Symbiose seminars

  • Soutenance de thèse de Gaëlle Garet

    Gaëlle Garet
    Tuesday, December 16, 2014 - 10:00
    Room Markov
    Talk abstract: 

    TBA

  • Soutenance de thèse de Sylvain Prigent

    Sylvain Prigent
    Friday, November 14, 2014 - 14:00
    Room Métivier
    Talk abstract: 

    Complétion combinatoire pour la reconstruction de réseaux métaboliques, et application au modèle des algues brunes Ectocarpus siliculosus.

     

     
    Durant cette thèse nous nous sommes attachés au développement d'une méthode globale de création de réseaux métaboliques chez des espèces biologiques non classiques pour lesquelles nous possédons peu d'informations. Classiquement cette reconstruction s'articule en trois points : la création d'une ébauche métabolique à partir d'un génome, la complétion du réseau et la vérification du résultat obtenu. Nous nous sommes particulièrement intéressé au problème d'optimisation combinatoire difficile que représente l'étape de complétion du réseau, en utilisant un paradigme de programmation par contraintes pour le résoudre : la programmation par ensemble réponse (ou ASP). Les modifications apportées à une méthode préexistante nous ont permis d'améliorer à la fois le temps de calcul pour résoudre ce problème combinatoire et la qualité de la modélisation.
    L'ensemble de ce processus de reconstruction de réseau métabolique a été appliqué au modèle des algues brunes, Ectocarpus siliculosus, nous permettant ainsi de reconstruire le premier réseau métabolique chez une macro-algue brune. La reconstruction de ce réseau nous a permis d'améliorer notre compréhension du métabolisme de cette espèce et d'améliorer l'annotation de son génome.
     
     
    Rapporteurs : 
    - Marie Beurton-Aimar, Maître de conférences, université de Bordeaux 2
    - Hubert Charles, Professeur, INSA Lyon
    - Claudine Médigue, Directrice de recherche CNRS, CEA-Génoscope
     
    Jury :
    - Alexander Bockmayr, Professeur, Freie Universität, Berlin
    - Arnaud Martin, Professeur, université de Rennes 1
    - Anne Siegel, Directrice de recherches CNRS (directrice de thèse)
    - Thierry Tonon, Maître de conférences, UMPC (co-directeur de thèse)
  • Soutenance de thèse de Valentin Wucher

    Valentin Wucher (INRA/Irisa)
    Monday, November 3, 2014 - 14:00
    Room Métivier
    Talk abstract: 

    Modélisation dun réseau de régulation dARN pour prédire des fonctions de gènes impliqués dans le mode de reproduction du puceron du pois
    Résumé
    Cette thèse cherche à discriminer au niveau génomique entre le développement d'embryons vers un mode de reproduction sexué et le développement vers un mode asexué chez le puceron du pois, Acyrthosiphon pisum. Cette discrimination passe par la création du réseau de régulation post-transcriptionnelle des microARN et des ARNm qui possèdent des cinétiques d'expression différentes entre ces deux embryogenèses ainsi que par l'analyse des modules d'interactions de ce réseau par l'utilisation de l'analyse de concepts formels. Pour ce faire, une stratégie en plusieurs étapes a été mise en place : la création d'un réseau d'interactions entre les microARN et les ARNm du puceron du pois ; l'extraction et la réduction du réseau aux microARN et ARNm qui possèdent des cinétiques différentes entre les deux embryogenèses à partir des données d'expression tirées du séquençage haut-débit ; l'analyse du réseau d'interactions réduit aux éléments d’intérêt par l'analyse de concepts formels. L'analyse du réseau a permis l'identification de différentes fonctions potentiellement importantes comme l'ovogenèse, la régulation transcriptionnelle ou encore le système neuroendocrinien. En plus de l'analyse du réseau, l'analyse de concepts formels a été utilisée pour définir une méthode de réparation de graphe biparti basée sur une topologie en concepts ainsi qu'une méthode de visualisation de graphes bipartis par ses concepts.

    Modeling of a gene network between mRNAs and miRNAs to predict gene functions involved in phenotypic plasticity in the pea aphid
    Abstract
    This thesis aims to discriminate between embryos development towards either sexual or asexual reproduction types in pea aphids, Acyrthosiphon pisum, at the genomic level. This discrimination involves the creation of a post-transcriptional regulation network between microRNAs and mRNAs whose kinetic expressions change depending on the embryogenesis. It also involves a study of this network's interaction modules using formal concept analysis. To do so, a three-step strategy was set up. First the creation of an interaction network between the pea aphid's microRNAs and mRNAs. The network is then reduced by keeping only microRNAs and mRNAs which possess differential kinetics between the two embryogeneses, these are obtained using high-throughput sequencing data. Finally the remaining network is analysed using formal concept analysis. Analysing the network allowed for the identification of several functions of potential interest such as oogenesis, transcriptional regulation or even neuroendocrine system. In addition to network analysis, formal concept analysis was used to create a new method to repair a bipartite graph based on its topology and a method to visualise a bipartite graph using its formal concepts.
     

  • Modélisation de la dynamique des réseaux de signalisation SBGN-AF à l'aide de programmes logiques normaux.

    Adrien Rougny (LRI)
    Thursday, October 16, 2014 - 10:30
    Room Minquiers
    Talk abstract: 

    Un grand nombre de réseaux de signalisation sont disponibles dans la littérature ou dans des bases de données sous forme de graphes d'intéractions. Afin de comprendre les systèmes sous-jacents à ces réseaux et de pouvoir les modifier dans un but principalement médical, il est nécessaire de comprendre leur comportement dynamique. C'est pourquoi un grand nombre de techniques de modélisation de la dynamique de ces réseaux moléculaires ont été développées. Il est notamment possible de modéliser la dynamique de ces systèmes par des réseaux booléens. La construction de ces réseaux booléens à partir de graphes d'intéractions nécessite une paramétrisation des fonctions booléennes, le plus souvent réalisée à partir de l'interprétation de résultats expérimentaux. Nous exposerons dans cette présentation une méthode de paramétrisation réalisée sans données expérimentales mais à partir de principes biologiques généraux régissant la dynamique des réseaux de signalisation. Dans notre méthode, les réseaux booléens sont exprimés sous forme de programmes logiques normaux, à partir desquels leurs états stationnaires et trajectoires sont calculés.

  • Modeling dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance

    Gregory Batt (INRIA, Rocquencourt)
    Thursday, October 9, 2014 - 10:30
    Room Minquiers
    Talk abstract: 

    TRAIL induces apoptosis selectively in cancer cells and is currently tested in clinics. Having a mechanistic understanding of TRAIL resistance could help to limit its apparition. Several observations suggested that protein level fluctuations play an important role in TRAIL resistance and its acquisition. However, quantitative, systems-level approaches to investigate their role in cellular decision-making processes are lacking. We propose a generic and principled approach to extend signal transduction models with protein fluctuation models for all proteins in the pathway. The key aspect is to use standard protein fluctuation models for long-lived proteins. We show that its application to TRAIL-induced apoptosis provide a quantitative, mechanistic explanation to previously published but yet unexplained critical observations.

  • Annoyances in metagenomic data analysis and interpretation

    Thomas Bruls (Genoscope)
    Thursday, September 25, 2014 - 10:30
    Room Minquiers
    Talk abstract: 
    Sustained developments in sequencing technology have fueled a range of
    new applications in various fields of life sciences, among which
    metagenomics (aka community genomics or environmental genomics), whose
    promise is to deliver deeper insights into the so-called "unseen majority".
    
    Beyond issues common to other data intensive applications, metagenomics 
    faces difficulties arising from the "in situ" structure of microbial 
    communities, which hinder the possibility of generating accurate 
    assemblies from even moderately complex metagenomes.
    
    These limitations have prompted or renewed interest in assembly-free
    methods for sequence analysis, which are nowadays intensively studied
    from both statistical and algorithmic point of views.
    
    In this talk, we will discuss and illustrate through various real
    world examples (and some less real ones) how such methods, including
    so-called "binning" methods, can help to increase biological
    interpretability of metagenome datasets.
    
    We will also sketch the layout of a software development project that
    aims at scalable variable selection for biomarker discovery from large
    and complex metagenomic datasets. It involves a nested clustering
    procedure combining two types of features extracted from the
    sequences: a coverage related signal (captured using long k-mers), and
    a composition related one (captured using shorter k-mers).
    
    If we have time left, we will evoke an intriguing spectral algorithm
    that has roots in the pre-genomic era, e.g. was succesfully applied in
    the context of physical mapping efforts, and that could be amenable to
    solve some sequence assembly problems.
  • Swarm: robust and fast clustering method for amplicon-based studies

    Frédéric Mahé (Department of Ecology Technische Universität Kaiserslautern )
    Thursday, September 4, 2014 - 10:30
    Room Minquiers
    Talk abstract: 

    Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units, improving the amount of meaningful biological information that can be extracted from amplicon-based studies.

  • Arthropod Genome Sequencing at the Baylor College of Medicine Human Genome Sequencing Center.

    Stephen Richards (Baylor College of Medicine Human Genome Sequencing Center.)
    Thursday, June 26, 2014 - 10:30
    Room Aurigny
    Talk abstract: 

    We have long been pioneered the sequencing of insects genomes, from Drosophila melanogaster to Aphids, Beetles and Centipedes.As decreasing sequencing costs have allowed, we are expanding our investigations to the phylum of Arthropods. As a pilot for the insect 5,000genomes project, we are sequencing a pilot of 30 arthropod genomes, to identify practical issues and solutions for the selection, DNA isolation, sequencing, assembly, annotation, analysis and publication of multiple arthropod genomes.Here we describe examples demonstrating the power of the de-novo genome to drive biology, and the successes, problems and lessons learned so far from our pilot project. We also present the automated annotation pipeline used for the project. We hope that this project will inform larger projects in the future.  

  • Deciphering respective genome wide roles of bacteria within a community responsible for copper bioleaching metabolic processes: an integrative systems ecology approach

    Philippe Bordon (Univ. of Chile)
    Thursday, May 22, 2014 - 10:30
    Room Aurigny
    Talk abstract: 
    Bioleaching process consists in the extraction of metals from ores
    through the cooperative participation of several extremophile
    microorganisms. Due to its great industrial interest, different studies
    have extensively focused on identifying isolated contributions of single
    strains to the process. Even though these studies achieved important
    advances, the functioning of a bioleaching consortium as a whole remains
    far from being understood. From a holistic perspective, this
    presentation proposes a novel integrative systems ecology approach that
    aims to give a functional sense to a metagenomic consortium through the
    integration of genomic and metabolic knowledge at genome scale. Using
    public genome data of five bacterial strains involved in copper
    bioleaching: Acidiphilium cryptum, Acidithiobacillus ferrooxidans,
    Acidithiobacillus thiooxidans, Leptospirillum ferriphilum and
    Sulfobacillus thermosulfidooxidans, we first reconstructed a global
    integrative metabolic network. Next, using a parsimony assumption, we
    decipher a set of genes, called SGS, that take an active part in
    metabolic pathways related to bioleaching and are consecutive on their
    respective genomes, adding the constraint that the associated metabolic
    reactions are also closely connected within metabolic networks. Finally,
    SGS analysis showed that no segment is shared by five bacteria,
    suggesting that no single organism allows alone the copper bioleaching,
    but also pinpoints to the combination of bacterial interactions
    necessary for promoting these pathways, as well as the major hub role of
     A. cryptum. Overall, the SGS paradigm depicts genomic functional units
    and their respective role to maintain metabolic pathways, information
    that is crucial to genetically monitor bacterial participation as a
    whole in environmental processes
    
  • Enhancing reuse in scientific workflows

    Sarah Cohen-Boulakia (LRI, Université Paris-Sud)
    Thursday, May 15, 2014 - 10:45
    Room Aurigny
    Talk abstract: 

    Scientific workflows have been introduced to enhance reproducibility, share and reuse of in-silico experiments. Their simple programming model appeals to bioinformaticians, who can use them to specify complex data processing pipelines.

    In this talk, I will first present the results of a study we performed on workflow (re)use based on a large set of public scientific workflows: While the number of available scientific workflows is increasing along with their popularity, workflows are not (re)used and shared as much as they could be.

    I will then present several projects which aim at enhancing workflow reuse while focusing more specifically on the recent DistillFlow project. DistillFlow proposes to reduce the structural complexity of workflows to make workflows easier to understand for users. The refactoring approach followed in DistillFlow has provided very interesting results both in the 1,500 public workflows from myexperiment.org and on the more curated workflow sets from the BioVel project (workflows to analyze biodiversity data).

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