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Vassily Hatzimanikatis

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Publications associées (124)

A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data

Julien Racle, Vassily Hatzimanikatis

Protein synthesis is a template polymerization process composed by three main steps: initiation, elongation, and termination. During translation, ribosomes are engaged into polysomes whose size is used for the quantitative characterization of translatome. ...

Public Library of Science2013

The interplay between tRNA competition and decoding on mRNA translation elongation rate modulation

Julien Racle, Vassily Hatzimanikatis, Joana Raquel Pinto Vieira

Springer2013

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Keng Cher Soh, Anirikh Chakrabarti

Mathematical modeling is an essential tool for a comprehensive understanding of cell metabolism and its interactions with the environmental and process conditions. Recent developments in the construction and analysis of stoichiometric models made it possib ...

2013

Metabolic modeling in biotechnology and medical research

Vassily Hatzimanikatis

Wiley-V C H Verlag Gmbh2013

Integrating computational methods to retrofit enzymes to synthetic pathways

Ursula Röthlisberger, Ivano Tavernelli, Vassily Hatzimanikatis, Marilisa Neri, Elizabeth Claire Brunk

Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target ...

Wiley-Blackwell2012

Exploration of trade-offs between steady-state and dynamic properties in signaling cycles

Dominique Bonvin, Benoît Chachuat, Vassily Hatzimanikatis, Andrijana Radivojevic

In the intracellular signaling networks that regulate important cell processes, the base pattern comprises the cycle of reversible phosphorylation of a protein, catalyzed by kinases and opposing phosphatases. Mathematical modeling and analysis have been us ...

Iop Publishing Ltd2012

A computational framework for the design of optimal protein synthesis

Jan Overney, Julien Racle, Vassily Hatzimanikatis

Despite the establishment of design principles to optimize codon choice for heterologous expression vector design, the relationship between codon sequence and final protein yield remains poorly understood. In this work, we present a computational framework ...

Wiley-Blackwell2012

Systems biology

Vassily Hatzimanikatis

Elsevier2011

DREAMS of metabolism

Vassily Hatzimanikatis, Keng Cher Soh

Metabolic networks have been studied for decades, and sophisticated computational frameworks are needed to augment experimental approaches to harness these complex networks. BNICE (Biochemical Network Integrated Computational Explorer), a computational app ...

Elsevier2010

Production of biofuels and biochemicals: in need of an ORACLE

Ljubisa Miskovic, Vassily Hatzimanikatis

The engineering of cells for the production of fuels and chemicals involves simultaneous optimization of multiple objectives, such as specific productivity, extended substrate range and improved tolerance – all under a great degree of uncertainty. The achi ...

Elsevier2010

The Origins of Time-Delay in Template Biopolymerization Processes

Vassily Hatzimanikatis

Time-delays are common in many physical and biological systems and they give rise to complex dynamic phenomena. The elementary processes involved in template biopolymerization, such as mRNA and protein synthesis, introduce significant time delays. However, ...

Public Library of Science2010

Modeling of uncertainties in biochemical reactions

Ljubisa Miskovic, Vassily Hatzimanikatis

Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual react ...

Wiley-Blackwell2010

Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks

Vassily Hatzimanikatis

Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the ...

Elsevier2010

In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene

Vassily Hatzimanikatis, Stacey Deleria Finley

Background: Bioremediation offers a promising pollution treatment method in the reduction and elimination of man-made compounds in the environment. Computational tools to predict novel biodegradation pathways for pollutants allow one to explore the capabil ...

BioMed Central2010

Discovery and Analysis of Novel Metabolic Pathways for the Biosynthesis of Industrial Chemicals: 3-Hydroxypropanoate

Vassily Hatzimanikatis

Sustainable microbial production of high-value organic compounds such as 3-hydroxypropanoate (3HP) is becoming an increasingly attractive alternative to organic syntheses that utilize petrochemical feedstocks. We applied the Biochemical Network Integrated ...

Wiley-Blackwell2010

Thermodynamic Analysis of Biodegradation Pathways

Vassily Hatzimanikatis, Stacey Deleria Finley

Microorganisms provide a wealth of bio-degradative potential in the reduction and elimination of xenobiotic compounds in the environment. One useful metric to evaluate potential biodegradation pathways is thermodynamic feasibility. However, experimental da ...

2009

Quantification of uncertainty in metabolic networks through the sampling of kinetic data space

Ljubisa Miskovic, Vassily Hatzimanikatis

Study of a metabolic network with respect to the sensitivity of the metabolite concentrations and the metabolic fluxes to genetic, biochemical, and environmental variations requires knowledge of the kinetic properties of the enzymes in the network. Experim ...

2009

Computational Framework for Predictive Biodegradation

Vassily Hatzimanikatis, Stacey Deleria Finley

As increasing amounts of anthropogenic chemicals are released into the environment, it is vital to human health and the preservation of ecosystems to evaluate the fate of these chemicals in the environment. It is useful to predict whether a particular comp ...

2009

Analysis of genome-scale metabolic model of mycobacterium tuberculosis for new combat strategies

Vassily Hatzimanikatis, John McKinney, Keng Cher Soh, Muhittin Emre Özdemir

2009

Effects of codon distributions and tRNA competition on protein translation

Vassily Hatzimanikatis

Translation is a central cellular process and the complexity of its mechanism necessitates mathematical frameworks to better understand system properties and make quantitative predictions. We have developed a gene sequence-specific mechanistic model for tr ...

2008

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