Publications by Pierre Guy Rémy Salvy

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Pierre Guy Rémy Salvy, Daniel Robert Weilandt

Kinetic models of metabolism relate metabolic fluxes, metabolite concentrations and enzyme levels through mechanistic relations, rendering them essential for understanding, predicting and optimizing the behaviour of living organisms. However, due to the la ...

NATURE PORTFOLIO2022

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

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

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 UNIV PRESS2022

Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Diauxie, or the sequential consumption of carbohydrates in bacteria such as Escherichia coli, has been hypothesized to be an evolutionary strategy which allows the organism to maximize its instantaneous specific growth-giving the bacterium a competitive ad ...

National Academy of Sciences2021

New and improved methods for integrated models of metabolism and gene expression

Pierre Guy Rémy Salvy

The beginning of the 21st century was marked by the advent of disruptive technologies, which ushered an era of groundbreaking advances in fundamental sciences, carried by the great pace at which computational capabilities spread and evolved. But the new ce ...

EPFL2021

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Pierre Guy Rémy Salvy, Maria Masid Barcon, Mohammadomid Oftadeh

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of ...

Nature Portfolio2021

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

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

Vassily Hatzimanikatis, Keng Cher Soh, Meriç Ataman, Georgios Fengos, 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 ...

2018