Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks

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Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism

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Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

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Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential

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Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors

(2018) Milenko Tokić et al.   ACS Synthetic Biology

Reserve Flux Capacity in the Pentose Phosphate Pathway Enables Escherichia coli 's Rapid Response to Oxidative Stress

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RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

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Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models

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Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

(2017) Anush Chiappino-Pepe et al.   PLoS Computational Biology

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

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Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants

(2016) Whitney D. Hollinshead et al.   Biotechnology for Biofuels

Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

(2016) Stefano Andreozzi et al.   METABOLIC ENGINEERING

iSCHRUNK – I n S ilico Approach to Ch aracterization and R eduction of Un certainty in the K inetic Models of Genome-scale Metabolic Networks

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Adaptation to different types of stress converge on mitochondrial metabolism

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BRENDA in 2017: new perspectives and new tools in BRENDA

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ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

(2016) Noushin Hadadi et al.   ACS Synthetic Biology

A Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in Pseudomonas putida

(2016) Max Chavarría et al.   mSystems

CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions

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Degradation kinetics and pathway of phenol byPseudomonasandBacillusspecies

(2015) Syed Adnan Hasan et al.   BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT

Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes

(2015) Ljubisa Miskovic et al.   CURRENT OPINION IN BIOTECHNOLOGY

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

(2015) Meric Ataman et al.   CURRENT OPINION IN BIOTECHNOLOGY

Pseudomonas putidaKT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways

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Tolerance engineering in bacteria for the production of advanced biofuels and chemicals

(2015) Aindrila Mukhopadhyay   TRENDS IN MICROBIOLOGY

Network Thermodynamic Curation of Human and Yeast Genome-Scale Metabolic Models

(2014) Verónica S. Martínez et al.   BIOPHYSICAL JOURNAL

Erratum to: A coupled thermodynamic and metabolic control analysis methodology and its evaluation on glycerol biosynthesis in Saccharomyces cerevisiae

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Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models

(2013) Joshua J. Hamilton et al.   BIOPHYSICAL JOURNAL

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints

(2013) Anirikh Chakrabarti et al.   Biotechnology Journal

Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition

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The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

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Extended kinetic model for DBT desulfurization using Pseudomonas Putida CECT5279 in resting cells

(2012) J. Calzada et al.   BIOCHEMICAL ENGINEERING JOURNAL

The Entner-Doudoroff pathway empowersPseudomonas putida KT2440 with a high tolerance to oxidative stress

(2012) Max Chavarría et al.   ENVIRONMENTAL MICROBIOLOGY

Analysis of solvent tolerance in Pseudomonas putida DOT-T1E based on its genome sequence and a collection of mutants

(2012) Zulema Udaondo et al.   FEBS LETTERS

In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates

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Regulatory Tasks of the Phosphoenolpyruvate-Phosphotransferase System of Pseudomonas putida in Central Carbon Metabolism

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Response of Pseudomonas putida KT2440 to Increased NADH and ATP Demand

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Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

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From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks

(2011) Keng Cher Soh et al.   FEMS YEAST RESEARCH

Stimulation of reactive oxygen species generation by disease-causing mutations of lipoamide dehydrogenase

(2011) Attila Ambrus et al.   HUMAN MOLECULAR GENETICS

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

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Redox Biocatalysis and Metabolism: Molecular Mechanisms and Metabolic Network Analysis

(2010) Lars M. Blank et al.   ANTIOXIDANTS & REDOX SIGNALING

Modeling of uncertainties in biochemical reactions

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In silicogenome-scale metabolic analysis ofPseudomonas putidaKT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival

(2010) Seung Bum Sohn et al.   Biotechnology Journal

Network thermodynamics in the post-genomic era

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Production of biofuels and biochemicals: in need of an ORACLE

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Selected Pseudomonas putida Strains Able To Grow in the Presence of High Butanol Concentrations

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Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering

(2009) Mohammad A. Asadollahi et al.   METABOLIC ENGINEERING

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

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Modeling of growth kinetics for Pseudomonas putida during toluene degradation

(2008) N.-C. Choi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

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

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

(2008) Juan Nogales et al.   BMC Systems Biology

A kinetic model for growth and biosynthesis of medium-chain-length poly-(3-hydroxyalkanoates) in Pseudomonas putida

(2008) M. S. M. Annuar et al.   BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING

Metabolic response of Pseudomonas putida during redox biocatalysis in the presence of a second octanol phase

(2008) Lars M. Blank et al.   FEBS Journal

Dual regulation of zwf-1 by both 2-keto-3-deoxy-6-phosphogluconate and oxidative stress in Pseudomonas putida

(2008) J. Kim et al.   MICROBIOLOGY-SGM

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

(2008) Jacek Puchałka et al.   PLoS Computational Biology