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Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism

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Escherichia coli metabolism under short-term repetitive substrate dynamics: adaptation and trade-offs

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Genomic diversity across the Rickettsia and ‘Candidatus Megaira’ genera and proposal of genus status for the Torix group

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CRISPR interference screens reveal growth–robustness tradeoffs inSynechocystissp. PCC 6803 across growth conditions

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Microbial physiological engineering increases the efficiency of microbial cell factories

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Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RubisCO) Is Essential for Growth of the Methanotroph Methylococcus capsulatus Strain Bath

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Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism

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Relationship between myo-inositol synthesis and carbohydrate metabolism changes in Mozambique tilapia (Oreochromis mossambicus) under acute hypersaline stress

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Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms

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Quantitative modeling of pentose phosphate pathway response to oxidative stress reveals a cooperative regulatory strategy

Hurbain, J., Thommen, Q., Anquez, F., & Pfeuty, B. (2022) · iScience · doi:10.1016/j.isci.2022.104681 · Cited by 37 · see citing works

Functional decomposition of metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions

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ROS-induced stress promotes enrichment and emergence of antibiotic resistance in conventional activated sludge processes

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Milligrams to kilograms: making microbes work at scale

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Dynamic Metabolomics for Engineering Biology: Accelerating Learning Cycles for Bioproduction

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Expanding the search for small-molecule antibacterials by multidimensional profiling

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Why is manganese so valuable to bacterial pathogens?

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Global insights into intermediate metabolites: Signaling, metabolic divergence and stress response modulation in plants

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Eat in or Take out? Metabolism of Intracellular Salmonella enterica

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Microbes with higher metabolic independence are enriched in human gut microbiomes under stressPreprint

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From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline

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Kinetic modeling of metabolism: Present and future

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Elucidating yeast glycolytic dynamics at steady state growth and glucose pulses through kinetic metabolic modeling

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Metabolomics and Microbial Metabolism: Toward a Systematic Understanding

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Dark accumulation of downstream glycolytic intermediates initiates robust photosynthesis in cyanobacteria

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Inside the phagosome: A bacterial perspective

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Fundamental Differences in Inactivation Mechanisms of Escherichia coli O157:H7 Between Chlorine Dioxide and Sodium Hypochlorite

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Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by Pseudomonas putida

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Redefining the Clostridioides difficile σ B Regulon: σ B Activates Genes Involved in Detoxifying Radicals That Can Result from the Exposure to Antimicrobials and Hydrogen Peroxide

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Metabolic plasticity enables lifestyle transitions of Porphyromonas gingivalis

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Is Galactose a Hormetic Sugar? An Exploratory Study of the Rat Hippocampal Redox Regulatory Network

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A critical bioenergetic switch is regulated by IGF2 during murine cartilage development

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The antenna-like domain of the cyanobacterial ferrochelatase can bind chlorophyll and carotenoids in an energy-dissipative configuration

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Design of microbial catalysts for two-stage processes

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Role of Premycofactocin Synthase in Growth, Microaerophilic Adaptation, and Metabolism of Mycobacterium tuberculosis

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Lactic acid fermentation: A maladaptive mechanism and an evolutionary throwback boosting cancer drug resistance

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Microbes with higher metabolic independence are enriched in human gut microbiomes under stress

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Engineering of Biosynthesis Pathway and NADPH Supply for Improved L-5-Methyltetrahydrofolate Production by Lactococcus lactis

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Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance

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Yeast increases glycolytic flux to support higher growth rates accompanied by decreased metabolite regulation and lower protein phosphorylation

Chen, M., Xie, T., Li, H., Zhuang, Y., Xia, J., & Nielsen, J. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2302779120 · Cited by 21 · see citing works

Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli

Bruckbauer, S. T., Minkoff, B. B., Yu, D., Cryns, V. L., Cox, M. M., & Sussman, M. R. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra120.002092 · Cited by 21 · see citing works

Analogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic Growth

Wilkes, R. A., Waldbauer, J., & Aristilde, L. (2021) · mBio · doi:10.1128/mbio.03259-21 · Cited by 21 · see citing works

Identifying metabolic features and engineering targets for productivity improvement in CHO cells by integrated transcriptomics and genome-scale metabolic model

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Enzymes of glycolysis and the pentose phosphate pathway as targets of oxidants: Role of redox reactions on the carbohydrate catabolism

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Dissolved iron released from nanoscale zero-valent iron (nZVI) activates the defense system in bacterium Pseudomonas putida, leading to high tolerance to oxidative stress

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Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast

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Dynamics in redox metabolism, from stoichiometry towards kinetics

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Beyond Resistance: Tolerance and Resilience of Bacteria to Photodynamic and Oxidative Stress

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Role of FruR transcriptional regulator in virulence of Listeria monocytogenes and identification of its regulon

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The Mar, Sox, and Rob Systems

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Effects of overexpression of STB5 in Saccharomyces cerevisiae on fatty acid biosynthesis, physiology and transcriptome

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A systems-level, semi-quantitative landscape of metabolic flux in C. elegans

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Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model

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Toxic reactive oxygen species stresses for reconfiguring central carbon metabolic fluxes in foodborne bacteria: Sources, mechanisms and pathways

Cheng, J., Zou, S., Ma, J., & Sun, D. (2023) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2023.2169245 · Cited by 16 · see citing works

From the metabolic profiling of drug response to drug mode of action

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Novel allosteric inhibition of phosphoribulokinase identified by ensemble kinetic modeling of Synechocystis sp. PCC 6803 metabolism

Nishiguchi, H., Liao, J. C., Shimizu, H., & Matsuda, F. (2020) · Metabolic Engineering Communications · doi:10.1016/j.mec.2020.e00153 · Cited by 15 · see citing works

Unraveling the Role of Acetic Acid Bacteria Comparing Two Acetification Profiles From Natural Raw Materials: A Quantitative Approach in Komagataeibacter europaeus

Román‐Camacho, J. J., Mauricio, J. C., Santos‐Dueñas, I. M., García‐Martínez, T., & García‐García, I. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.840119 · Cited by 15 · see citing works

Protein cost allocation explains metabolic strategies in Escherichia coli

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Competitive oxidation of key pentose phosphate pathway enzymes modulates the fate of intermediates and NAPDH production

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Identifying the Growth Modulon of Corynebacterium glutamicum

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Comparative 13C‐metabolic flux analysis indicates elevation of ATP regeneration, carbon dioxide, and heat production in industrial Saccharomyces cerevisiae strains

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Dynamic models for metabolomics data integration

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Disrupting Central Carbon Metabolism Increases β-Lactam Antibiotic Susceptibility in Vibrio cholerae

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Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

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Optimized expression of Hfq protein increases Escherichia coli growth

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Model Balancing: A Search for In-Vivo Kinetic Constants and Consistent Metabolic States

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Bayesian Regression Facilitates Quantitative Modeling of Cell Metabolism

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Quantitative metabolic fluxes regulated by trans-omic networks

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Reserve Flux Capacity in the Pentose Phosphate Pathway by NADPH Binding Is Conserved across Kingdoms

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Activation of the pentose phosphate pathway flux by hydrogen peroxide is not regulated by NADPH‐mediated feedback inhibition

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Acute stimulation of glucose metabolism by H2O2 sustains the NADPH steady-state under oxidative stress

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Acute stimulation of glucose metabolism by H₂O₂ sustains the NADPH steady-state under oxidative stressPreprint

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Quantitative modeling of pentose phosphate pathway response to oxidative stress reveals a cooperative regulatory strategy

Hurbain, J., Thommen, Q., Anquez, F., & Pfeuty, B. (2022) · iScience · doi:10.1016/j.isci.2022.104681 · Cited by 37 · see citing works