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Marília Dias Vieira Braga
I am currently a staff researcher at the Genome Informatics group
Contact | Interests | Teaching | Languages | Academic Info | Experience | Software | Publications


Every human being is the union of two worlds: the inner one and the outer one. Both are infinite and equally important. Freedom is closely connected to the inner world. The outer one, of relationships to the society and to the environment, is closely connected to responsibility. Deeper responsibility allows higher flights in the spiritual development of the inner world.

Therefore, true freedom can only be achieved with responsibility. Talking about true freedom necessarily implies responsibility. Responsibility is an inseparable property of true freedom. I like to insist on this point, just to make it clear what kind of freedom we are talking about.

How else can we identify true freedom? In addition to being accompanied by a deep responsibility, true freedom is the most fertile ground for empathy, ecology, patience, solidarity, courage and the virtue that surrounds everything: deep love, with full respect for the environment.


Contact

e-mails: mbraga AT cebitec.uni-bielefeld.de
mdvbraga AT posteo.net

Universität Bielefeld
Technische Fakultät
AG Genominformatik
Postfach 10 01 31
33501 Bielefeld
Germany

Office U10-139

Office hours: TBA

Phone: +49 (0)521 106-3840
Fax....: +49 (0)521 106-6495

Interests

Professional interests:
  • Bioinformatics: evolution, genome rearrangements
  • Computer Science: algorithms, combinatorics, software engineering, Java
  • Research organization

Main personal interests:

  • Being a mother!
  • Ecology & Urban ecology
Teaching

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)

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2023 - Summer Semester:

Algorithms in Comparative Genomics (with R. Wittler)

More details in GI website      Uni-Bielefeld eKVV: Lecture | Exercises  

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2022/2023 - Winter Semester:

Research Café - (Computer) Science and Society

More details in GI website      Uni-Bielefeld eKVV: Seminar 

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2021/2022 - Winter Semester:

Algorithms in Comparative Genomics

More details in GI website      Uni-Bielefeld eKVV: Lecture | Exercises  

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2020/2021 - Winter Semester:

Algorithms in Comparative Genomics

More details in GI website      Uni-Bielefeld eKVV: Lecture | Exercises  

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2018/2019 - Winter Semester:

Algorithms in Genome Research (with Jens Stoye)

More details in GI website      Uni-Bielefeld eKVV: Lecture | Exercises  

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2016 - Summer Semester:

Algorithms in Bioinformatics (Seminar)    Uni-Bielefeld eKVV  


COPPE/UFRJ (Rio de Janeiro, Brazil)

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2011 - from March to May:

Computational Biology (with Celina M. H. de Figueiredo)


Bielefeld University (Germany)

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2010 - Summer Semester:

Classical Papers in Bioinformatics (Seminar)    Uni-Bielefeld eKVV  

Combinatorics of Genome Rearrangements (Seminar)    Uni-Bielefeld eKVV  

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2009/2010 - Winter Semester:

Bioinformatics Journal Club    Uni-Bielefeld eKVV  

Algorithmen in der Genomforschung (with Jens Stoye)    Uni-Bielefeld eKVV  

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2009 - Summer Semester:

Bioinformatics JOurnal Club (with Jens Stoye)    Uni-Bielefeld eKVV  

Algorithms in English (Seminar)    Uni-Bielefeld eKVV  


Languages
  • Portuguese
  • English
  • French
  • German
  • Spanish
Academic information


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)



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



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)


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


CV in Portuguese


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


Professional experience

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


Software
 
[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
 
[Nov 2008]  A java framework to deal with (signed) permutations which represent genomes in bioinformatics  >>  baobabLUNA


List of publications

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



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



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).