[BBC] [Gtpb] CSDM14 - Chromosome structure determination using modelling and Hi-C data - Bioinformatics Training Course - Announcement/Reminder

[Pedro Fernandes]

TRAINING COURSE ANNOUNCEMNT/REMINDER

The training course CSDM14 is open for applications.

    IMPORTANT DATES for this Course
    Deadline for applications: November 15th 2014
    Notification of acceptance within 72 hours of application
    Course date: November 25th to November 28th 2014

http://gtpb.igc.gulbenkian.pt/bicourses/CSDM14/

CSDM14 - Chromosome structure determination using modelling and Hi-C data
with Marc Marti-Renom, Davide Baù and François Serra

Welcome to the world of using Hi-C data -  
http://www.ncbi.nlm.nih.gov/pubmed/22652625 - in the context of  
discovering genome organization.

Course description
The sequence of a genome alone does not carry enough information to  
fully understand how genomic processes are carried out in the cell  
nucleus; to achieve this, the knowledge of the three-dimensional (3D)  
architecture of a genome is necessary. Advances in genomic  
technologies and the development of new analytical methods, such as  
3C-based methods, have allowed getting insights at unprecedented  
resolution into how the genome is organized. Recently, it has been  
shown that chromatin is organized in Topologically Associating Domains  
(TADs), large interaction domains that appear to be conserved among  
different cell types. In this course, participants will learn to use  
TADbit, a software for the analysis and modeling of Hi-C data.

The course will cover all the aspects of modeling with Hi-C data:

     Generation of Hi-C contact matrices from raw data (that is,  
iterative mapping of the fastq reads to the reference genome, cleaning  
and normalization)
     Analysis of Hi-C matrices (Hi-C map visualization, TAD  
identification, experiment comparison, and TAD selection)
     3D modeling and analysis of TADs

The 3D module of TADbit is based on a computational module of the  
Integrative Modeling Platform (IMP,  
http://www.integrativemodeling.org) that uses chromosome conformation  
capture data to determine the 3D architecture of genomic domains and  
entire genomes at unprecedented resolutions. Participants can bring-in  
specific biological questions and/or their on data to work on during  
the course. At the end of the course, participants will be familiar  
with the TADbit software, enabling them to fully analyze and model  
Hi-C data.
Target Audience

The course is oriented to experimental researchers and  
bioinformaticians at the graduate and post-graduate levels. The last  
edition of this course was attended by people with different  
backgrounds and interested in the genome organization.
Moreover, Hi-C data have recently been used in metagenomics studies to  
accurately cluster metagenome assembly contigs into groups that  
contain nearly complete genomes of each species.
It is likely that the participants to this course aim at getting  
involved in generating Hi-C data for chromosome structure  
determination or that they just want to be able to correctly interpret  
and analyze publicly available data.

The Linux and Programming skills are really only recommended, not essential.

Thank you for your interest

Pedro Fernandes
-- 
Pedro Fernandes
Instituto Gulbenkian de Ciência
Apartado 14
2781-901 OEIRAS
PORTUGAL
Tel +351 21 4407912
http://gtpb.igc.gulbenkian.pt






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