An Algorithm That Builds a Set of Strings Given Its Overlap Graph. - Marília D. V. Braga; Joao Meidanis (LATIN, 2002)

The Solution Space of Sorting by Reversals. - Marília D. V. Braga; Marie-France Sagot; Céline Scornavacca; Eric Tannier (ISBRA, 2007)

Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution. - Marília D. V. Braga; Marie-France Sagot; Céline Scornavacca; Eric Tannier (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Counting All DCJ Sorting Scenarios. - Marília D. V. Braga; Jens Stoye (RECOMB-CG, 2009)

An asymmetric approach to preserve common intervals while sorting by reversals. - Marília D. V. Braga; Christian Gautier; Marie-France Sagot (Algorithms Mol. Biol., 2009)

baobabLUNA: the solution space of sorting by reversals. - Marília D. V. Braga (Bioinform., 2009)

On Sorting Genomes with DCJ and Indels. - Marília D. V. Braga (RECOMB-CG, 2010)

The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. - Jakub Kovác; Marília D. V. Braga; Jens Stoye (RECOMB-CG, 2010)

Genomic Distance with DCJ and Indels. - Marília D. V. Braga; Eyla Willing; Jens Stoye (WABI, 2010)

Repetition-free longest common subsequence. - Said Sadique Adi; Marília D. V. Braga; Cristina G. Fernandes; Carlos Eduardo Ferreira; Fábio Viduani Martinez; Marie-France Sagot; Marco Aurelio Stefanes; Christian Tjandraatmadja; Yoshiko Wakabayashi (Discret. Appl. Math., 2010)

The Solution Space of Sorting by DCJ. - Marília D. V. Braga; Jens Stoye (J. Comput. Biol., 2010)

Analysis and Implementation of Sorting by Transpositions Using Permutation Trees. - Marcelo P. Lopes; Marília D. V. Braga; Celina M. H. de Figueiredo; Rodrigo de A. Hausen; Luis Antonio Brasil Kowada (BSB, 2011)

Genomic distance under gene substitutions. - Marília D. V. Braga; Raphael Machado; Leonardo Costa Ribeiro; Jens Stoye (BMC Bioinform., 2011)

On the weight of indels in genomic distances. - Marília D. V. Braga; Raphael Machado; Leonardo Costa Ribeiro; Jens Stoye (BMC Bioinform., 2011)

Double Cut and Join with Insertions and Deletions. - Marília D. V. Braga; Eyla Willing; Jens Stoye (J. Comput. Biol., 2011)

Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation. - Jakub Kovác; Robert Warren; Marília D. V. Braga; Jens Stoye (J. Comput. Biol., 2011)

DCJ-indel Distance with Distinct Operation Costs. - Poly H. da Silva; Marília D. V. Braga; Raphael Machado; Simone Dantas (WABI, 2012)

Restricted DCJ-indel model: sorting linear genomes with DCJ and indels. - Poly H. da Silva; Raphael Machado; Simone Dantas; Marília D. V. Braga (BMC Bioinform., 2012)

The Potential of Family-Free Genome Comparison. - Marília D. V. Braga; Cédric Chauve; Daniel Doerr; Katharina Jahn 001; Jens Stoye; Annelyse Thévenin; Roland Wittler (Models and Algorithms for Genome Evolution, 2013)

An Overview of Genomic Distances Modeled with Indels. - Marília D. V. Braga (CiE, 2013)

Restricted DCJ-Indel Model Revisited. - Marília D. V. Braga; Jens Stoye (BSB, 2013)

DCJ-indel and DCJ-substitution distances with distinct operation costs. - Poly H. da Silva; Raphael Machado; Simone Dantas; Marília D. V. Braga (Algorithms Mol. Biol., 2013)

On the inversion-indel distance. - Eyla Willing; Simone Zaccaria; Marília D. V. Braga; Jens Stoye (BMC Bioinform., 2013)

On the Family-Free DCJ Distance. - Fábio Viduani Martinez; Pedro Feijão; Marília D. V. Braga; Jens Stoye (WABI, 2014)

On the family-free DCJ distance and similarity. - Fábio Viduani Martinez; Pedro Feijão; Marília D. V. Braga; Jens Stoye (Algorithms Mol. Biol., 2015)

Sorting Linear Genomes with Rearrangements and Indels. - Marília D. V. Braga; Jens Stoye (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates. - Diego P. Rubert; Pedro Feijão; Marília D. V. Braga; Jens Stoye; Fábio Viduani Martinez (WABI, 2016)

Algorithms for Computing the Family-Free Genomic Similarity Under DCJ. - Diego P. Rubert; Gabriela Medeiros; Edna Ayako Hoshino; Marília D. V. Braga; Jens Stoye; Fábio Viduani Martinez (RECOMB-CG, 2017)

Approximating the DCJ distance of balanced genomes in linear time. - Diego P. Rubert; Pedro Feijão; Marília Dias Vieira Braga; Jens Stoye; Fábio Viduani Martinez (Algorithms Mol. Biol., 2017)

Genomic Distance with High Indel Costs. - Poly H. da Silva; Raphael Machado; Simone Dantas; Marília D. V. Braga (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Computing the family-free DCJ similarity. - Diego P. Rubert; Edna Ayako Hoshino; Marília D. V. Braga; Jens Stoye; Fábio Viduani Martinez (BMC Bioinform., 2018)

Natural family-free genomic distance. - Diego P. Rubert; Fábio Viduani Martinez; Marília D. V. Braga (Algorithms Mol. Biol., 2021)

The potential of family-free rearrangements towards gene orthology inference. - Diego P. Rubert; Daniel Doerr; Marília D. V. Braga (J. Bioinform. Comput. Biol., 2021)

Computing the Rearrangement Distance of Natural Genomes. - Leonard Bohnenkämper; Marília D. V. Braga; Daniel Doerr; Jens Stoye (J. Comput. Biol., 2021)

Computing the Inversion-Indel Distance. - Eyla Willing; Jens Stoye; Marília D. V. Braga (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. - Marília D. V. Braga; Leonie R. Brockmann; Katharina Klerx; Jens Stoye (WABI, 2022)

Gene Orthology Inference via Large-Scale Rearrangements for Partially Assembled Genomes. - Diego P. Rubert; Marília D. V. Braga (WABI, 2022)

On the Class of Double Distance Problems. - Marília D. V. Braga; Leonie R. Brockmann; Katharina Klerx; Jens Stoye (RECOMB-CG, 2023)

Efficient gene orthology inference via large-scale rearrangements. - Diego P. Rubert; Marília D. V. Braga (Algorithms Mol. Biol., 2023)

Closing the complexity gap of the double distance problem. - Luís Cunha 001; Thiago Lopes; Uéverton S. Souza; Marília D. V. Braga; Jens Stoye (CoRR, 2024)

Investigating the complexity of the double distance problems. - Marília D. V. Braga; Leonie R. Brockmann; Katharina Klerx; Jens Stoye (Algorithms Mol. Biol., 2024)