BioInfo Seminars

Invited seminars usually take place on Thursdays at 14:30 in Ada Lovelace building (PCRI/650, access indications).

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  • [PSay CompBio] Parsimony meets our understanding of recent human evolution: from phylogenetic trees to admixture galore
    By Luca Pagani (University of Padova, Italy & Estonian Biocentre, Tartu, Estonia) on Thursday 23 November 2017, 14:30 (LRI, room 435).

    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.

  • [PSay CompBio] SBGNlog: a logical framework based on SBGN to reason on molecular networks
    By Adrien Rougny (Biotechnology Research Institute for Drug Discovery, AIST, Japon) on Thursday 30 November 2017, 14:30 (LRI, room 435).

    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.

  • [PSay CompBio] How mathematics can help us elucidate lipid metabolism
    By Stefan Schuster (Dept. of Bioinformatics, University of Jena) on Thursday 07 December 2017, 14:30 (LRI, room 435).

    Elementary-modes analysis [1] 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.


  • Perfect sampling of closed queueing networks and random generation of combinatorial objects
    By Christelle Rovetta (LIX/LRI) on Thursday 09 November 2017, 14:30 (LIX, room Marcel-Paul Schützenberger).

    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.

  • RNALands: Understanding Cellular Mechanisms through Simulation of RNA Folding Kinetics
    By Andrea Tanzer (Department of Theoretical Chemistry, University of Vienna, Austria) on Thursday 26 October 2017, 14:30 (LIX, room Philippe Flajolet).

    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.

  • Modélisation énergétique qualitative de l'organisme humain assimilé à un système dynamique
    By Marc Irigoin-Guichandut (médecin nutritioniste, Hôpital Avicenne) on Thursday 21 September 2017, 14:30 (LRI, Ada Lovelace, room 465).

    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.

  • Data analyses in functional genomics: two different stories based on deep sequencing technologies in micro-organisms
    By Gaëlle Lelandais (I2BC, Université Paris-Sud) on Thursday 23 March 2017, 14:30 (LRI, Ada Lovelace, room 465).

    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.

  • Comprehensive and Formal Modelling Platform for Biological Processes
    By David Safranek (Masaryk University, Czech Republic) on Thursday 02 February 2017, 14:30 (LRI, Ada Lovelace, room 465).

    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.

  • Protein coevolution and the viral world
    By Alessandra Carbone (UPMC) on Thursday 26 January 2017, 14:30 (LRI, Ada Lovelace, room 465).

    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.

  • Finding a gene tree in a phylogenetic network
    By Philippe Gambette (Univ. Marne-la-Vallée) on Thursday 19 January 2017, 14:30 (LIX).

    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.

  • Inférence de réseaux à partir de données RNA-seq
    By Mélina Gallopin (Univ. Paris-Sud) on Thursday 15 December 2016, 14:30 (Ada Lovelace, room 465).

    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.

  • Dynamic metabolic model of yeast for lipid production
    By Jorgelindo da Veiga Moreira (LIX/LRI) on Thursday 17 November 2016, 14:30 (Ada Lovelace, room 465).

    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.

  • Assessing the robustness of predictions algorithms for ancestral adjacencies
    By Yann Ponty (CNRS/LIX, École Polytechnique) on Thursday 11 February 2016, 14:30 (Ada Lovelace, room 465).

    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.

  • Counting, generating and sampling tree alignments
    By Julien Courtiel (University of British Columbia, Vancouver, Canada) on Thursday 14 January 2016, 11:00 (Ada Lovelace, room 465).

    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.

  • A Rule-based driven knowledge representation model for signalling networks
    By Adrien Basso-Blandin (LIP, ÉNS Lyon) on Thursday 17 December 2015, 14:30 (Ada Lovelace, room 465).

    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.

  • Biological Network inference by quantitative and nonparametric modeling
    By Florence d’Alché-Buc (Télécom ParisTech) on Thursday 19 November 2015, 16:00 (Ada Lovelace, room 465).

    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.

  • Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
    By Nicolas Le Novère (Babraham Institute, Cambridge, UK) on Wednesday 28 October 2015, 14:30 (Ada Lovelace, room 465).

    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.

  • Formal Modeling, Data Integration and Quantitative Verification of large-scale cell-based models.
    By Louis Fippo Fitime (IRCCyN, École Centrale de Nantes) on Thursday 08 October 2015, 14:30 (Ada Lovelace, room 475).

    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.

  • Computing with synthetic protocells
    By Patrick Amar (LRI) on Monday 22 June 2015, 14:30 (Ada Lovelace, room 475).

    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.

  • Horizontal and Vertical Ensemble methods for biomarkers dicovery: overview and outlook
    By Philippe Rinaudo (CEA) on Thursday 04 June 2015, 14:30 (Ada Lovelace, room 445).

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For older invited seminars, please refer to seminar archives.