Since the late 90s the first available DNA sequences from Neanderthal have fuelled a debate on putative admixture between “us” and our closest relatives. Back then, the available evidence were in agreement with the parsimony principle, stating that to explain the observed genetic and palaeoanthropology data no archaic admixture was... more info.
Invited seminars usually take place on Thursdays at 14:30 in Ada Lovelace building (PCRI/650, access indications).
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The Systems Biology Graphical Notation (SBGN) is a standard that allows representing molecular networks in an unambiguous way.
SBGN maps can be stored and exchanged using the SBGN-ML format, and programmatically manipulated using the libSBGN library.
This latter was designed in order to ease the support (writing, reading, editing and... more info.
Elementary-modes analysis  has become a well-established theoretical tool in metabolic pathway analysis. It allows one to decompose complex metabolic networks into the smallest functional entities, which can be interpreted as biochemical pathways. It led to successful theoretical prediction of novel pathways, such as in carbohydrate metabolism in Escherichia coli... more info.
Random generation of combinatorial objects is an important problem in many fields of research (communication networks, theoretical computing, combinatorics, statistical physics, ...). This often requires to sample the stationary distribution of an ergodic Markov chain. In 1996, Propp and Wilson introduced an algorithm to produce unbiased samples of the stationary distribution... more info.
RNAs play a fundamental role in cellular processes: gene expression and its regulation, activation and inactivation of genomic domains, genomic rearrangements, defense against pathogens, and regulation of the epitranscriptome.
The function of most RNAs is determined by the structure of the molecule. RNAs are long polymers that fold back onto... more info.
Il est proposé un modèle de l'organisme humain simplifié par la non prise en compte des facteurs sociaux et environnementaux. Ce modèle énergétique qualitatif assimile l'organisme à un système dynamique dont les variables sont dérivées du principe de la conservation de l'énergie appliqué à un système thermodynamique ouvert. En distinguant... more info.
I am a new Professor at the University Paris Sud (since September 2016). I joined the I2BC institute, in the research team of Olivier Lespinet. My research interests are related to the analyses of experimental datasets in functional genomic projects. During this seminar, I will present original results we obtained... more info.
The goal of computational systems biology is to develop models that can predict and explain uknown facts about the dynamics of biological systems, especially, non-trivial behaviour emerging from the interplay among the enormous number of individual biochemical components. Models are typically based on known first principles, wet-lab measurements, and existing... more info.
A fundamental question in computational biology is the extraction of evolutionary information from DNA sequences. Here, we consider protein sequences and structures, and describe how important biological information on protein-protein binding sites and on mechanical and allosteric properties of proteins can be extracted. Among different examples, we shall present a... more info.
Phylogenetic networks have been introduced as a model generalizing phylogenetic trees in order to represent the evolution of species. Contrary to trees, it allows to represent the transfer of genetic material between coexisting species or populations, through recombination, hybridization or horizontal gene transfers. Several methods have been proposed to reconstruct... more info.
Mes travaux portent sur l'analyse statistique des données issues de la technologie de séquençage RNA-seq. Dans un premier temps, je m'intéresserai à la question de la modélisation (discrète ou continue) des données RNA-seq pour l'inférence de réseaux. Puis je présenterai une approche non-asymptotique pour sélectionner des sous-ensembles de variables pertinentes... more info.
The oleaginous yeast, Yarrowia lipolytica, is emerging as an important cell factory for lipid production. In order to understand this metabolic phenotype and internal regulations leading to lipid accumulation, we used genome-scale metabolic models (GEM) and metabolomics data to construct a reduced dynamic model. The resulting model shows energetic variations... more info.
In this work, we revisit the prediction of gene adjacencies within ancestral genomes, a problem solved in polynomial-time by the DeCo algorithm contributed by Berard et al, which relies on a complex dynamic-programming scheme. More precisely, we assess the robustness of predictions obtained in a parsimonious model by: 1) positing... more info.
Pairwise ordered tree alignment are combinatorial objects that appear in important applications, such as RNA secondary structure comparison. However, the usual representation of tree alignments is ambiguous, which is detrimental to any probabilistic analysis.
In this talk, we see how to remove this ambiguity. We give for that a context-free... more info.
The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their literatures and data are consequently fragmented, distributed and sometimes—at least apparently—inconsistent. This... more info.
We consider the task of biological network inference and re-visit this task using the idea of Jacobian estimation. We propose a new nonparametric approach to vector autoregressive models that imposes sparsity on the elements of the Jacobian. The method is based on the definition of multiple output regression models and... more info.
PIP3 is synthesized by PI3Ks and regulates complex cell responses, such as growth and migration. Signals that drive long-term reshaping of cell phenotypes are difficult to resolve because of complex feedback networks that operate over extended times. It is clear PIP3-dependent modulation of mRNA accumulation is important in this process... more info.
In this work we propose an automatic way of generating and verifying formal hybrid models of signaling and transcriptional events, gathered in large-scale regulatory networks.This is done by integrating temporal and stochastic aspects of the expression of some biological components. The hybrid approach lies in the fact that measurements... more info.
In this article we present a new kind of computing device that uses biochemical reactions networks as building blocks to implement logic gates. The architecture of a computing machine relies on these generic and composable building blocks, computation units, that can be used in multiple instances to perform complex boolean... more info.
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For older invited seminars, please refer to seminar archives.