Symbiose seminars

  • TBA

    Marc Tramier
    Thursday, December 20, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    TBA

  • Soutenance de thèse Clémence FRIOUX

    Clémence FRIOUX
    Monday, November 19, 2018 - 14:00
    Room Métivier
    Talk abstract: 

    TBA

  • Looking inside the dark proteome universe. A tale on protein regions that do not correspond to protein domain families.

    Tristan Bitard Feildel (UPMC)
    Thursday, November 15, 2018 - 10:30 to 12:00
    Room Aurigny
    Talk abstract: 

    71% is the percentage of the Human proteins with at least one domain annotation (Pfam v31) and 45% is the percentage of Human protein amino acid sequences corresponding to a domain (set made of canonical proteins and isoforms). Surprisingly not much isn'it? And these percentages is for the Human proteome, the most (probably?) extensively studied Eukaryotic organisms even if a huge bias has been recently pointed out regarding which genes are studied or left out. To what correspond the remaining amino acids? Very often they are viewed as intrinsically disordered regions (IDRs) or proteins (IDPs), part or whole proteins that do not fold into a stable structure. In this presentation, I will present an other view on these proteins and protein regions. Particularly I will show that restricting sequence analyses to annotation from protein domain databases is a too stringent approaches as to be part of a protein domain databases, a sequence must either have been lucky enough to have a corresponding X-Ray/NMR structure or be conserved and old enough to be in many different proteins and different organisms. I will present two examples, an evolutionary analyses of novel (recent) protein domains on Insect and a comparative  analyses of the dark proteome from Uniprot/Swissprot, to illustrate that the dark proteome might not be as dark as thought, but as often it is a matter of which tools to use.Keywords: protein domain, intrinsically disordered domains, novel domain

  • TBA

    Léa Cabioch (BioGenouest)
    Thursday, November 8, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    TBA

  • PhD Defend - From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing

    Camille Marchet - Irisa
    Friday, September 28, 2018 - 14:00
    Room Métivier
    Talk abstract: 

    The purpose of this thesis work is to allow the processing of transcriptome sequencing data, i.e. messenger RNA sequences, which reflect gene expression. More precisely, it is a question of taking advantage of the characteristics of the data produced by the new sequencing technologies, known as third generation (TGS). These technologies produce large sequences, which cover the total length of RNA molecules. This has the advantage of avoiding the sequence assembly phase, which was tricky, though necessary with the data generated by previous sequencing technologies called NGS. On the other hand, TGS data are noisy (up to 15% sequencing errors), requiring the development of new algorithms to analyze this data. The core work of this thesis consisted in the methodological development and implementation of new algorithms allowing the grouping of TGS sequences by gene, then their correction and finally the detection of the different isoforms of each gene.

  • Computing Birds Acoustic Social Network

    Hédi Soula (UPMC)
    Thursday, September 27, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    For public health, economical and environmental reasons, surveying of bird populations is a major issue because of their proximity with humans. We propose passive acoustic methods that allow to assess the social structure of wild-type population and estimate several parameters of social groups.  Whole population acoustic network assessment can be a powerful tool to analyze and study important social groups of birds. However studies have focused mostly on vocal communication between two individuals and little is known about properties emerging from an acoustical network where several individuals are involved. On the other hand, animal social network analysis relies on static graphs of proximity -- proximal -- and most of the time ignore more distal information such as acoustic network of whole groups. We propose several methods and results to assess such acoustic networks and model to explain their dynamics in relation to their known social structure. 

     
  • Epissage alternatif et modèles grammaticaux

    Aymeric Antoine-Lorquin
    Thursday, September 13, 2018 - 10:30
    Room Markov
    Talk abstract: 

    Les modèles grammaticaux permettent de modéliser des motifs de séquences génomiques, notamment en décrivant comment se structurent les différents éléments présents au sein de ces motifs. Ces modèles semblent donc particulièrement adaptés pour la rechercher des transcrits alternatifs, qui résultent de sélections différentes des exons d'un gène lors de l'épissage alternatif.Dans cet exposé, je présenterai rapidement ce que sont les modèles grammaticaux. Je décrirai ensuite quelques travaux menés dans le cadre de ma thèse et de mon post-doc sur la recherche ex nihilo de transcrits alternatifs dans des séquences de gènes, la recherche de transcrits alternatifs basée sur l'information d'orthologie et enfin la recherche de transcrits alternatifs au sein de long-reads issus de séquençage nanopore.

  • Reference-free approach for population genomic analysis using metagenomic and metranscriptomic data

    Amin Madoui (Genoscope CEA)
    Thursday, July 5, 2018 - 14:00
    Room Aurigny
    Talk abstract: 

    The availability of large datasets of metagenomic sequences offers new opportunities for population genetics research. However, for many non-model species, the lack of reference genomes remains an important issue and constitutes an obstacle for population genomics studies. We took advantages of the discoSnp++ program and proved first its usefulness in the context of metagenomics. Then we developed a new reference-free method to identify species named metavariants species (MVS) by analogy to the metagenomic species (MGS). After detecting biallelic loci directly from metagenomic reads using discoSnp++, MVSs are identified by density-based clustering on biallelic loci depth sequencing coverage across all sampled populations. Then, the allele frequencies of MVS can be used for population genomic analyses to identify population differentiation and loci under natural selection. We applied this method to decipher population structure and differentiation on Tara Oceans metagenomic data. We also combined metatranscriptomic and metagenomic data with discoSnp++ to identify allele-specific expression (ASE) at the population level and detected a strong link between loci under natural selection and loci under ASE.

     

  • Spectral methods for reconstructing latent orderings, and applications to de novo genome assembly.

    Antoine Recanati (ENS)
    Thursday, June 28, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    The seriation problem seeks to recover a latent ordering from similarity information. We typically observe a matrix measuring pairwise similarity between a set of n elements and assume they have a serial structure, i.e. they can be ordered along a chain where the similarity between elements decreases with their distance within this chain. In the context of de novo prokaryotic genome assembly, within the Overlap-Layout-Consensus paradigm, we collect fragments of DNA (reads) randomly sampled across the genome, with sufficient coverage so that a given read overlaps with the neighboring reads. However, the position of the reads within the genome is unknown, so one has to solve a sort of jigsaw puzzle (the layout). This layout step can fit in the framework of Seriation, where the similarity measures the overlap (if any) between two reads, and we wish to reorder the reads such that two neighboring reads have a large overlap, and two reads far apart do not overlap.

    In this talk, I will present a basic spectral method for Seriation, akin to the Spectral Clustering method widely used in Machine Learning, together with a simple extension that allows to deal with circular orderings and improves robustness to noise. I will then present results of this method applied to finding the layout of E. coli reads sequenced with Oxford Nanopore Technology MinION device.

     

  • Thèses encadrées en bioinformatique

    Mourad Elloumi (univ. Tunis)
    Thursday, June 21, 2018 - 10:30
    Room Aurigny
    Talk abstract: 

    Dans cet exposé, je vais présenter les activités de notre groupe,
    le BioInformatics Group (BIG), à travers les thèses encadrées.

    Je présente, particulièrement, nos travaux sur :

     . Le Biregroupement des Données Biopuces

     . Correction des Données de Séquençage de 3ème Génération

    Je termine cet exposé, par présenter mes autres activités

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