Genome Rearrangement Problems Viewed Through Permutations, Matrices and Other Algebraic Concepts

• Grant number: 12/14104-0
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: January 01, 2013
• End date: August 31, 2016
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Theory of Computation
• Principal Investigator: João Meidanis
• Grantee: Priscila Do Nascimento Biller
• Host Institution: Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated scholarship(s): 13/25084-2 - Ancestral artificial genomes, BE.EP.DR

Abstract

Rearrangements are evolutionary events that modify in different ways the order of large segments in genomes. To explain the evolutionary history of a set of species with rearrangements can be seen as an computational optimization problem, called Genome Rearrangement Problem. This problem consists in finding a tree which relates the set of genomes received, minimizing the sum of edge weights, where the weight of an edge is the number of rearrangements that explains the evolution between the genomes of incident vertices. The quality of the inference and the complexity of the problem depend on the rearrangement model used, which formally defines how the genomes can be modified. In this project we will investigate rearrangement problems with the algebraic model, introduced by Meidanis and Dias and extended by Feijão and Meidanis. It is not yet known the efficiency of the algebraic model in rearrangement problems with three or more genomes, in connection with the algebraic model. In this project we intend to investigate these complexities and seeking new forms, more efficient, to solve genome rearrangement problems.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

PEREIRA ZANETTI, JOAO PAULO; BILLER, PRISCILA; MEIDANIS, JOAO. Median Approximations for Genomes Modeled as Matrices. Bulletin of Mathematical Biology, v. 78, n. 4, p. 786-814, APR 2016. (12/14104-0, 12/13865-7)

BILLER, PRISCILA; PEREIRA ZANETTI, JOAO PAULO; MEIDANIS, JOAO; SETUBAL, JC; SILVA, WM. Center Genome with Respect to the Rank Distance. ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, BSB 2020, v. 12558, p. 9-pg., 2020-01-01. (12/13865-7, 12/14104-0, 18/00031-7)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

BILLER, Priscila Do Nascimento. Análise estatística da evolução por rearranjo de genomas. 2016. Doctoral Thesis - Universidade Estadual de Campinas (UNICAMP). Instituto de Computação Campinas, SP.