João Paulo Pereira Zanetti

• Abstract

  Genome comparison can be made in several ways. In many applications, reducing the differences between two genomes to a single real number expressing their distance is important. In recent years, a measure called DCJ distance, which combines biological appeal with computational efficiency, has been heavily used. Another measure called algebraic distance, related to the rank distance in mat…

  Advances in Matrix-based Genome Rearrangement Theory, BP.PD

• Abstract

  The genome rearrangement problem consists in minimizing the number of evolutionary events between two given genomes. This is the basis of one of the most studied themes in bioinformatics. The Algebraic Model for Genome Rearrangements is a way to define genome rearrangement using proven tools from group theory.This doctorate aims to apply the algebraic model to the genome median problem an…

  Algebraic Model for Genome Rearrangements, BP.DR

• Abstract

  This project intends to investigate the computational complexity of PQR tree construction. PQR trees are data structures relevant for the problem of permuting the columns of a binary matrix in order to leave their rows with all their 1s in consecutive positions, with applications in planarity, interval graphs, and problems in computational biology. Both online and offline algorithms wil…

  Complexity of PQR Tree Construction, BP.MS

(Only some records are available in English at this moment)

• Abstract

  The genome median problem is a very important problem in bioinformatics. We still do not know whether it is easy under the new Adjacency Algebraic Theory, or NP-Hard. We are interested in a generalization of it, the matrix median problem, that we believe is easier.We plan to study the matrix median problem, and its relation with the genome median problem. (AU)

  Algebraic model for genome rearrangements, BE.EP.DR