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.
Invited seminars usually take place on Thursdays at 14:30 in Ada Lovelace building (PCRI/650, access indications).
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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.
The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA-seq data, since coverage information cannot be used to flag repeated sequences, of which transposable elements are one of the main examples. Most... more info.
As technological advances allow a better identification of cellular networks, more and more molecular data are produced allowing the construction of detailed molecular interaction maps. One strategy to get insights into the dynamical properties of such systems is to derive compact dynamical models from these maps, which would then be... more info.
Logical (discrete) models have been used to study numerous biological regulatory networks over the last 40 years. The increasing size of the networks of interest calls for formal methods for their dynamical analysis. Model reduction aims at constructing "simpler" version of the models by taking out selected components while preserving... more info.
Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the 168 proteins of the Mintseris Benchmark 2.0. On the one hand... more info.
La biologie de synthèse est un domaine de recherche émergeant ayant pour objectif de définir des principes et des outils afin de créer des composants biologiques inter-opérables et programmables tout en veillant à définir un cadre sûr pour leur conception.
Dans ce cadre, les environnements de conception assistés par ordinateur... more info.
In bioinformatics, metabolism is usually modeled by directed graphs where nodes represent reactions and edges represent substrate/product exchanges between them. Subsets of these networks are often used to represent collections of reactions involved in a same biological process, also called metabolic pathways. Enzymes recruited in these pathways have often... more info.
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For older invited seminars, please refer to seminar archives.