CSDM14 - Chromosome structure determination using modelling and Hi-C data

Nov/25 09:00 - Nov/28 18:00
Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal
Tuesday, November 25, 2014 - 09:00 to Friday, November 28, 2014 - 18:00

Instituto Gulbenkian de Ciência,
Apartado 14, 2781-901 Oeiras, Portugal

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


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.


Related resources

Event contact information

Pedro Fernandes
Instituto Gulbenkian de Ciência
Apartado 14
2781-901 OEIRAS
Tel +351 21 4407912