[BBC] [Gtpb] GTPB Bioinformatics Training course REMINDER - 3DAROC16 - 3C-based data analysis and 3D reconstruction of chromatin folding

[Pedro Fernandes]

The Gulbenkian Training Programme in Bioinformatics

Applications for the bioinformatics training course

3DAROC16
3C-based data analysis and 3D reconstruction of chromatin folding
are open.
with Marc Marti-Renom, François Serra and Davide Baù

   IMPORTANT DATES for this Course
    Deadline for applications: September 30th 2016
    Notification of acceptance within 72 hours of application (working  
days count)
    Course date: Oct 10th to Oct 14th 2016

Please refer to the course website
http://gtpb.igc.gulbenkian.pt/bicourses/3DAROC16
for details.


Course Description
3C-based methods, such as Hi-C, produce a huge amount of raw data as  
pairs of DNA reads that are in close spatial proximity in the cell  
nucleus. Overall, those interaction matrices have been used to study  
how the genome folds within the nucleus, which is one of the most  
fascinating problems in modern biology. The rigorous analysis of those  
paired-reads using computational tools has been essential to fully  
exploit the experimental technique, and to study how the genome is  
folded in the space. Currently, there is a clear expansion on the  
wealth of data on genome structure with the availability of many  
datasets of Hi-C experiments down to 1Kb resolution (see for example:  
http://hic.umassmed.edu/welcome/welcome.php ;  
http://promoter.bx.psu.edu/hi-c/view.php or  
http://www.aidenlab.org/data.html ). In this course, participants will  
learn to use TADbit, a software designed and developed to manage all  
dimensionalities of the Hi-C data:

     1D - Map paired-end sequences to generate Hi-C interaction matrices
     2D - Normalize matrices and identify constitutive domains (TADs,  
compartments)
     3D - Generate populations of structures which satisfy the Hi-C  
interaction matrices
     4D - Analyze and compare different samples.

Participants can bring- specific biological questions and/or their own  
3C-based data to analyse during the course. At the end of the course,  
participants will be familiar with the TADbit software and will be  
able to fully analyse Hi-C data. Note: Although the TADbit software is  
central in this course, alternative software will be discussed for  
each part of the analysis.


Best regards
Pedro Fernandes

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



_______________________________________________
GTPB mailing list
GTPB at igc.gulbenkian.pt
https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb