. ,
Glycolytic strategy as a tradeoff between energy yield and protein cost, Proc Natl Acad Sci, vol.110, pp.10039-10044, 2013. ,
, Transcription regulation of central carbon metabolism V Chubukov et al
Complex coordination of multi-scale cellular responses to environmental stress, Mol BioSyst, vol.7, pp.731-741, 2011. ,
High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry, Anal Chem, vol.83, pp.7074-7080, 2011. ,
Purification and properties of fructose-1,6-bisphosphatase of Bacillus subtilis, J Biol Chem, vol.254, pp.5340-5349, 1979. ,
Identification and expression of the Bacillus subtilis fructose-1,6-bisphosphatase gene (fbp), J Bacteriol, vol.180, pp.4309-4313, 1998. ,
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae, Mol Syst Biol, vol.6, p.430, 2010. ,
Regulation and control of metabolic fluxes in microbes, Curr Opin Biotechnol, vol.22, pp.566-575, 2011. ,
Achieving optimal growth through product feedback inhibition in metabolism, PLoS Comput Biol, vol.6, p.1000802, 2010. ,
Simultaneous genomic overexpression of seven glycolytic enzymes in the yeast Saccharomyces cerevisiae, Enzyme Microb Technol, vol.26, pp.688-698, 2000. ,
Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli, Mol Syst Biol, vol.7, p.477, 2011. ,
Genetic regulatory mechanisms in the synthesis of proteins, J Mol Biol, vol.3, pp.318-356, 1961. ,
Estimating regression coefficients by minimizing the dispersion of the residuals, Ann Math Stat, vol.43, pp.1449-1458, 1972. ,
Identification of two distinct Bacillus subtilis citrate synthase genes, J Bacteriol, vol.176, pp.4669-4679, 1994. ,
A universal method for achieving increases in metabolite production, Eur J Biochem, vol.216, pp.361-367, 1993. ,
Metabolic fluxes during strong carbon catabolite repression by malate in Bacillus subtilis, J Biol Chem, vol.285, pp.1587-1596, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-02663413
Growth rate-dependent global effects on gene expression in bacteria, Cell, vol.139, pp.1366-1375, 2009. ,
Somewhat in controlthe role of transcription in regulating metabolic fluxes, Curr Opin Biotechnol, vol.24, pp.987-993, 2013. ,
Functioning of a metabolic flux sensor in Escherichia coli, Proc Natl Acad Sci, vol.110, pp.1130-1135, 2013. ,
Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses, Cell, vol.143, pp.639-650, 2010. ,
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis, Mol Cell Proteomics, vol.6, pp.697-707, 2007. ,
Shifts in growth strategies reflect tradeoffs in cellular economics, Mol Syst Biol, vol.5, p.323, 2009. ,
Conditiondependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis, Science, vol.335, pp.1103-1106, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01000245
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data, J Biol Chem, vol.282, pp.28791-28799, 2007. ,
Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation, J Biol Chem, vol.283, pp.23524-23532, 2008. ,
Indirect and suboptimal control of gene expression is widespread in bacteria, Mol Syst Biol, vol.9, p.660, 2013. ,
Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase, Biochemistry, vol.47, pp.5881-5888, 2008. ,
Stochastic gene expression and its consequences, Cell, vol.135, pp.216-226, 2008. ,
Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response, Nat Biotechnol, vol.27, pp.604-605, 2009. ,
Mixed and diverse metabolic and gene-expression regulation of the glycolytic and fermentative pathways in response to a HXK2 deletion in Saccharomyces cerevisiae, FEMS Yeast Res, vol.8, pp.155-164, 2008. ,
Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae, FEMS Yeast Res, vol.5, pp.611-619, 2005. ,
Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae, Proc Natl Acad Sci, vol.103, pp.2166-2171, 2006. ,
Recasting nonlinear differential equations as S-systems: a canonical nonlinear form, Math Biosci, vol.87, pp.83-115, 1987. ,
Transcriptional and metabolic responses of Bacillus subtilis to the availability of organic acids: Transcription regulation is important but not sufficient to account for metabolic adaptation, Appl Environ Microbiol, vol.73, pp.499-507, 2007. ,
Interdependence of cell growth and gene expression: origins and consequences, Science, vol.330, pp.1099-1102, 2010. ,
CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of Bacillus subtilis gluconeogenic genes, Mol Microbiol, vol.55, pp.1435-1451, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-02683556
Principles of transcriptional regulation and evolution of the metabolic system in E. coli, Genome Res, vol.19, pp.79-91, 2009. ,
Getting started in gene expression microarray analysis, PLoS Comput Biol, vol.5, p.1000543, 2009. ,
Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway, FEBS Lett, vol.500, pp.169-171, 2001. ,
Maintenance metabolism and carbon fluxes in Bacillus species, Microb Cell Fact, vol.7, p.19, 2008. ,
CcpN controls central carbon fluxes in Bacillus subtilis, J Bacteriol, vol.190, pp.6178-6187, 2008. ,
Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker's yeast, FEBS J, vol.276, pp.5521-5536, 2009. ,
Chapter twenty-seven-quantitative analysis of flux regulation through hierarchical regulation analysis, pp.571-595, 2011. ,
Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of 13C-labeled primary metabolites, FEMS Yeast Res, vol.5, pp.559-568, 2005. ,
Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors, J Theor Biol, vol.165, pp.477-502, 1993. ,
Design of gene circuits: lessons from bacteria, Nat Rev Genet, vol.5, pp.34-42, 2004. ,
Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux, Science, vol.327, pp.1004-1007, 2010. ,
RNA-Seq: a revolutionary tool for transcriptomics, Nat Rev Genet, vol.10, pp.57-63, 2009. ,
Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems, Biotechnol Bioeng, vol.66, pp.69-85, 1999. ,
Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase, Nat Chem Biol, vol.8, pp.562-568, 2012. ,
)C-based metabolic flux analysis, Nat Protoc, vol.4, issue.13, pp.878-892, 2009. ,
Inducer-modulated cooperative binding of the tetrameric CggR repressor to operator DNA, Biophys J, vol.92, pp.3215-3227, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00164236
Just-in-time transcription program in metabolic pathways, Nat Genet, vol.36, pp.486-491, 2004. ,
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