Research Projects

Integration of experimental data into a single framework to 3D genomics models

National Center for Genomic Analysis (CNAG-CRG) / National Genome Sequencing Centre

Barcelona

Spain

3/13

Objectives

Develop a single framework to model 3D genomes based on diverse datasets obtained by ESRs. The global aim will be accomplished with 3 objectives:
1. Proper genome description/representation.
2. Implementation of new restraints types to represent the input data.
3. Development of new sampling strategies to identify the minima that satisfies the input restraints.

Methodology

Computational development of a Python modules to TADbit for the use of diverse and additional input restraints.

Expected Results

An updated TADbit module to deal with diverse datasets interrogating the genome structure. The resulting methods and software will be used within the ETN for modelling genomes and genomic domains.

Planned Secondments

FMI, Switzerland (3 months):
Imaging
EMBL, Germany (3 months):
Hi-C experiments
ELISAVA, Spain (1 month):
Design of new ways of representing genomes
MPIMG, Germany (4 months):
Analysis of genetic alterations

Enrolment in doctoral programs

PhD in Biochemistry from Universitat Pompeu Fabra, Barcelona

References

Goodstadt, M. & Marti-Renom, M. A. Challenges for visualizing three-dimensional data in genomic browsers. FEBS Lett 591, 2505-2519, doi:10.1002/1873-3468.12778 (2017).

Serra, F. et al. Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors. PLoS Comput Biol 13, e1005665, doi:10.1371/journal.pcbi.1005665 (2017).

Trussart, M. et al. Assessing the limits of restraint-based 3D modeling of genomes and genomic domains. Nucleic Acids Res 43, 3465-3477, doi:10.1093/nar/gkv221 (2015).