Vassily Hatzimanikatis

Dr. Vassily Hatzimanikatis is currently Associate Professor of Chemical Engineering and Bioengineering at Ecole Polytechnique Federale de Lausanne (EPFL), in Lausanne, Switzerland. Vassily received a PhD and an MS in Chemical Engineering from the California Institute of Technology, and his Diploma in Chemical Engineering from the University of Patras, in Greece. After the completion of his doctoral studies, he held a research group leader position at the Swiss Federal Institute of Technology in Zurich (ETHZ), Switzerland. Prior to joining EPFL, Vassily worked for three years in DuPont, Cargill, and Cargill Dow, and he has been assistant professor at Northwestern University, at Illinois, USA.

Vassilys research interests are in the areas of computational systems biology, biotechnology, and complexity. He is associate editor of the journals Biotechnology & Bioengineering, Metabolic Engineering and Integrative Biology, and he serves on the editorial advisory board of the journals Bioprocess and Biosystems Engineering, Journal of Chemical Technology and Biotechnology, and Industrial Biotechnology. He has written over 70 technical publications and he is co-inventor in three patents and patent applications.

Vassily is a fellow of the American Institute for Medical and Biological Engineering (2010), he was a DuPont Young Professor (2001-2004), and he has also received the Jay Bailey Young Investigator Award in Metabolic Engineering (2000), and the ACS Elmar Gaden Award (2011).

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ChE-411: Principles and applications of systems biology

The course introduces and develops the key concepts from systems biology and systems engineering in the context of complex biological networks. The lectures elaborate on techniques and methods to mode

ChE-201: Introduction to chemical engineering

Introduction to Chemical Engineering is an introductory course that provides a basic overview of the chemical engineering field. It addresses the formulation and solution of material and energy balanc

ChE-320: Bioreactor modeling and simulation

The course of Bioreactor modeling and simulation focuses on the principles of algorithmic design and analysis of biochemical reactors. The application of these designed reactors would be in the produc

Supplementary datasets for the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" -Part 2

Vassily Hatzimanikatis, Ljubisa Miskovic, Michaël Roger Germain Moret

Supplementary files containing datasets needed to reproduce the results of the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic stat

EPFL Infoscience2023

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

Vassily Hatzimanikatis, Ljubisa Miskovic, Michaël Roger Germain Moret

Large omics datasets are nowadays routinely generated to provide insights into cellular processes. Nevertheless, making sense of omics data and determining intracellular metabolic states remains chall

2023

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

Vassily Hatzimanikatis, Daniel Robert Weilandt

One of the main challenges hampering the development of kinetic models is the lack of kinetic parameters for many enzymatic reactions. Here, the authors introduce a framework to explore the catalytica

NATURE PORTFOLIO2023

Le métabolisme est l'ensemble des réactions chimiques qui se déroulent à l'intérieur de chaque cellule d'un être vivant et lui permettent notamment de se maintenir en vie, de se reproduire (se diviser), de se développer et de répondre aux stimuli de son environnement (échanges par exemple). Certaines de ces réactions chimiques se déroulent en dehors des cellules de l'organisme, comme la digestion ou le transport de substances entre cellules. Cependant, la plupart de ces réactions ont lieu dans les cellules elles-mêmes et constituent le métabolisme intermédiaire.

Un réseau métabolique est l'ensemble des processus métaboliques et physiques qui déterminent les propriétés physiologiques et biochimiques d'une cellule. Par conséquent, ces réseaux comprennent les réactions chimiques du métabolisme, les voies métaboliques, ainsi que les interactions régulatrices qui guident ces réactions. Avec le séquençage complet des génomes, il est maintenant possible de reconstituer le réseau de réactions biochimiques dans de nombreux organismes, des bactéries aux humains.

Metabolic engineering is the practice of optimizing genetic and regulatory processes within cells to increase the cell's production of a certain substance. These processes are chemical networks that use a series of biochemical reactions and enzymes that allow cells to convert raw materials into molecules necessary for the cell's survival. Metabolic engineering specifically seeks to mathematically model these networks, calculate a yield of useful products, and pin point parts of the network that constrain the production of these products.