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A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Nature communications, 2021-08, Vol.12 (1), p.4790-4790, Article 4790

2021

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Rational strain design with minimal phenotype perturbation

Nature communications, 2024-01, Vol.15 (1), p.723-14, Article 723

2024

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Production of biofuels and biochemicals: in need of an ORACLE

Trends in biotechnology (Regular ed.), 2010-08, Vol.28 (8), p.391-397

2010

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Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches

Current pharmaceutical design, 2015-01, Vol.21 (6), p.806

2015

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

Biotechnology journal, 2013-09, Vol.8 (9), p.1043-1057

2013

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

Current opinion in biotechnology, 2015-12, Vol.36, p.146-153

2015

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Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

PLoS computational biology, 2019-08, Vol.15 (8), p.e1007242-e1007242

2019

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

Metabolic engineering, 2016-05, Vol.35, p.148-159

2016

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

FEMS yeast research, 2012-03, Vol.12 (2), p.129-143

2012

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Antihypertensive Drugs Metabolism: An Update to Pharmacokinetic Profiles and Computational Approaches

Current pharmaceutical design, 2014-12, Vol.21 (6), p.806-822

2014

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Modeling of uncertainties in biochemical reactions

Biotechnology and bioengineering, 2011-02, Vol.108 (2), p.413-423

2011

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Iterative minimization of H 2 control performance criteria

Automatica (Oxford), 2008-10, Vol.44 (10), p.2549-2559

2008

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Identification and the Information Matrix: How to Get Just Sufficiently Rich?

IEEE transactions on automatic control, 2009-12, Vol.54 (12), p.2828-2840

2009

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

Biotechnology for biofuels, 2020-02, Vol.13 (1), Article 33

2020

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Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

Proceedings of the National Academy of Sciences - PNAS, 2019-04, Vol.116 (15), p.7298-7307

2019

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iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Metabolic engineering, 2016-01, Vol.33, p.158-168

2016

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

Industrial & engineering chemistry research, 2019-07, Vol.58 (30), p.13544-13554

2019

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Constraint-based metabolic control analysis for rational strain engineering

Metabolic engineering, 2021-07, Vol.66, p.191-203

2021

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Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

Metabolic engineering, 2019-03, Vol.52, p.29-41

2019

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Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

Nature machine intelligence, 2022-08, Vol.4 (8), p.710-719

2022

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Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

Nature catalysis, 2024, Vol.7 (10), p.1086-1098

2024

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A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

Biotechnology for biofuels, 2017-06, Vol.10 (1), Article 166

2017

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

ACS synthetic biology, 2018-08, Vol.7 (8), p.1858-1873

2018

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On the integration of process engineering with metabolomics for the production of muconic acid: the case for Saccharomyces Cerevisiae

Computer Aided Chemical Engineering, 2022, Vol.51, p.541-546

2022

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Closed-Loop Identification of MIMO Systems: A New Look at Identifiability and Experiment Design

European journal of control, 2010, Vol.16 (3), p.228-239

2010

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A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Rational strain design with minimal phenotype perturbation

Production of biofuels and biochemicals: in need of an ORACLE

Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches

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

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

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

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

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

Antihypertensive Drugs Metabolism: An Update to Pharmacokinetic Profiles and Computational Approaches

Modeling of uncertainties in biochemical reactions

Iterative minimization of H 2 control performance criteria

Identification and the Information Matrix: How to Get Just Sufficiently Rich?

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

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

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

Constraint-based metabolic control analysis for rational strain engineering

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

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

On the integration of process engineering with metabolomics for the production of muconic acid: the case for Saccharomyces Cerevisiae

Closed-Loop Identification of MIMO Systems: A New Look at Identifiability and Experiment Design

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