2011

Marília D. V. Braga, Raphael Machado, Leonardo C. Ribeiro and Jens Stoye. Genomic distance under gene substitutions. In Proceedings of RECOMB-CG 2011. [Talk (pdf)]

Marília D. V. Braga, Raphael Machado, Leonardo C. Ribeiro and Jens Stoye. On the weight of indels in genomic distances. In Proceedings of RECOMB-CG 2011. [Talk (pptx)]

Marília D. V. Braga, Eyla Willing and Jens Stoye. Double cut and join with insertions and deletions. In Journal of Computational Biology (JCB), 18(9), p. 1167-1184, 2011.

Jakub Kovác, Robert Warren, Marília D. V. Braga and Jens Stoye. Restricted DCJ Model (The Problem of Chromosome Reincorporation). In Journal of Computational Biology (JCB), 18(9), p. 1231-1241, 2011.

Marcelo P. Lopes, Marília D. V. Braga, Celina M. H. de Figueiredo, Rodrigo de A. Hausen and Luis Antonio B. Kowada. Analysis and Implementation of Sorting by Transpositions using Permutation Trees. In Proceedings of BSB 2011, Lecture Notes in Bioinformatics (LNBI), vol. 6832, p. 42-49, 2011.

2010

Marília D. V. Braga. On sorting genomes with DCJ and indels. In Proceedings of RECOMB-CG 2010, Lecture Notes in Bioinformatics (LNBI), vol. 6398, p. 62-73, 2010. [Talk (pdf)]

Jakub Kovac, Marília D. V. Braga and Jens Stoye. The problem of chromosome reincorporation in DCJ sorting and halving. In Proceedings of RECOMB-CG 2010, Lecture Notes in Bioinformatics (LNBI), vol. 6398, p. 13-24, 2010.

Marília D. V. Braga, Eyla Willing and Jens Stoye. Genomic distance with DCJ and indels. In Proceedings of WABI 2010, Lecture Notes in Bioinformatics (LNBI), vol. 6293, p. 90-101, 2010.

Marília D. V. Braga and Jens Stoye. The solution space of sorting by DCJ. In Journal of Computational Biology (JCB), 17(9), p. 1145-1165, 2010.

2009

Marília D. V. Braga, Christian Gautier and Marie-France Sagot. An asymmetric approach to preserve common intervals while sorting by reversals. Algorithms for Molecular Biology, 2009.

Marília D. V. Braga and Jens Stoye. Counting all DCJ sorting scenarios. In Proceedings of RECOMB-CG 2009, Lecture Notes in Bioinformatics (LNBI), vol. 5817, p. 36-47, 2009. [Talk (pdf)]

Said S. Adi, Marília D. V. Braga, Cristina G. Fernandes, Carlos E. Ferreira, Fábio V. Martinez, Marie-France Sagot, Marco A. Stefanes, Christian Tjandraatmadja and Yoshiko Wakabayashi. Repetition-free longest common subsequence. Discrete Applied Mathematics, 2009.

Marília D. V. Braga. babobabLUNA: the solution space of sorting by reversals. Bioinformatics, vol. 25, no. 14, 1833--1835, 2009.

Marília D. V. Braga. Exploring the solution space of sorting by reversals when analyzing genome rearrangements. PhD thesis, 2009. Available here. Research supported by Program Alßan - European Union (grant no. E05D053131BR).

Claire Lemaitre, Marília D. V. Braga, Christian Gautier, Marie-France Sagot, Eric Tannier and Gabriel A. B. Marais. Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes. Genome Biology and Evolution, 2009.

2008

Marília D. V. Braga, Marie-France Sagot, Celine Scornavacca and Eric Tannier. Exploring the solution space of sorting by reversals with experiments and an application to evolution. Transactions on Computational Biology and Bioinformatics, vol. 5, no. 3, 348--356, 2008.

Said S. Adi, Marília D. V. Braga, Cristina G. Fernandes, Carlos E. Ferreira, Fábio V. Martinez, Marie-France Sagot, Marco A. Stefanes, Christian Tjandraatmadja, Yoshiko Wakabayashi. Repetition-free longest common subsequence. Latin-American Algorithms, Graphs and Optimization Symposium (LAGOS), 2007. Electronic Notes in Discrete Mathematics, vol. 30, p. 243-248, 2008.

2007

Marília D. V. Braga, Marie-France Sagot, Celine Scornavacca and Eric Tannier. The solution space of sorting by reversals. International Symposium on Bioinformatics Research and Applications (ISBRA). Lecture Notes in Bioinformatics (LNBI), vol. 4463, p. 293-304, May 2007. [Talk (pdf)]

2003

André L. Vettore et al. Analysis and functional annotation of an expressed sequence tag collection for tropical crop Sugarcane. Genome Research, 13, p. 2725-2735, 2003.

2002

João Meidanis, Marília D. V. Braga and Sergio Verjovski-Almeida. Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa. Microbiology and Molecular Biology Reviews, vol. 66, no. 2, p. 272-299, June 2002.

Marília D. V. Braga and João Meidanis. An algorithm that builds a set of strings given its overlap graph. Latin American Theoretical Informatics (LATIN). Lecture Notes in Computer Science (LNCS), vol. 2286, p. 52-63, April 2002.

2001

Guilherme P. Telles, Marília D. V. Braga, Zanoni Dias, Tzy-Li Lin, José A. A. Quitzau, Felipe R. da Silva and João Meidanis. Bioinformatics of the Sugarcane EST Project. Genetics and Molecular Biology, vol. 24, no. 1-4, p. 9-15, 2001.

2000

Marília D. V. Braga. Grafos de sequências de DNA. Master thesis (in portuguese), 2000. Available here. Research supported by FAPESP Brazilian agency (Grant 97/11629-2).