About Rodrigo
Read about Rodrigo’s project.
Supervision
Marc A. Marti-Renom
CNAG-CRG, 1st Supervisor
Luca Giorgetti
FMI, 2nd Supervisor
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).