Vincent Noel

Vincent Noel
Institut Curie · Département de Bioinformatique et Biologie des systèmes

PhD in Applied Mathematics
My research focuses on modelling biological systems and its computational aspects

About

36
Publications
3,194
Reads
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275
Citations
Introduction
Research Engineer at Institut Curie. My research focuses on modelling biological systems and its computational aspects
Additional affiliations
July 2021 - present
Institut Curie
Position
  • Engineer
July 2018 - June 2021
Institut Curie
Position
  • PostDoc Position
March 2014 - June 2018
Instituto Butantan
Position
  • PostDoc Position
Education
October 2008 - December 2012
Université de Rennes 1
Field of study
  • Applied Mathematics
September 2006 - June 2008
Université de Rennes 1
Field of study
  • Bioinformatics
September 2003 - June 2004
Université de Rennes 1
Field of study
  • Computer Science

Publications

Publications (36)
Conference Paper
Full-text available
The construction of models of biological networks from prior knowledge and experimental data often leads to a multitude of candidate models. Devising a single model from them can require arbitrary choices, which may lead to strong biases in subsequent predictions. We introduce here a methodology for a) synthesizing Boolean model ensembles satisfyin...
Poster
Full-text available
In this work we present PhysiBoSS-COVID, an effort to integrate MaBoSS, a stochastic Boolean modelling software, into PhysiCell-COVID to allow the leverage of cell- and pathway-specific Boolean models in this framework. To obtain these COVID-19-specific models, we have taken advantage of CaSQ ability to convert all Covid19 Disease maps into SBML-qu...
Article
Full-text available
WebMaBoSS is an easy-to-use web interface for conversion, storage, simulation and analysis of Boolean models that allows to get insight from these models without any specific knowledge of modeling or coding. It relies on an existing software, MaBoSS, which simulates Boolean models using a stochastic approach: it applies continuous time Markov proce...
Preprint
Full-text available
Motivation Cancer progression is a complex phenomenon that spans multiple scales from molecular to cellular and intercellular. Simulations can be used to perturb the underlying mechanisms of those systems and to generate hypotheses on novel therapies. We present a new version of PhysiBoSS, a multiscale modelling framework designed to cover multiple...
Article
Full-text available
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 mole...
Article
Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the reusability of these models and their ability to reproduce virtual experiments becomes critical. Correct and effective model annotation in community-supported...
Article
Full-text available
Mathematical modeling aims at understanding the effects of biological perturbations, suggesting ways to intervene and to reestablish proper cell functioning in diseases such as cancer or in autoimmune disorders. This is a difficult task for obvious reasons: the level of details needed to describe the intra-cellular processes involved, the numerous...
Article
Full-text available
The study of response to cancer treatments has benefited greatly from the contribution of different omics data but their interpretation is sometimes difficult. Some mathematical models based on prior biological knowledge of signaling pathways, facilitate this interpretation but often require fitting of their parameters using perturbation data. We p...
Article
Full-text available
As opposed to the standard tolerogenic apoptosis, immunogenic cell death (ICD) constitutes a type of cellular demise that elicits an adaptive immune response. ICD has been characterized in malignant cells following cytotoxic interventions, such as chemotherapy or radiotherapy. Briefly, ICD of cancer cells releases some stress/danger signals that at...
Chapter
The construction of models of biological networks from prior knowledge and experimental data often leads to a multitude of candidate models. Devising a single model from them can require arbitrary choices, which may lead to strong biases in subsequent predictions. We introduce here a methodology for a) synthesizing Boolean model ensembles satisfyin...
Article
Full-text available
Background: Solutions to stochastic Boolean models are usually estimated by Monte Carlo simulations, but as the state space of these models can be enormous, there is an inherent uncertainty about the accuracy of Monte Carlo estimates and whether simulations have reached all attractors. Moreover, these models have timescale parameters (transition r...
Preprint
Full-text available
One of the aims of mathematical modeling is to understand and simulate the effects of biological perturbations and suggest ways to intervene and reestablish proper cell functioning. However, it remains a challenge, especially when considering the dynamics at the level of a cell population, with cells dying, dividing and interacting. Here, we introd...
Preprint
Full-text available
The study of response to cancer treatments has benefited greatly from the contribution of different omics data but their interpretation is sometimes difficult. Some mathematical models based on prior biological knowledge of signalling pathways, facilitate this interpretation but often require fitting of their parameters using perturbation data. We...
Preprint
Full-text available
Motivation Solutions to stochastic Boolean models are usually estimated by Monte Carlo simulations, but as the state space of these models can be enormous, there is an inherent uncertainty about the accuracy of Monte Carlo estimates and whether simulations have reached all asymptotic solutions. Moreover, these models have timescale parameters (tran...
Data
Fig. S1. The tuning of MAPK‐ERK1/2, but not p38 signaling underlies FGF2 sensitization to ATR‐checkpoint or proteasome inhibition in murine K‐Ras‐driven and ESFT cancer cells.
Article
Full-text available
In malignant transformation, cellular stress response pathways are dynamically mobilized to counterbalance oncogenic activity, keeping cancer cells viable. Therapeutic disruption of this vulnerable homeostasis might change the outcome of many human cancers, particularly those for which no effective therapy is available. Here, we report the use of F...
Preprint
Full-text available
In malignant transformation, cellular stress response pathways are dynamically mobilized to counterbalance oncogenic activity, keeping cancer cells viable. Therapeutic disruption of this riskily balanced homeostasis might change the outcome of many human cancers, particularly those for which no effective therapy is available. Here, we report the us...
Chapter
We present in this article a methodology for designing kinetic models of molecular signaling networks, which was exemplarily applied for modeling one of the Ras/MAPK signaling pathways in the mouse Y1 adrenocortical cell line. The methodology is interdisciplinary, that is, it was developed in a way that both dry and wet lab teams worked together al...
Article
Full-text available
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a classical metabolic enzyme involved in energy production and plays a role in additional nuclear functions, including transcriptional control, recognition of misincorporated nucleotides in DNA and maintenance of telomere structure. Here, we show that the recombinant protein T. cruzi GAPDH (rTcGAP...
Article
Full-text available
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a classical metabolic enzyme involved in energy production and plays a role in additional nuclear functions, including tran-scriptional control, recognition of misincorporated nucleotides in DNA and maintenance of telomere structure. Here, we show that the recombinant protein T. cruzi GAPDH (rTcGA...
Conference Paper
Full-text available
Background / Purpose: The Ras family of proto-oncoproteins are involved in several types of human tumors. Hence, they are intensely studied to unravel mechanisms underlying malignant progression, which might lead to the development of new therapies. To this end, the mouse Y1 adrenocortical tumor cell line is an interesting model, since it display...
Conference Paper
Full-text available
Background / Purpose: The Ras family of proto-oncoproteins are involved in several types of human tumors. Hence, they are intensely studied to unravel mechanisms underlying malignant progression, which might lead to the development of new therapies. To this end, the mouse Y1 adrenocortical tumor cell line is an interesting model, since it display...
Article
Full-text available
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle, leading to cell division and proliferation, combines slow growth, spatio-temporal re-organisation of the cell, a...
Article
Full-text available
Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be described as a sequence of successive equilibrations of different subsets of variables of the system. Polynomial...
Article
Full-text available
Modeling of complex biological systems, especially at a molecular scale, is an emerging field of research, inspired by the recent development of high throughput techniques in molecular biology. The corresponding objective for mathematical modeling is to be able to analyze the behavior of these high dimensional dynamical systems. This is an importan...
Article
Full-text available
Piecewise smooth hybrid systems, involving continuous and discrete variables, are suitable models for describing the multiscale regulatory machinery of the biological cells. In hybrid models, the discrete variables can switch on and off some molecular interactions, simulating cell progression through a series of functioning modes. The advancement t...
Article
Full-text available
Biochemical networks are used in computational biology, to model mechanistic details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multiscaleness, an impo...
Article
Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be described as a sequence of successive equilibrations of different subsets of variables of the system. Polynomial...
Article
Full-text available
We use the Litvinov-Maslov correspondence principle to reduce and hybridize networks of biochemical reactions. We apply this method to a cell cycle oscillator model. The reduced and hybridized model can be used as a hybrid model for the cell cycle. We also propose a practical recipe for detecting quasi-equilibrium QE reactions and quasi-steady stat...
Conference Paper
Full-text available
We discuss piecewise smooth hybrid systems as models for regulatory networks in molecular biology. These systems involve both continuous and discrete variables. The discrete variables allow to switch on and off some of the molecular interactions in the model of the biological system. Piecewise smooth hybrid models are well adapted to approximate th...
Chapter
Full-text available
We discuss piecewise smooth hybrid systems as models for regulatory networks in molecular biology. These systems involve both continuous and discrete variables. The discrete variables allow to switch on and off some of the molecular interactions in the model of the biological system. Piecewise smooth hybrid models are well adapted to approximate th...
Article
Full-text available
Systems biology use networks of biochemical reactions as models for cellular process. The dynamics of reaction networks with many well sep-arated time scales, is well captured by asymptotic models obtained by trop-icalization of the smooth dynamics, via the Litvinov-Maslov correspondence principle. The tropicalized models can be used to check the g...

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Projects

Project (1)
Project
Development of an agent-based model of SARS-Cov-2 infection of an epithelial tissue, using boolean models for intracellular signalling. This project is an example of what can be done with PhysiBoSS, which integrates intracellular boolean models into PhysiCell.