Training – Morning sessions – Data analysis using R – Starting 8th March 2016

EVENT : C3BI Training – Morning sessions


Trainers : Marie-Agnès Dillies, Anne Biton, Stevenn Volant, Hugo Varet, from Bioinformatics and Biostatistic Hub, Felix Cheysson from Unité de pharmacoépidémiologie et maladies infectieuses, Institut Pasteur, Paris Time : 09:00 am – 12:00 am From : 08/03/2016     To: 12/04/2016 Every Tuesday

Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris


Le Hub Bioinformatique et Biostatistique de l’Institut Pasteur organise des cours thématiques ouverts à tous. La première session intitulée « Analyse de données avec R » aura lieu tous les mardis matins, du 8 mars au 12 avril, en salle rétrovirus n°14, rez-de-chaussée du bâtiment Lwoff. Les cours seront donnés en Français et alterneront théorie et pratique avec RStudio. Il est demandé à chaque participant de venir avec un ordinateur portable chargé sur lequel il aura préalablement installé les éléments nécessaires (R, Rstudio et les fichiers de données sur lesquels nous travaillerons). La liste complète des fichiers et logiciels nécessaires sera disponible sur la page web du cours une dizaine de jours avant le début de la session.

Ce cours est une initiation à l’analyse de données. Il est préférable d’avoir une connaissance minimale de R. Dans le cas contraire, un tutoriel d’initiation est disponible sur la page web du cours et les notions de base de R seront rappelées pendant la pratique. Pour les personnes n’ayant jamais utilisé R, il peut être utile d’avoir des connaissances de base en programmation, quel que soit le langage. Le cours s’adresse à des personnes qui veulent apprendre ou ré-apprendre à utiliser les statistiques à bon escient pour leurs propres projets. L’objectif est de présenter et expliquer les principales notions de statistiques utiles pour décrire un jeu de données, en explorer les propriétés afin d’en tirer des conclusions robustes, utiliser à bon escient les méthodes les plus courantes (tests d’hypothèse, ACP, …) et savoir lire, interpréter (et éventuellement aborder d’un œil critique) les résultats présentés dans les publications. Nous utiliserons le moins possible le formalisme mathématique mais insisterons sur les propriétés des méthodes, leurs pré-requis, l’interprétation des résultats. Nous aborderons les notions d’analyse exploratoire, ACP, clustering, estimation, échantillonnage, régression, tests d’hypothèse, planification d’expérience. Les inscriptions sont maintenant fermées.
Installation requise:

Documents

Programme Support de cours Commandes R Jeux de données Evaluation

Programme Training_MorningSessions_Stat

Supports de cours

Intro R :

Training_MorningSessions_Stat_IntroR

Session 1 : statsSessionLecture1 Session 2 : statsSessionLecture2

Session 3 : Session3_MultivariateAnalaysis Session 4: statisticalLawsCourse expDesigns Session 5 et 6: Stat_Session5_6

Commandes R

CommandesSession1.R CommandesSession3.R CommandesSession4.R CommandesSession5.R CommandesInternal.R

Jeux de données

LungA LungB LungC Session3_dat_pca_clus Session4_exprs Session5-6

Evaluation

Sorry. This form is no longer available.

Training – Session d’hiver : programmation et scripting – 11 February 2016

EVENT : C3BI Training – Programmation & Scripting

Ecole Du C3BI : Session d’hiver : programmation et scripting


From : 11/02/2015

To : 25/02/2015


Objectif de la formation : Ce cours s’adresse à toute personne du campus souhaitant acquérir des bases de la programmation et du scripting utiles à la bioinformatique et ayant du mal à trouver du temps pour se former tout le long de l’année.
Pré-requis :Aptitude à travailler onze jours en continu en informatique et avoir des besoins confirmés par des projets en cours ou à venir.

Cette formation n’est accessible qu’aux personnes de l’Institut Pasteur, retrouvez les modalités d’inscription sur le site intranet de Pasteur.

Seminars – Human population genetics – 4 February 2016

EVENT : C3BI Seminars

 Human population genetics: genetic adaptation and epigenetic responses to environmental change


Speaker : Lluis Quintana-Murci, from Human Evolutionary Genetics Unit – Institut Pasteur Time : 02:00 pm Starting Date : 04/02/2016     

Location : Retrovirus room – LWOFF (22), Institut Pasteur, Paris


Human population genetics: genetic adaptation and epigenetic responses to environmental change

Different environmental, demographic and selective forces, together with cultural and social characteristics of human lifestyle, shape the patterns of variability of the human genome at the population level. In particular, infectious diseases have been a major cause of human mortality, so natural selection is expected to act strongly on host defence genes. This is particularly expected for innate immunity genes, as they represent the first line of host defence against pathogens. I will present different cases of how some of these genes and the pathways they trigger have been targeted by natural selection, in its different forms and intensities, helping to delineate genes that are important for host defence, with respect to those exhibiting higher immunological redundancy. I will also discuss how population-specific genetic variation can profoundly impact immune-related molecular phenotypes, such mRNA and miRNA expression upon infection (expression quantitative trait loci – eQTL – mapping), and how these studies increase our understanding of immunological mechanisms under genetic control that have been crucial for our past and present survival against infection. Finally, I will discuss how the differences in lifestyle and habitat of human populations, together with their distinct patterns of genetic diversity, affect the epigenetic landscape of the human genome. Specifically, our studies of populations of African rainforest hunter-gatherers and sedentary farmers show that methylation variation associated with recent changes in habitat mostly involves immune functions, whereas that associated with historical lifestyle primarily affects developmental processes. Our work increases our understanding of whether and how populations are able to respond/adapt to environmental changes, including those related to pathogen pressures, over different time scales.

Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting

Seminars – P-Metagenomic Analysis Group – Paris – 29 January 2016

EVENT : C3BI Seminars – Large audience

P-MAG – Paris – Metagenomic Analysis Group


Speakers : Stevenn Volant research engineer, from Institut Pasteur, Amine Ghozlane researche engineer, from Institut Pasteur, Etienne Ruppé researcher from Hôpitaux Universitaire de Genève and Eric Pelletier researcher from Genoscope/CEA

    Time : 02:00 pm till 05:00 pm

      Starting Date : 29/01/2016

Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris


P-MAG_pasteur  

Registrations are now closed.

Seminars – Conservation and co-evolution – 21 January 2016

EVENT : C3BI Seminars

Conservation and co-evolution: from sequence analysis to protein-protein interactions


Speaker : Alessandra Carbone, from  Laboratory of Computational and Quantitative Biology, CNRS Université Pierre et Marie Curie, Paris

     Time : 02:00 pm     

Starting Date : 21/01/2016     

Location : Retrovirus room – LWOFF (22), Institut Pasteur, Paris


Conservation and co-evolution: from sequence analysis to protein-protein interactions

In computational biology, a fundamental question is the extraction of evolutionary information from DNA sequences. Here, we consider protein sequences and structures. Given a family of protein sequences and the associated distance tree, we shall explain how a fine reading of the conservation and co-evolution signals between residues in sequences can be used to identify protein binding sites, mechanical and allosteric properties, protein-protein interactions. Based on this novel approach to coevolution analysis, we reconstructed the protein-protein interaction network of the Hepatitis C Virus at the residue resolution. For the first time, coevolution analysis of an entire virus was realised, based on a limited set of protein sequences with high sequence identity within genotypes. The identified coevolving residues constitute highly relevant predictions of protein-protein interactions for further experimental identification of HCV protein complexes. The method can be used for interaction predictions for other viral protein interaction networks.

Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting

Trainings – Leishield Training Course on Next Generation Sequencing

EVENT : C3BI Training – NGS Data Analysis

Leishield – Training Course on Next Generation Sequencing


Organizing Committee & Module coordinators : Fatma Z. Guerfali, Antonio V. Borderia,  Marie-Agnès Dillies, Christophe Malabat, from Institut Pasteur Tunis & C3BI

Date : from 30/11/2015 to 04/12/2015

Location : Pacific room – CIS (22), Institut Pasteur, Paris


The primary aim of this course was to provide a basic understanding of the Leishmania genome, NGS technology and analysis tools, and to develop a basic pipeline for the students to start working on their data. This first pipeline will help to standardize all analysis done in the consortium and should facilitate a posterior paper publication. This pipeline will evolve in the context of a collaboration between the Leishield partners and the C3BI, taking into account the difficulties to analyze and interpret the sequence data generated, and the specific needs of each Consortium node. A future Workshop will be organized in June 2016 to tackle all these questions, and to have a follow-up on the analysis.

CoursLeishield

The secondary aim of this course was to have a first contact between the C3BI and Leishield in order to establish a future collaboration. This course provided to the teachers and students, fertile ground to work together and exchange ideas.

 
LeiSHield_NGS_WORKSHOP

Seminars – Network biology and Salmonella infection mechanisms

EVENT : C3BI Seminars – Methodological

Network biology approaches to uncover the mechanisms of Salmonella infection and its autophagy modulating features in the gut


Speaker : Tamas Korcsmaros, Research Leader from TGAC, The Genome Analysis Centre, Norwich Research Park, Norwich, UK – Institute of Food Research, Norwich Research Park, Norwich, UK      Time : 02:00 pm      Starting Date : 07/12/2015     

Location : Retrovirus room – LWOFF (22), Institut Pasteur, Paris


In the last decade, networks became a novel approach in understanding how changes in cellular processes can lead to diseases, such as cancer, infection and inflammatory bowel disease (IBD). In our studies we focus on autophagy (cellular self-degradation) and its regulation. Autophagy is a stress response mechanism also important in development, immune regulation, ageing and cancer, where it could act as both pro- and anti-tumorigenic. Autophagy malfunction is also known to be related to IBD, and it is often manipulated by intestinal pathogenic bacteria, such as Salmonella.

To investigate how Salmonella is modulating autophagy we developed the first large-scale network resource for Salmonella enterica, integrating known and predicted regulatory, metabolic and signalling interactions. We investigated the variation and commonality in the networks of Salmonella serovars with either a predominantly intestinal or extra-intestinal pathogenicity. We analysed the differences (e.g., regulatory connections) for 10 strains of two niche groups (intestinal / extraintestinal), as well as defined a “core” Salmonella consensus network. Then, built on the combination of earlier identified Salmonella-host interactions and our recently published Autophagy Regulatory Network resource (http://autophagy-regulation.org), we predicted novel genes responsible for autophagy modulation in the gut using the intestine specific Salmonella networks. Finally, we have designed a fluorescence reporter system to monitor autophagy of Salmonella and to validate the role of predicted genes. The developed bioinformatics workflows and experimental validation system could be used for other strains or pathogens to iteratively predict genes for biological validation with the potential to provide additional insight or model refinement.

Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting

Available Positions – C3BI 2016 – Job Application

Performance evaluation of DNA copy number segmentation methods

Thursday 3rd of December, Pierre Neuvial will talk about performance evaluation of DNA copy number segmentation methods. #C3BIPasteur

EVENT : C3BI Seminars – Large audience

Performance evaluation of DNA copy number segmentation methods


Speaker : Pierre Neuvial, CNRS researcher from Laboratoire de Mathématiques et Modélisation d’Evry (LaMME) – Équipe Statistique & Génome – Université d’Evry Val d’Essonne      Time : 02:00 pm      Starting Date : 03/12/2015     

Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris


A number of bioinformatic or biostatistical methods are available for segmenting DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these methods is generally assessed using unrealistic simulation studies, or based on small real data analyses.

In order to make an objective and reproducible performance assessment, we have designed and implemented a resampling-based framework to generate realistic DNA copy number profiles of cancer samples with known truth. In this talk, I will describe this framework and its application to a comparison study between methods for segmenting DNA copy number profiles from SNP microarrays.

This study indicates that no single method is uniformly better than all others. It also helps identifying pros and cons of the compared methods as a function of biologically informative parameters, such as the fraction of tumor cells in the sample and the proportion of heterozygous markers.

Reference: M. Pierre-Jean, G. Rigaill and P. Neuvial Performance evaluation of DNA copy number segmentation methods. Briefings in Bioinformatics (2015) http://bib.oxfordjournals.org/content/16/4/600


Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting

Protein superfamily evolution: algorithms and applications

Kimmen Sjölander will present “Protein superfamily evolution: algorithms and applications” in Institut Pasteur, Paris #C3BISeminars 22 Oct15

EVENT : C3BI Seminars – Large audience

Protein superfamily evolution: algorithms and applications


Speaker : Kimmen Sjölander, Professor from Department of Bioengineering, University of California, Berkeley  Time : 02:00 pm Starting Date : 22/10/2015

Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris


Protein superfamilies evolve through diverse mechanisms, including insertions, deletions, point mutations, gene duplications and domain architecture rearrangements.   Each of these events can modify the function or structure of the encoded protein. It is not surprising, therefore, that bioinformatics algorithms for virtually every conceivable task depend on accurately reconstructed phylogenetic trees.    In this talk, I will present the SATCHMO (Simultaneous Alignment and Tree Construction using Hidden Markov mOdels) algorithm. SATCHMO is designed to handle extreme levels of sequence and structural divergence, using Hidden Markov Models and other statistical modeling techniques to model the conserved structure within nested subgroups, and HMM-HMM scoring and alignment to construct a hierarchical tree and output a multiple sequence alignment. On benchmark datasets of structurally aligned proteins, SATCHMO outperforms MUSCLE, MAFFT, and ClustalW algorithms.    In the second half of this talk, I will present phylogenomic methods for ortholog identification. Ortholog identification is fundamental to phylogenetic tree estimation as well as automatic function prediction. While most standard orthology prediction methods employ computationally efficient graph-based approaches, their accuracy is generally lower than phylogenomic approaches.   Benchmark experiments using the TreeFam dataset show the superior performance of our methods, particularly in cases where proteins contain “promiscuous” domains.


Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting