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- Poly H. da Silva, Raphael Machado, Simone Dantas, Marília D. V. Braga
- Algorithms for Molecular Biology
- 2012

Classical approaches to compute the genomic distance are usually limited to genomes with the same content and take into consideration only rearrangements that change the organization of the genome (i.e. positions and orientation of pieces of DNA, number and type of chromosomes, etc.), such as inversions, translocations, fusions and fissions. These… (More)

- Poly H. da Silva, Raphael Machado, Simone Dantas, Marília D. V. Braga
- BMC Bioinformatics
- 2012

The double-cut-and-join (DCJ) is a model that is able to efficiently sort a genome into another, generalizing the typical mutations (inversions, fusions, fissions, translocations) to which genomes are subject, but allowing the existence of circular chromosomes at the intermediate steps. In the general model many circular chromosomes can coexist in some… (More)

- Marília D. V. Braga, Raphael Machado, Leonardo C. Ribeiro, Jens Stoye
- BMC Bioinformatics
- 2011

Classical approaches to compute the genomic distance are usually limited to genomes with the same content, without duplicated markers. However, differences in the gene content are frequently observed and can reflect important evolutionary aspects. A few polynomial time algorithms that include genome rearrangements, insertions and deletions (or… (More)

- Marília D. V. Braga, Raphael Machado, Leonardo C. Ribeiro, Jens Stoye
- BMC Bioinformatics
- 2011

The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of such markers. In these models, a deletion and a subsequent insertion that occur at the same position of the genome count for two sorting steps. Here we… (More)

- Raphael Machado, Celina M. H. de Figueiredo
- Discrete Applied Mathematics
- 2011

- Raphael Machado, Celina M. H. de Figueiredo, Nicolas Trotignon
- Discrete Mathematics
- 2013

A graph G is chordless if no cycle in G has a chord. In the present work we investigate the chromatic index and total chromatic number of chordless graphs. We describe a known decomposition result for chordless graphs and use it to establish that every chordless graph of maximum degree ∆ ≥ 3 has chromatic index ∆ and total chromatic number ∆+1. The proofs… (More)

- Hélio B. Macêdo Filho, Raphael Machado, Celina M. H. de Figueiredo
- Algorithmica
- 2012

The class of unichord-free graphs was recently investigated in the context of vertex-colouring (Trotignon and Vušković in J Graph Theory 63(1): 31–67, 2010), edge-colouring (Machado et al. in Theor Comput Sci 411(7–9): 1221–1234, 2010) and total-colouring (Machado and de Figueiredo in Discrete Appl Math 159(16): 1851–1864, 2011). Unichord-free graphs proved… (More)

- Guilherme Dias da Fonseca, Celina M. H. de Figueiredo, Vinícius G. P. de Sá, Raphael Machado
- Theor. Comput. Sci.
- 2014

A unit disk graph is the intersection graph of n congruent disks in the plane. Dominating sets in unit disk graphs are widely studied due to their applicability in wireless ad-hoc networks. Because the minimum dominating set problem for unit disk graphs is NP-hard, numerous approximation algorithms have been proposed in the literature, including some PTASs.… (More)