|
2023
-
Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx and Jens Stoye.
Investigating the complexity of the double distance problems.
Accepted for publication in Algorithms for Molecular Biology.
-
Diego Rubert and Marília D. V. Braga.
Efficient gene orthology inference via large-scale rearrangements.
Algorithms for Molecular Biology 18: 14.
-
Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx and Jens Stoye.
On the class of double distance problems.
In Proceedings of RECOMB-CG 2023. LNBI, 13883.
2022
-
Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx and Jens Stoye.
A linear time algorithm for an extended version of the breakpoint double distance.
In Proceedings of WABI 2022. LIPIcs, 242(13), 1-16.
-
Diego Rubert and Marília D. V. Braga.
Gene orthology inference via large-scale rearrangements for partially assembled genomes.
In Proceedings of WABI 2022. LIPIcs, 242(24), 1-22.
2021
-
Diego Rubert, Daniel Doerr and Marília D. V. Braga.
The potential of family-free rearrangements towards gene orthology inference.
Journal of Bioinformatics and Computational Biology (JBCB), 19(6):2140014.
-
Diego Rubert, Fábio V. Martinez and Marília D. V. Braga.
Natural family-free genomic distance.
Algorithms for Molecular Biology 16: 4.
-
Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr and Jens Stoye.
Computing the rearrangement distance of natural genomes.
Journal of Computational Biology (JCB) 28(4), pages 410-431.
-
Eyla Willing, Jens Stoye and Marília D. V. Braga.
Computing the inversion-indel distance.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(6):2314-2326.
2020
- Diego Rubert, Fábio V. Martinez and Marília D. V. Braga.
Natural family-free genomic distance.
In Proceedings of WABI 2020. LIPIcs, 172(3), 1-23.
-
Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr and Jens Stoye.
Computing the rearrangement distance of natural genomes.
In Proceedings of RECOMB 2020. LNBI, 12074. 3-18.
2018
- Diego Rubert, Edna A. Hoshino, Marília D. V. Braga, Jens Stoye and Fábio V. Martinez.
Computing the family-free DCJ similarity.
BMC Bioinformatics 19(Suppl. 6): 152.
2017
- Diego Rubert, Gabriel L. Medeiros, Edna A. Hoshino, Marília D. V. Braga, Jens Stoye and Fábio V. Martinez.
Algorithms for Computing the Family-Free Genomic Similarity under DCJ.
In Proceedings of RECOMB-CG 2017, Lecture Notes in Bioinformatics (LNBI), vol. 10562, p. 76-100.
-
Diego Rubert, Pedro Feijão, Marília D. V. Braga, Jens Stoye and Fábio V. Martinez. Approximating the DCJ distance of balanced genomes in linear time.
Algorithms for Molecular Biology 12: 3.
-
Poly H. Da Silva, Raphael Machado, Simone Dantas and Marília D. V. Braga. Genomic Distance with High Indel Costs.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 14(3): 728-732.
2016
- Diego Rubert, Pedro Feijão, Marília D. V. Braga, Jens Stoye and Fábio V. Martinez. A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates.
In Proceedings of WABI 2016, Lecture Notes in Bioinformatics (LNBI), vol. 9838, p. 293-306.
2015
- Fábio V. Martinez, Pedro Feijão, Marília D. V. Braga and Jens Stoye. On the family-free DCJ distance and similarity.
Algorithms for Molecular Biology 10: 13.
- Marília D. V. Braga and Jens Stoye. Sorting linear genomes with rearrangements and indels.
Transactions on Computational Biology and Bioinformatics (TCBB), 12(3), p. 500-506.
2014
- Fábio V. Martinez, Pedro Feijão, Marília D. V. Braga and Jens Stoye. On the family-free DCJ distance.
In Proceedings of WABI 2014, Lecture Notes in Bioinformatics (LNBI), vol. 8701, p. 174-186.
2013
- Eyla Willing, Simone Zaccaria, Marília D. V. Braga and Jens Stoye. On the inversion-indel distance.
In proceedings of
RECOMB-CG 2013.
- Marília D. V. Braga and Jens Stoye. Restricted DCJ-Indel Model Revisited. In proceedings of
BSB 2013,
Lecture Notes in Bioinformatics (LNBI), vol. 8213, p. 36-46. [Talk (pdf)]
- Marília D. V. Braga, Cedric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin and Roland Wittler. The Potential of Family-Free Genome Comparison. In Models and Algorithms for Genome Evolution (MAGE), pages 287-307 (chapter 13).
- Poly H. Da Silva, Raphael Machado, Simone Dantas and Marília D. V. Braga. DCJ-indel and DCJ-substitution distances with distinct operation costs. Algorithms for Molecular Biology, 8:21.
- Marília D. V. Braga. An overview of genomic distances modeled with indels. In proceedings of Computability in Europe (CiE) 2013, Lecture Notes in Computer Science (LNCS), vol. 7921, p. 22-31. [Talk (pdf)]
2012
- Poly H. Da Silva, Raphael Machado, Simone Dantas and Marília D. V. Braga. Restricted DCJ-indel model: sorting linear genomes with DCJ and indels. In proceedings of
RECOMB-CG 2012.
- Marília D. V. Braga. DCJ-substitution distance with distinct costs. Short paper in digital proceedings of BSB 2012.
- Poly H. Da Silva, Marília D. V. Braga, Raphael Machado and Simone Dantas. DCJ-indel distance with distinct operation costs. In Proceedings of
WABI 2012,
Lecture Notes in Bioinformatics (LNBI), vol. 7534, p. 378-390.
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 (TCBB), 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
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).
|
M. D. V. Braga's Lattes CV (Brazilian platform) - CNPq/Brazil