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Vassily Hatzimanikatis

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Publications associées (124)

Principles of Systems Biology, No. 11

Vassily Hatzimanikatis, Noushin Hadadi, Laurent Potvin-Trottier, Jasmin Maria Hafner

This month: AI that learns patterns and facts, new protein-RNA and protein-protein relationships, engineering signaling and metabolism, and more variants of Cas9. ...

Cell Press2016

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Stefano Andreozzi

Accurate determination of physiological states of cellular metabolism requires detailed information about metabolic fluxes, metabolite concentrations and distribution of enzyme states. Integration of fluxomics and metabolomics data, and thermodynamics-base ...

Academic Press Inc Elsevier Science2016

A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism

Paolo Angelino, Vassily Hatzimanikatis, Howard Riezman, Georgios Savoglidis

We present a model-based method, designated Inverse Metabolic Control Analysis (IMCA), which can be used in conjunction with classical Metabolic Control Analysis for the analysis and design of cellular metabolism. We demonstrate the capabilities of the met ...

Academic Press Inc Elsevier Science2016

Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin

Françoise Gisou van der Goot Grunberg, Laurence Gouzi Abrami, Vassily Hatzimanikatis, Patrick Alain Sandoz, Georgios Savoglidis, Tiziano Dallavilla

Cellular functions are largely regulated by reversible post-translational modifications of proteins which act as switches. Amongst these, S-palmitoylation is unique in that it confers hydrophobicity. Due to technical difficulties, the understanding of this ...

Public Library of Science2016

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Keng Cher Soh, Stefano Andreozzi

Rational metabolic engineering methods are increasingly employed in designing the commercially viable processes for the production of chemicals relevant to pharmaceutical, biotechnology, and food and beverage industries. With the growing availability of om ...

Elsevier2016

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

Vassily Hatzimanikatis, Bart Deplancke, Alina Isakova, Yves Berset

Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its i ...

American Society for Biochemistry and Molecular Biology2016

Do genome-scale models need exact solvers or clearer standards?

Jens Nielsen, Vassily Hatzimanikatis

Wiley-Blackwell2015

Noise analysis of genome-scale protein synthesis using a discrete computational model of translation

Julien Racle, Adam Stefaniuk, Vassily Hatzimanikatis

Noise in genetic networks has been the subject of extensive experimental and computational studies. However, very few of these studies have considered noise properties using mechanistic models that account for the discrete movement of ribosomes and RNA pol ...

Amer Inst Physics2015

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

Vassily Hatzimanikatis, Noushin Hadadi, Meriç Ataman

The present work is the first of a series of papers aiming at a coherent and unified development of the thermodynamics of metabolism and the rationalization of feasibility analysis of metabolic pathways. The focus in this part is on high-level quantum chem ...

Royal Soc Chemistry2015

Integrative approaches for signalling and metabolic networks

Vassily Hatzimanikatis

Royal Soc Chemistry2015

Solvation quantities from a COSMO-RS equation of state

Vassily Hatzimanikatis

This work focuses on the extension of the successful COSMO-RS model of mixtures into an equation-of-state model of fluids and its application for the estimation of solvation/hydration quantities of a variety of chemical substances. These quantities include ...

Elsevier2015

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Milenko Tokic, Georgios Fengos

The overarching ambition of kinetic metabolic modeling is to capture the dynamic behavior of metabolism to such an extent that systems and synthetic biology strategies can reliably be tested in silico. The lack of kinetic data hampers the development of ki ...

Elsevier2015

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

Jens Nielsen, Rebecca Oppenheim, Vassily Hatzimanikatis, Stepan Tymoshenko, Dominique Soldati-Favre

Toxoplasma gondii is a human pathogen prevalent worldwide that poses a challenging and unmet need for novel treatment of toxoplasmosis. Using a semi-automated reconstruction algorithm, we reconstructed a genome-scale metabolic model, ToxoNet1. The reconstr ...

Public Library Science2015

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

Vassily Hatzimanikatis, Noushin Hadadi

Designing putative metabolic pathways is of great interest in synthetic biology. Retrobiosynthesis is a discipline that involves the design, evaluation, and optimization of de novo biosynthetic pathways for the production of high-value compounds and drugs ...

Elsevier Sci Ltd2015

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

Vassily Hatzimanikatis, Meriç Ataman

Thermodynamics-based network analysis through the introduction of thermodynamic constraints in metabolic models allows a deeper analysis of metabolism and guides pathway engineering. The number and the areas of applications of thermodynamics-based network ...

Elsevier2015

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Aikaterini Zisaki

Drug discovery and development is a high-risk enterprise that requires significant investments in capital, time and scientific expertise. The studies of xenobiotic metabolism remain as one of the main topics in the research and development of drugs, cosmet ...

Bentham Science Publishers2015

Kinetic models in industrial biotechnology - Improving cell factory performance

Jens Nielsen, Vassily Hatzimanikatis

An increasing number of industrial bioprocesses capitalize on living cells by using them as cell factories that convert sugars into chemicals. These processes range from the production of bulk chemicals in yeasts and bacteria to the synthesis of therapeuti ...

Academic Press Inc Elsevier Science2014

Functional genomics of Plasmodium falciparum using metabolic modelling and analysis

Rebecca Oppenheim, Vassily Hatzimanikatis, Stepan Tymoshenko, Dominique Soldati-Favre

Plasmodium falciparum is an obligate intracellular parasite and the leading cause of severe malaria responsible for tremendous morbidity and mortality particularly in sub-Saharan Africa. Successful completion of the P. falciparum genome sequencing project ...

Oxford Univ Press2013

Tunable reporter signal production in feedback-uncoupled arsenic bioreporters

Jan Roelof van der Meer, Vassily Hatzimanikatis

Escherichia coli-based bioreporters for arsenic detection are typically based on the natural feedback loop that controls ars operon transcription. Feedback loops are known to show a wide range linear response to the detriment of the overall amplification o ...

Wiley-Blackwell2013

Mechanistically Consistent Reduced Models of Synthetic Gene Networks

Vassily Hatzimanikatis

Designing genetic networks with desired functionalities requires an accurate mathematical framework that accounts for the essential mechanistic details of the system. Here, we formulate a time-delay model of protein translation and mRNA degradation by syst ...

Cell Press2013

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