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Vassily Hatzimanikatis

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Publications associées (123)

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Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell

Vassily Hatzimanikatis, Julien Racle, Joana Raquel Pinto Vieira

Understanding the mechanisms behind translation and its rate-limiting steps is crucial for both the development of drug targets and improvement of heterologous protein production with many biotechnological applications, such as in pharmaceutical and biofue ...

Elsevier2016

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

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

Vassily Hatzimanikatis, Françoise Gisou van der Goot Grunberg, Laurence Gouzi Abrami, 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

Redefining solubility parameters: Bulk and surface properties from unified molecular descriptors

Vassily Hatzimanikatis

The central objective of this work is to revisit the development of the widely used solubility parameters and linear solvation energy relationships (LSER) and seek interconnections and possibilities for secure exchange of information. Partial solvation par ...

Academic Press Ltd- Elsevier Science Ltd2017

Integration of Metabolic, Regulatory and Signaling Networks Towards Analysis of Perturbation and Dynamic Responses

Vassily Hatzimanikatis, Meriç Ataman, Anush Chiappino-Pepe, Vikash Kumar Pandey

The expanding generation of dynamic biological data requires approaches that integrate and analyze information from different types of cellular processes –metabolism, regulation, and signaling–, and ultimately increase our insights into the cell behavior u ...

2017

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Vassily Hatzimanikatis, Noushin Hadadi, Vikash Kumar Pandey

The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Current ...

2019

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

Vassily Hatzimanikatis, Ljubisa Miskovic, Georgios Savoglidis, Milenko Tokic

Analysis of the dynamic and steady-state properties of biochemical networks hinges on information about the parameters of enzyme kinetics. The lack of experimental data characterizing enzyme activities and kinetics along with the associated uncertainties i ...

2019

Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli

Vassily Hatzimanikatis, Anastasia Sveshnikova

Developing efficient bioprocesses requires selecting the best biosynthetic pathways, which can be challenging and time-consuming due to the vast amount of data available in databases and literature. The extension of the shikimate pathway for the biosynthes ...

2024

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

Vassily Hatzimanikatis, Meriç Ataman

In the post-genomic era, Genome-scale metabolic networks (GEMs) have emerged as invaluable tools to understand metabolic capabilities of organisms. Different parts of these metabolic networks are defined as subsystems/pathways, which are sets of functional ...

2017

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Vassily Hatzimanikatis, Meriç Ataman, Georgios Fengos, Keng Cher Soh, Pierre Guy Rémy Salvy

Summary: pyTFA and matTFA are the first published implementations of the original TFA paper. Specifically, they include explicit formulation of Gibbs energies and metabolite concentrations, which enables straightforward integration of metabolite concentrat ...

Oxford University Press2018

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

Vassily Hatzimanikatis, Sofia Tsouka

Over the last decades, yeast has become a key model organism for the study of lipid biochemistry. Because the regulation of lipids has been closely linked to various physiopathologies, the study of these biomolecules could lead to new diagnostics and treat ...

2020

A computational framework for the design of optimal protein synthesis

Vassily Hatzimanikatis, Julien Racle

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

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

Vassily Hatzimanikatis, Ljubisa Miskovic, Noushin Hadadi, Marianne Seijo

Thousands of biochemical reactions with characterized activities are “orphan,” meaning they cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel reactions predicted by pathway-generation tools also lack associated sequences, l ...

National Academy of Sciences2019

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks

Dimitrios Alexandros Kyparissidis, Vassily Hatzimanikatis

The increasing availability of large metabolomics datasets enhances the need for computational methodologies that can organize the data in a way that can lead to the inference of meaningful relationships. Knowledge of the metabolic state of a cell and how ...

Elsevier2017

ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds

Vassily Hatzimanikatis, Anastasia Sveshnikova

Synthetic biology and metabolic engineering rely on computational search tools for predictions of novel biosynthetic pathways to industrially important compounds, many of which are derived from aromatic amino acids. Pathway search tools vary in their scope ...

2022

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

Vassily Hatzimanikatis, Julien Racle, Adam Stefaniuk

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

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flu ...

Nature Research2020

Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models

Vassily Hatzimanikatis, Maria Masid Barcon, Georgios Fengos, Daniel Robert Weilandt, Pierre Guy Rémy Salvy, Zhaleh Hosseini

Motivation: Large-scale kinetic models are an invaluable tool to understand the dynamic and adaptive responses of biological systems. The development and application of these models have been limited by the availability of computational tools to build and ...

Oxford University Press2022

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

Vassily Hatzimanikatis, Ljubisa Miskovic, Michaël Roger Germain Moret

A persistent obstacle for constructing kinetic models of metabolism is uncertainty in the kinetic properties of enzymes. Currently, available methods for building kinetic models can cope indirectly with uncertainties by integrating data from different biol ...

2019

Modeling of uncertainties in biochemical reactions

Vassily Hatzimanikatis, Ljubisa Miskovic

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