| 2026 | WABI | On the Complexity of the (ℓ, k)-Median Problems. | Lus Cunha, Thiago Nascimento, Marlia D. V. Braga, Jens Stoye |
| 2022 | WABI | A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. | Marlia D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye |
| 2022 | WABI | Gene Orthology Inference via Large-Scale Rearrangements for Partially Assembled Genomes. | Diego P. Rubert, Marlia D. V. Braga |
| 2020 | RECOMB | Computing the Rearrangement Distance of Natural Genomes. | Leonard Bohnenkmper, Marlia D. V. Braga, Daniel Doerr, Jens Stoye |
| 2020 | WABI | Natural Family-Free Genomic Distance. | Diego P. Rubert, Fbio Viduani Martinez, Marlia D. V. Braga |
| 2017 | RECOMB | Algorithms for Computing the Family-Free Genomic Similarity Under DCJ. | Diego P. Rubert, Gabriela Medeiros, Edna Ayako Hoshino, Marlia D. V. Braga, Jens Stoye, Fbio Viduani Martinez |
| 2016 | WABI | A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates. | Diego P. Rubert, Pedro Feijo, Marlia D. V. Braga, Jens Stoye, Fbio Viduani Martinez |
| 2014 | WABI | On the Family-Free DCJ Distance. | Fbio Viduani Martinez, Pedro Feijo, Marlia D. V. Braga, Jens Stoye |
| 2013 | CiE | An Overview of Genomic Distances Modeled with Indels. | Marlia D. V. Braga |
| 2012 | WABI | DCJ-indel Distance with Distinct Operation Costs. | Poly H. da Silva, Marlia D. V. Braga, Raphael Machado, Simone Dantas |
| 2010 | RECOMB | On Sorting Genomes with DCJ and Indels. | Marlia D. V. Braga |
| 2010 | RECOMB | The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. | Jakub Kovc, Marlia D. V. Braga, Jens Stoye |
| 2010 | WABI | Genomic Distance with DCJ and Indels. | Marlia D. V. Braga, Eyla Willing, Jens Stoye |
| 2009 | RECOMB | Counting All DCJ Sorting Scenarios. | Marlia D. V. Braga, Jens Stoye |
| 2002 | LATIN | An Algorithm That Builds a Set of Strings Given Its Overlap Graph. | Marlia D. V. Braga, Joao Meidanis |