Chromosome structure determination using modelling and Hi-C data

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   IMPORTANT DATES for this Course
   Deadline for applications: November 20th 2013
   Notification of acceptance within 72 hours of application (working days count)
   Course date: November 27th to November 29th 2013


Davide Baù
After obtaining a Masters degree in Chemistry at the University of Padua and completing a one-year course in bioinformatics at the University of Cologne, Davide moved to the University College Dublin, where, in 2008, he got his PhD at the School of Computer Science and Informatics under the supervision of Dr. Gianluca Pollastri. His thesis focused on the development of an optimization algorithm that searched the space of protein C-alpha trace configurations under the guidance of a statistical potential based on features predicted by machine learning techniques.
After his PhD, Davide moved to Dr. Marc Marti-Renom´s laboratory where he started to work on genomic domains and genome structures determination by integrating 3C-based and FISH data into the Integrative Modeling Platform (IMP). During this time, he developed the methods that led to the determination of the first high-resolution model of a human genomic region, the alpha-globin genomic domain, and of the first three-dimensional model of an entire bacterial genome, the Caulobacter Crescentus. He is currently involved in different collaborations that aim at determining the genome architecture of several organisms including Human, Yeast, Mycoplasma Pneumoniae, Fly and Mouse.

Affiliation: Centro Nacional de Análisis Genómico (CNAG) and Center for Genomic Regulation (CRG), Barcelona, ES

François Serra
François Serra obtained his Degree in Biology, specialized in Physiology and Neurophysiology, his Master's Degree in Structural genomics and bioinformatics (Strasbourg I Universty, France) and it's PhD in Evolutionary Genomics in the Department of Bioinformatics at the CIPF (Valencia). He is now part of the Structural Genomics team of Marc Marti-Renom at CNAG and at CRG (Barcelona).
His main research interests are grounded on comparative genomics and evolution with a special focus on the effect of evolution in the structural arrangement of genomes. He has taught MEPA three times for GTPB, and similar courses at CIPF (Valencia, ES) and the Department of Genetics of the University of Cambridge, UK.

Affiliation: Centro Nacional de Análisis Genómico (CNAG) and Center for Genomic Regulation (CRG), Barcelona, ES

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 3D modeling of Topologically Associated Domains (TADs) and genomes. 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.

Target Audience

The course is oriented to experimental researchers with minimal computational skills, at the graduate and post-graduate levels. It is also suitable for bioinformatics developers at all levels. We anticipate that this course is attended by people with several types of interests in genome organization. It is likely that they may also aim at getting involved in generating Hi-C data for chromosome structure determination and that they want to model its 3D representation, but that does not need to be the case for all the participants: they may, for example, just want to explore publicly available data.

Course Pre-requisites

Recommended Linux and basic Python programming skills, graduate level in Life Sciences.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

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Last updated:  October 29th 2013