Marília Dias Vieira Braga
I am currently a staff researcher at the Genome Informatics group I will offer a workshop in the DFH Festival of Uni Bielefeld: The only future is ancestral: inspirations from Krenak's provocative words

         - Nêgo Bispo quoting Mãe Joana, the one who couldn't read or write, but knew how to speak

Why using compost toilets? Why, indeed, would anyone take that path, when we are surrounded by infrastructure that can simply drive the 'work' away from us?

For me, it's a direct outgrowth of my deepest understanding of the beauty of the Earth - that she is life itself - and that connection with the Earth means embracing the sacredness of all of life. Moreover, that this world itself is the terrain of our spiritual journey, the place where our growth and development is enacted, where our challenges are faced and our truths are lived.

From that point of view, taking responsibility for our own existence, and especially not following the established absurdity of simply flushing toilet residues into clean water every day, is a spiritual necessity. There is no myth more fascinating, no realm of spirit or faerie more strange, exotic and entrancing, than the amazing creatures of the microbial world whose birth, growth, death and decay makes compost out of organic residues. For gardeners, soil builders and earth healers, there is no greater treasure than compost, with its recycled nutrients and complex colonies of microbial life.

Disconnecting from the infrastructure that has been granted is also a good step toward freeing yourself from the alienation imposed on your mind by that infrastructure and taking some of the many pernicious consequences (both local and far reaching) of that infrastructure off your shoulders.

(Freely adapted from Starhawk)

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Interests

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Professional interests: Bioinformatics: evolution, genome rearrangements Computer Science: algorithms, combinatorics, software engineering, Java Research organization Main personal interests: Being a mother! Ecology & Urban ecology

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Teaching

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Current teaching activities at Bielefeld University (Germany) 2023/2024 - Winter Semester: Research Café - (Computer) Science and Society More details in GI website      Uni-Bielefeld eKVV: Seminar  Former teaching activities Bielefeld University (Germany) ..................................................................... 2023 - Summer Semester: Algorithms in Comparative Genomics (with R. Wittler) More details in GI website      Uni-Bielefeld eKVV: Lecture | Exercises   ..................................................................... 2022/2023 - Winter Semester: Research Café - (Computer) Science and Society More details in GI website      Uni-Bielefeld eKVV: Seminar  ..................................................................... 2021/2022 - Winter Semester: Algorithms in Comparative Genomics More details in GI website      Uni-Bielefeld eKVV: Lecture | Exercises   ..................................................................... 2020/2021 - Winter Semester: Algorithms in Comparative Genomics More details in GI website      Uni-Bielefeld eKVV: Lecture | Exercises   ..................................................................... 2018/2019 - Winter Semester: Algorithms in Genome Research (with Jens Stoye) More details in GI website      Uni-Bielefeld eKVV: Lecture | Exercises   ..................................................................... 2016 - Summer Semester: Algorithms in Bioinformatics (Seminar)    Uni-Bielefeld eKVV   COPPE/UFRJ (Rio de Janeiro, Brazil) ..................................................................... 2011 - from March to May: Computational Biology (with Celina M. H. de Figueiredo) Bielefeld University (Germany) ..................................................................... 2010 - Summer Semester: Classical Papers in Bioinformatics (Seminar)    Uni-Bielefeld eKVV   Combinatorics of Genome Rearrangements (Seminar)    Uni-Bielefeld eKVV   ..................................................................... 2009/2010 - Winter Semester: Bioinformatics Journal Club    Uni-Bielefeld eKVV   Algorithmen in der Genomforschung (with Jens Stoye)    Uni-Bielefeld eKVV   ..................................................................... 2009 - Summer Semester: Bioinformatics JOurnal Club (with Jens Stoye)    Uni-Bielefeld eKVV   Algorithms in English (Seminar)    Uni-Bielefeld eKVV

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Languages

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Portuguese English French German Spanish

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Academic information

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Academic background

2011-2015	Research Project Leader in Bioinformatics at Inmetro - Brazil Grant PROMETRO no. 563087/10-2 (CNPq & Inmetro) Research fields: algorithms, genome rearrangements and evolution
2009-2010	Post-doc position in Bioinformatics at AG Genominformatik (Genome Informatics) - University of Bielefeld - Germany Research fields: algorithms, genome rearrangements and evolution
2005-2008	PhD in Bioinformatics - Laboratoire de Biométrie et Biologie Evolutive (LBBE) - University of Lyon (UCBL - France) Advisors: Marie-France Sagot and Eric Tannier Research fields: algorithms, genome rearrangements and evolution Available here. Research supported by Program Alßan - European Union (grant no. E05D053131BR).
1998-2000	Master's degree in Computer Science - Institute of Computing - University of Campinas (Unicamp - SP - Brazil) Advisor: João Meidanis Research fields: theory of computing and computational biology Version in Portuguese available here. Research supported by FAPESP Brazilian agency (grant no. 97/11629-2).
1994-1997	Bachelor's degree in Computer Science - Institute of Computing - University of Campinas (Unicamp - SP - Brazil)

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Participation on projects at the Bioinformatics Laboratory (LBI) - Institute of Computing - University of Campinas (Unicamp - SP - Brazil)

2001-2002	Bioinformatics support on the Human Cancer Genome project1,2
2000-2002	Automatic gene categorization on the Sugar Cane EST project (SUCEST)1,3
1999-2000	DNA Sequence assembling on Xylella fastidiosa bacterium genome project1

1	Project supported by Foundation for Research Support (FAPESP), São Paulo, Brazil
2	Project supported by Ludwig Institute for Cancer Research - Brazil
3	Project supported by Copersucar - Brazil

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Grants

Research project, 2011 to 2015 CNPq & Inmetro - Brazil (grant PROMETRO no. 563087/2010-2) Participation in Scientific Events, 2013 CNPq - Brazil (grant AVG no. 451784/2013-8) Promotion of Scientific Events, 2012 CNPq - Brazil (grant ARC no. 452871/2012-3) Doctoral scholarship, 2005 to 2008 Program Alßan, European Union (grant no. E05D053131BR) Master scholarship, 1998 to 2000 Foundation for Research Support (FAPESP), São Paulo, Brazil (grant no. 97/11629-2)

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Awards

Master thesis ''Graphs of DNA Sequences'' (in Portuguese - Grafos de Sequências de DNA) chosen among the best twelve in the year 2000 by the Brazilian Computer Society (SBC). Medal of Technologic and Scientific Merit, 2000, State of São Paulo Government, Brazil

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CV in Portuguese

   M. D. V. Braga's Lattes CV (Brazilian platform) - CNPq/Brazil

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Professional experience

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2004-2005	Software analyst Ci&T - Campinas - SP - Brazil
2003-2004	Bioinformatics system analyst Alellyx Applied Genomics - Campinas - SP - Brazil
2002-2003	Bioinformatics system analyst Scylla Bioinformatics - Campinas - SP - Brazil

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Software

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[Oct 2021]	A pipeline for inferring orthologs based on genome rearrangements	>>	OrthoFFGC
[Sep 2020]	An ILP for computing a family-free rearrangement distance	>>	gen-diff
[Jun 2020]	An ILP for computing the DCJ-indel distance of natural genomes	>>	ding

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List of publications

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2024 Marília D. V. Braga, Daniel Doerr, Diego P. Rubert and Jens Stoye. Family-Free Genome Comparison. In Comparative Genomics: Methods and Protocols, volume 2802 of Methods in Molecular Biology, 2024. Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx and Jens Stoye. Investigating the complexity of the double distance problems. Algorithms for Molecular Biology 19: 1. 2023 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. BMC Bioinformatics 14 (Suppl 15):S3. 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. BMC Bioinformatics 13 (Suppl 19):S14. 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. BMC Bioinformatics 12 (Suppl 9):S8. [Talk (pdf)] Marília D. V. Braga, Raphael Machado, Leonardo C. Ribeiro and Jens Stoye. On the weight of indels in genomic distances. BMC Bioinformatics 12(Suppl 9):S13. [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 4:16, 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 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).

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