Chromosome structure determination using modelling and Hi-C data

Downloadable poster in PDF
A Testimonial:
I do not have the time to come this year, however I should say that it is a course that introduces one of the most fascinating problem of modern computational biology that of building 3D models of genome structures. Both the organisation and the instructors are excellent and I really enjoyed it last year.

Costas Bouyioukos,
Institute of Systems and Synthetic Biology
Évry, Ile-De-France, FR

You may be interested in reading the review paper
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
Nature Reviews Genetics 14, 390-403 (2013) doi:10.1038/nrg3454 (Open Access)

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


Marc A. Marti-Renom
I obtained a Ph.D. in Biophysics from the UAB where I worked on protein folding under the supervision of Professors B. Oliva, F.X. Aviles and M. Karplus. After that, I went to the US for a postdoctoral training on protein structure modeling at the Sali Lab (Rockefeller University) as the recipient of the Burroughs Wellcome Fund fellowship. Later on, I was appointed Assistant Adjunct Professor at UCSF. Between 2006 and 2011, I headed of the Structural Genomics Group at the CIPF in Valencia (Spain). Currently, I am ICREA research professor and lead the Genome Biology Group at the National Center for Genomic Analysis (CNAG) and the Structural Genomics Group at the Centre for Genomic Regulation (CRG), both in Barcelona. Our group is broadly interested on how RNA, proteins and genomes organize and regulate cell fate. I am Associate Editor of the PLoS Computational Biology journal and have published over 70 articles in international peer-reviewed journal.

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

Davide Baù
After obtaining a Master 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 Genomic 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 modeling of Hi-C data.

The course will cover all the aspect of modeling with Hi-C data:
  1. Generation of Hi-C contact matrices from raw data (that is, iterative mapping of the fastq reads to the reference genome, cleaning and normalization)
  2. Analysis of Hi-C matrices (Hi-C map visualization, TAD identification, experiment comparison, and TAD selection)
  3. 3D modeling and analysis of TADs
The 3D module of TADbit is based on a computational module of the Integrative Modeling Platform 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.

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

IGC Homepage

Last updated:  Oct11th 2014