C3BI Meeting – Seminar – Methodological – Approximate Bayesian Computation (ABC) in population genomics: historical inferences and detection of natural selection in humans

Upcoming Events : Seminar – Methodological 05/28/2015 at 02:00 pm at Retrovirus room – LWOFF (22)

Date : 05/28/2015 at 02:00 pm Location : Retrovirus room – LWOFF (22) Speakers : Guillaume Laval For any questions, suggestions (or to volunteer) for future talks or general feedback please contact us at bioinfo-hub@pasteur.fr

Approximate Bayesian Computation (ABC) in population genomics: historical inferences and detection of natural selection in humans

In population genetics inferences, we aim to evaluate various evolutionary/demographical models (e.g. population growth, recent adaptive selection events) and estimate the underlying parameters (e.g. expansion rates, age and intensity of selection events). Consequently, we need to analytically or numerically compute likelihood functions, i.e. the probability to observe genetics data (SNP genotyped or DNA region re-sequenced in many individuals/populations) given such evolutionary/demographical models. Unfortunately, in many situations, the analytical formulas are unknown, can only be approximated (composite likelihood) or cannot be numerically evaluated. However, the Approximate Bayesian Computation (ABC) approaches bypass such computational difficulties by simulating genetic data according to evolutionary/demographical models. These methods provide high degree of freedom in the choice of models to be tested, but usually involve simulating large amounts of genetic data and, therefore, are highly computational intensive. Here, I present new ABC algorithms aiming to estimate demographical/adaptive parameters in complex scenarios and using genomic data. First, I focus on the estimation of divergence times and migration/admixture patterns between populations using ascertained genome-wide SNPs genotyped in rainforest hunter-gatherers and agriculturalists African populations. Next, I present new ABC approaches to estimate the genome-wide effects (extent and intensity) of recent selection in humans using the whole-genome sequence data of 1000 Genomes (Phase 1, several populations world-wide). Please join us and share your experience, views and thoughts on the talk. We want this meeting to have an interactive and lively atmosphere with many debates.

C3BI

C3BI Meeting – Seminar – Large audience – SRTS2, Short Read Sequence Typing for Bacterial Pathogens

Upcoming Events : Seminar – Large audience 05/12/2015 at 03:00 pm at Retrovirus room – LWOFF (22)

Date : 05/12/2015 at 03:00 pm Location : Retrovirus room – LWOFF (22) Speakers : Kathryn E. HOLT For any questions, suggestions (or to volunteer) for future talks or general feedback please contact us at bioinfo-hub@pasteur.fr

SRST2, Short Read Sequence Typing for Bacterial Pathogens

Kathryn E. HOLT will present SRST2 program, designed to take sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, etc) and report the presence of STs and/or reference genes. For more information, see: Inouye et al, 2014. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs, available at http://genomemedicine.com/content/6/11/90 Please join us and share your experience, views and thoughts on the talk.

 C3BI

C3BI Team – !hacking@pasteur

Upcoming Events : !hacking@pasteur Thursday MAY 7th at 3.00PM at room Retrovirus in building LWOFF

Date : Thursday May 7th at 3.00PM Location : room Retrovirus in building LWOFF Speakers : Vincent ROUILLY For any questions, suggestions (or to volunteer) for future talks or general feedback please contact us at hacking-adm@pasteur.fr

Hands-on session on the R Shiny Framework

Vincent ROUILLY will present on his experience with the R web application framework “Shiny”. If you have always struggled to provide friendly interfaces to your super-smart R scripts, there is a Shiny light at the end of the tunnel. Shiny, provided by RStudio, is a web application framework for R. It can turn your analyses into interactive web applications. No HTML, CSS, or Javascript knowledge is required. During this session, we will introduce the basic features and architecture of a Shiny App, and we will go through all the necessary steps involved in deploying a simple Shiny App. Shiny Project websitehttp://shiny.rstudio.com/ Gallery of Shiny applications: http://www.showmeshiny.com/ To make the session more interactive, bring your laptop with you with the latest R and Rstudio pre-installed + installed packages (ggplot2, shiny) Please join us and share your experience, views and thoughts on the talk and coding in general. We want this meeting to have an interactive and lively atmosphere with many debates on what is considered the “best” way.

C3BI

Working Group : Best Practices and the particularities of mammalian genomes

Working Group : Best Practices and the particularities of mammalian genomes

Date : Thursday 16th April 2015 – 2PM Location : Retrovirus room – Lwoff building – ground floor Speakers : Bernd JAGLA

Best Practices and the particularities of mammalian genomes

  A potential list of topics to be discussed during these meetings :

– Recent papers related to this subject (see e.g. http://www.biomedcentral.com/1471-2164/16/97) – Difference between the different versions of the genomes and annotations – How to handle reads (from a sequencing machine) that align to multiple places in the genome – How to handle different individuals (e.g. from sequencing multiple patients), from a reference genome point of view – How to deal with transcripts / differential analysis of splice variants.

C3BI

C3BI Seminar : High throughput approaches for studying the genomic and epigenetic landscapes of human replication origins

C3BI Seminar : High throughput approaches for studying the genomic and epigenetic landscapes of human replication origins Franck Picard Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard – Lyon

Date : 2nd April 2015 – 11 AM Location : Salle Jean-Paul Aubert, ground floor Building Fernbach Speakers : Franck Picard – Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard – Lyon

Abstract

Replication is the mechanism by which genomes are duplicated into two exact copies. Genomic stability is under the control of a spatiotemporal program that orchestrates both the positioning and the timing of firing of about 50,000 replication starting points, also called replication origins. Replication bubbles found at origins have been very difficult to map due to their short lifespan. Moreover, with the flood of data characterizing new sequencing technologies, the precise statistical analysis of replication data has become an additional challenge. We propose a new method to map replication origins on the human genome, and we assess the reliability of our finding using experimental validation and comparison with origins maps obtained by bubble trapping.

This fine mapping then allowed us to identify potential regulators of the replication dynamics. Our study highlights the key role of CpG Islands and identifies new potential epigenetic regulators (methylation of lysine 4 on histone H4, and tri-methylation of lysine 27 on histone H3) whose coupling is correlated with an increase in the efficiency of replication origins, suggesting those marks as potential key regulators of replication. Overall, our study defines new potentially important pathways that might regulate the sequential firing of origins during genome duplication.

C3BI Team

C3BI Seminar : Uncovering Somatic Mutations in Genomically Unstable Mouse Lymphomas using Next-Generation Sequencing Technologies

Our next meeting will be …

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Upcoming Events : C3BI Seminar – Uncovering Somatic Mutations in Genomically Unstable Mouse Lymphomas using Next-Generation Sequencing Technologies Thursday 9th April 2015 – 2PM – Retrovirus Room – André LWOFF building

Date : April, Thursday 9th – 2PM Location : Retrovirus room – André LWOFF building Speekers: Valentine Murigneux, in Lymphocyte Development & Oncogenesis group, led by Ludovic Deriano

Uncovering Somatic Mutations in Genomically Unstable Mouse Lymphomas using Next-Generation Sequencing Technologies.

Genomic instability is a hallmark of many cancer cells and is thought to lead to the rapid evolution of subclones that are then selected for invasiveness, metastatic potential, and drug resistance. Specifically, failure to properly repair DNA double strand breaks can lead to complex chromosomal and genomic rearrangements characteristic of many cancers. In this study, using next generation sequencing technologies, we have analyzed the genomes and transcriptomes of T cell lymphomas originating from a series of genetically modified mouse models that carry specific deficiencies in genes maintaining genome stability during the physiological process of V(D)J recombination. We have developed bioinformatic pipelines to identify somatic mutations from whole-genome sequencing and RNA-sequencing. We have identified a set of tumor-specific variants (single nucleotide, copy number and structural variants), revealing the tumor landscape of V(D)J recombinase-induced lymphomas.

C3BI Team

C3BI Seminar : Network-based analysis of large-scale datasets

Our next meeting will be …

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Upcoming Events : C3BI Seminar – Network-based analysis of large-scale datasets Thursday 26th March 2015  – 2PM – Retrovirus Room – André LWOFF building

Date : March, Thursday 26th – 2PM Location : Retrovirus room – André LWOFF building Speekers: Benno Schwikowski, Head of Systems Biology Lab in Institut Pasteur

Network-based analysis of large-scale datasets.

The ongoing development of molecular measurement technology allow us to observe cellular systems at an increasing number of levels and in increasing detail, which can then be integrated to form models to identify those observations that contribute to cellular or organismal phenotype. Our laboratory researches principles, and develops methodology and tools for computational elements of the measurement technology, as well as the integration of various observations, in the context of infectious disease and immunity.  One important ingredient for the integration of various observations are functional molecular interaction networks, such as STRING, which can be understood as noisy, but increasingly complete blueprints of the cellular machinery. The integration of such networks with functional ‘omics data (such as genotypes or transcriptomes) enables the detection of true ‘hot spots’ in the cellular machinery that would go unnoticed in non-network-based analyses. In my talk, I will discuss approaches and tools we are developing around network-based integration, along with their statistical and algorithmic bases, and the computational challenges.

C3BI Team

IGDA Kickoff meeting

We are please to inform you that our next meeting will be the IGDA Kickoff Meeting, held in Amphithéâtre Duclaux, Tuesday 17th of March 2015 at 1:30 PM more details

Our next meeting will be …

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Upcoming Events : IGDA Kickoff meeting Tuesday 17th March 2015 – Grand Amphithéâtre de l’Institut Pasteur, bâtiment Duclaux

Date : March, Tuesday 17th Location : Amphithéâtre Duclaux Download the program

The International Group for Data Analysis (IGDA) led by Magnus Fontes is part of the Center for Bioinformatics, BioStatistics and Integrative Biology (C3BI) and the International Division in IP Paris. This is the Parisian node of the International Network for Data analysis (INDA). Its mission is to push the boundaries of data analysis in Biology within Institut Pasteur and its International Network (IPIN). INDA was envisioned, within the IP, as a network linking, data handling, and analysis produced in the IPIN. Such a network would be very advantageous to boost international collaborations between experimentalist and modelers/bioinformaticians, as well as, increasing education in data analysis in the network. We promote openness, collaboration, dynamism, and education and provide an invaluable asset to the IPIN.

The first INDA conference will be held on March 17 from 1.30-5.30pm in the Émile Duclaux lecture hall. The event will feature presentations from experts in the Institut Pasteur International Network on the application of bioinformatics to biomedicine. This conference is open to anyone on campus who is interested in attending the presentations and meeting staff from the International Network. It will also be possible to follow the event on the Institut Pasteur’s YouTube channel. The decision to broadcast the event live is an opportunity to test the technical capabilities of this communication tool. @IGDA_Pasteur

C3BI Team

C3BI Kickoff Meeting

We are please to inform you that our next meeting will be the C3BI Kickoff Meeting, held in Amphithéâtre Duclaux, Monday 16th of March 2015 at 9:15 AM more details

Our next meeting will be …

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Upcoming Events : C3BI Kickoff meeting Monday 16th March 2015 – Grand Amphithéâtre de l’Institut Pasteur, bâtiment Duclaux

Date : March, Monday 16th Location : Amphithéâtre Duclaux Program: 9h15 – Welcome & Coffee 9h30 – Welcome 9h40 – Machine learning for personalized genomics – Jean-Philippe Vert – Mines ParisTech, Center for Computational Biology, France – Institut Curie, Centre de recherche en Biologie du développement, France Website : http://cbio.ensmp.fr/?page_name=Overview 10h10 – Computational imaging & modelling of nuclear architecture in yeast – Christophe Zimmer – Unité Imagerie et modélisation – Institut Pasteur Website : https://sites.google.com/site/imagingandmodeling/ 10h40 – Coffee break & croissants 11h10 – Molecular modeling in structural biology – Michael Nilges Unité de Bio-Informatique Structurale – Institut Pasteur Website : http://www.pasteur.fr/recherche/unites/Binfs/ 11h40 – Reproducible Science in Bioinformatics – Sarah Cohen-Boulakia Laboratoire de Recherche en Informatique, Orsay Website : https://www.lri.fr/presentation.php 12h10 – Alignement/Phylogeny : new advances and challenges – Cedric Notredame Centre for Genomic Regulation, Barcelona Website : http://www.crg.eu/en/programmes-groups/comparative-bioinformatics 12h40 – Lunch & Coffee 14h15 – Welcome – Christian Bréchot – Head of Institut Pasteur 14h30 – One year of reflection – Didier Mazel – Responsible for the implementation committee of C3BI 14h50 – Informatic services and their evolution – Michaël Pressigout – Head of the Information Systems Department (DSI) 15h10 – Goals and organisation of C3BI – Olivier Gascuel – Head of C3BI 15h30 – The Institut Pasteur International Network for Data Analysis (INDA) -Magnus Fontes – Directeur de l’INDA 15h50 – First steps of the Bioinformatics and Biostatistics Hub – Marie-Agnès Dillies – Co-Head of Hub team 16h10 – A new bioinformatics unit – Martin Weigt – Head of Integrative statistical modeling of biological sequences Unit – Institut Pasteur 16h30 – Discussions & Cocktail Download pdf program

Scientific research has entered the era of big data: the ability to analyze, store, share and protect a considerable amount of data has become a key strategic issue for all world-class research institutions. The Institut Pasteur has embraced this revolution, creating the Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI). This center aims to facilitate research and collaborations in bioinformatics between all Institut Pasteur resources.

The launching of C3BI will take place on March 16. There will be presentations by leading researchers in the field in the morning, followed by an introduction to the operation of the center, its organization and its goals in the afternoon. We will conclude the day with cocktails and plenty of time for discussion.

C3BI Team