Course single-cell transcriptomics and epigenomics 2019
Single-cell transcriptomics and epigenomics: theory and practice (sincellTE)
Du 03-02-2019 au 08-02-2019 à Station Biologique Roscoff
Date limite d'inscription: 15-11-2018

   

Duration

The workshop will take place  3 - 8 February 2019 at Station Biologique de Roscoff, France

Objectives

This workshop focuses on the large-scale study of heterogeneity across individual cells from a genomic, transcriptomic and epigenomic point of view. New technological developments enable the characterization of molecular information at a single cell resolution for large numbers of cells. The high dimensional omics data that these technologies produce come with novel methodological challenges for the analysis. In this regard, specific bioinformatics and statistical methods have been developed in order to extract robust information.

The workshop aims to provide such methods for engineers and researchers directly involved in functional genomics project making use of single-cell. A wide range of single cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines.

Audience

This course is directed towards engineers and researchers who regularly need to undertake single-cell data analysis as well as PhD Student and Post Doc in computational biology or bioinformatics that are interested in the development of methods and pipelines for highly dimensional single-cell data analysis.

Working environment

Unix command will be used for bioinformatic analysis, and R programming language for statistical analysis.

Requirements

Understanding of bioinformatics tools and pipelines for next generation sequencing data (RNA-seq or Hi-C or ATAC-seq bulk). Participants must have prior experience on NGS data analysis with R and basic Unix command line skills.

Registration

Deadline 15th novembre 2018 (participants selection: end of November 2018). As the number of participants is limited (30 participants), the steering committee will retain candidates on the basis of the information inquired on the registration form.

Frais d’inscription pour les personnels académiques

Registration fees. A) Academy/University: 600€HT=720€TTC ; B) Private sector: 1.750€HT=2.100€TTC. The registration fee includes accommodation and meals.

Scientific coordination:​ ​ Marc Deloger (Institut Curie, INSERM U900, Mines ParisTech), Marie-Agnès Dillies, C3BI (USR 3756 IP CNRS), Agnès Paquet, UCAGenomiX (IPMC CNRS), Antonio Rausell (Institut Imagine, INSERM UMR-1163), Nicolas Servant (Institut Curie, INSERM U900, Mines ParisTech), Morgane Thomas-Chollier, IBENS (CNRS UMR8197, ENS, INSERM U1024).

Technical coordination :​ ​ Erwan Corre (ABIMS FR2424 CNRS-UPMC, Station Biologique de Roscoff)

Administrative management​ :​ ​ C3BI (Institut Pasteur)


Version française

 

English version


program




Applications are closed since 15/11/2018.

La formation commencera le dimanche 3 février à 18h et finira le vendredi 8 à 14h / The workshop will start Sunday, February 3 at 6pm and will end Friday, February 8 at 2pm
Les travaux pratiques seront réalisés sur ordinateur portable pour lequel vous devez avoir les droits administrateur / Hands-on computer sessions will be held on a laptop on which you need to have administrator rights
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Nous nous occupons de la réservation de l’hôtel. L’organisation de votre voyage et le paiement de vos frais de transport sont à votre charge.

Pour vous aider, voici quelques informations pratiques que vous retrouverez sur notre page web : https://www.france-bioinformatique.fr/en/evenements/sincellTE_2019

    En train : TGV entre Paris Montparnasse et Morlaix (durée 3h) puis autocar de Morlaix à Roscoff (durée 32 mn)
    En avion : vols au départ de Roissy et d’Orly à destination de Brest, puis taxi de Brest à Roscoff.

Si vous pouvez partager le taxi à plusieurs, le tarif est intéressant. Nous pouvons vous fournir sur demande les coordonnées de compagnies de taxi avec lesquelles travaille le centre de Roscoff.

Pour vous aider à organiser votre voyage, merci de remplir ce document partagé :

Qui vous permettra d’entrer en contact avec les personnes voyageant dans le même train / avion.

Nous reviendrons vers vous dans le courant de la semaine prochaine pour vous donner les informations nécessaires au règlement des frais d’inscription.

Au plaisir de vous retrouver à Roscoff,

Bien cordialement


Erwan Corre (ABIMS FR2424 CNRS-UPMC, Station Biologique de Roscoff)

 

Marc Deloger (Institut Curie, INSERM U900, Mines ParisTech)

Dr Marc Deloger is project leader and trainings manager in the "Bioinformatics and biostatistics data analysis" team of the Institut Curie's bioinformatics platform. He has expertise in analysis of many different type of NGS data but mainly in RNA-seq, WES and ChIP-seq. He is also part of the Bio-Informatics French Society (SFBI) council.

Marie-Agnès Dillies (C3BI USR 3756 IP CNRS)

Dr Marie-Agnès Dillies is co-head of the Bioinformatics and Biostatistics Hub of the Institut Pasteur. She has expertise in statistical analysis of gene expression data (Dillies et al, Briefings in Bioinformatics 2013). She is co-animating the StatOmique group. Recently she joined the Pasteur Single Cell Initiative.

Agnès Paquet (UCAGenomiX IPMC CNRS)

Agnes Paquet is an expert in statistical analysis and mining of large datasets from high-throughput assays (microarrays, NGS data such as RNAseq and single cell RNAseq). She is specialized in biomarkers discovery and in development of assays for diagnostic and resistance assessment in HIV, HCV, breast and lung cancers. She is currently the head of biostatistics for the Functional Genomics Plateforme of the Institut de Pharmacologie Moleculaire et Cellulaire (Sophia Antipolis, France).

Antonio Rausell (Institut Imagine, INSERM UMR-1163)

Dr. Antonio Rausell is the Director of the Clinical Bioinformatics Lab of the Institut Imagine. He has an extensive expertise in bioinformatics and high-dimensional single-cell data analysis. He led the development of an R/Bioconductor package for the statistical assessment of cell hierarchies from single-cell RNA-seq data (http://bioconductor.org/packages/sincell, Julia et al Bioinformatics 2015). He then analyzed CD4+ T cells heterogeneity through single-cell RNA-seq data of from individuals with extreme phenotypes of HIV infection and uncovered cell surface markers of the HIV-permissive cell (Rato*, Rausell* et al, Plos Pathogens 2017). Ongoing research at his lab includes the development of a new methodology to predict cell types at single-cell resolution with a main focus in hematopoietic stem and progenitors cells (MCXpress software, https://github.com/cbl-imagine/MCXpress).

Nicolas Servant (Institut Curie, INSERM U900, Mines ParisTech)

Morgane Thomas-Chollier (IBENS CNRS UMR8197, ENS, INSERM U1024)

Dr. Morgane Thomas-Chollier is Associate Professor in Bioinformatics at Ecole Normale Supérieure Paris, in the team Computational Systems Biology at IBENS. She has expertise in epigenomics (ChIP-seq, ChIP-exo) and motif analysis in genomic sequences. She is part of the Bio-Informatics French Society (SFBI) council.

 

Luca Albergante (Institut Curie, INSERM U900, Mines ParisTech)

Akira Cortal (Institut Imagine, INSERM UMR-1163)

Akira Cortal is a Phd student at Imagine Institute of Genetic Disease in the Clinical Bioinformatics Lab.
He is currently working on the development of R package for single cell RNA-Seq analysis.

Hervé Isambert (Institut Curie, UMR168)

Kevin Lebrigand (UCAGenomiX IPMC CNRS)

Nathalie Lehmann (IBENS CNRS UMR8197, ENS, INSERM U1024)

Nathalie Lehmann is an engineer in bioinformatics at the Institute of
Biology of Ecole normale supérieure (IBENS) in the team Computational
Systems Biology. She is working on single-cell RNA seq data in both
analysis and pipeline development.

Heather Marlow (Institut Pasteur, UMR3738)

François Spitz (Institut Pasteur, UMR3738)

 


Q. Le matériel (slides, etc) sera-t-il disponible en ligne après l'évènement pour celles et ceux qui ne peuvent pas participer ?

R. Généralement pour ce genre d'école nous demandons aux intervenants de faire une version publiable sur le site web (c'est à dire avec toutes les sourcesclairement indiquées, en retirant les résultats confidentiels ou non encore publiés etc...). Toutefois c'est à la discrétion de l'intervenant.

Q. Comment savoir si je peux bénéficier du tarif "académique" ou pas ?

R. Tout dépend de votre "employeur" officiel et non du laboratoire/institut auquel vous êtes rattaché. Le tarif académique s'applique aux personnels financés par établissement public c'est à dire ayant une fiche de paye provenant d'un EPST (CNRS, IFSTTAR, INED, INRA, INRIA, INSERM, IRD, IRSTEA) ou d'une Université. De plus cette école étant une école CNRS, cela est gratuit pour les agents CNRS.

Q. Est-il possible d'effectuer plusieurs candidatures par laboratoire ?

R. Il faut "prioritiser" en interne vos candidatures car vue la demande attendue, le nombre de places restreint et la volonté de diffusion la plus large possible au niveau national, il y a quasiment aucune chance que 2 candidatures d'un même laboratoire soient sélectionnées.

Q. La formation est-elle en anglais ou en français ?

R. La formation sera dispensée en anglais

Q. Est-il possible de régler une inscription par bon de commande ?

R. 


If you have a question or need addition information regarding the single-cell school 2019, please fill the form below. We will contact you as soon as possible.

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