| Grant number: | 13/25084-2 |
| Support Opportunities: | Scholarships abroad - Research Internship - Doctorate |
| Start date: | May 01, 2014 |
| End date: | April 30, 2015 |
| Field of knowledge: | Physical Sciences and Mathematics - Computer Science - Theory of Computation |
| Principal Investigator: | João Meidanis |
| Grantee: | Priscila Do Nascimento Biller |
| Supervisor: | Eric Tannier |
| Host Institution: | Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil |
| Institution abroad: | Institut National de Recherche en Informatique et en Automatique (INRIA Rhône-Alpes), France |
| Associated to the scholarship: | 12/14104-0 - Genome Rearrangement Problems Viewed Through Permutations, Matrices and Other Algebraic Concepts, BP.DR |
Abstract Molecular evolutionary studies systematically face a validation issue as we have no direct access to ancient molecules beyond a million years. So hypotheses about the shape of ancestral genomes which can be orders of magnitude older are difficult to test and to confirm. Methods to reconstruct ancestral genomes may be tested with simulated data, producing full scenarios they can compare with. But often simulations are designed to confirm the validity of a particular method, while they should be blind to the methods. A solution might be found in artificial life systems and in silico models of genome evolution. Aevol, developed in the Beagle INRIA project-team, was designed to understand processes of genome structural evolution, and is based on more sophisticate biology principles than most ad hoc simulators. We propose to use it to generate artificial data, of which we know the history, in order to test methods of inference of ancient genome structures. Aevol would have to be adapted to include speciation processes, a tracking procedure to record gene histories, and possibly lateral gene transfers between species. Several ancestral genome reconstruction methods have been designed both by the Beagle team and by the University of Campinas, as well as by several other teams around the world, in all cases independently from Aevol. The internship will consist in adapting Aevol and testing some of these methods, assessing the relevance of simplifying assumptions beyond each of them, and comparing the efficiency of different principles. (AU) | |
| News published in Agência FAPESP Newsletter about the scholarship: | |
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