PUB - Publikationen an der Universität Bielefeld

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• [28]
  

  2024 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2990270

  Dias Vieira Braga, M., Doerr, D., Rubert, D. P., & Stoye, J. (2024). Family-Free Genome Comparison. In J. C. Setubal, P. F. Stadler, & J. Stoye (Eds.), Methods in Molecular Biology: Vol. 2802. Comparative Genomics. Methods and Protocols (2nd ed., pp. 57-72). New York, NY: Humana. https://doi.org/10.1007/978-1-0716-3838-5_3

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• [27]
  

  2024 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2985702

  Dias Vieira Braga, M., Brockmann, L. R., Klerx, K., & Stoye, J. (2024). Investigating the complexity of the double distance problems. Algorithms for Molecular Biology, 19, 1. https://doi.org/10.1186/s13015-023-00246-y

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• [26]
  

  2023 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2981606

  Dias Vieira Braga, M., Brockmann, L. R., Klerx, K., & Stoye, J. (2023). On the Class of Double Distance Problems. In K. Jahn & T. Vinař (Eds.), Lecture Notes in Computer Science: Vol. 13883. Comparative Genomics. 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14–15, 2023, Proceedings (pp. 35-50). Cham: Springer Nature . https://doi.org/10.1007/978-3-031-36911-7_3

  PUB | DOI | WoS
   
• [25]
  

  2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2983338

  Rubert, D., & Dias Vieira Braga, M. (2023). Efficient gene orthology inference via large-scale rearrangements. Algorithms for Molecular Biology , 18(1), 14. https://doi.org/10.1186/s13015-023-00238-y

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• [24]
  

  2022 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2968237

  Rubert, D., & Dias Vieira Braga, M. (2022). Gene Orthology Inference via Large-Scale Rearrangements for Partially Assembled Genomes. In C. Boucher & S. Rahmann (Eds.), Leibniz International Proceedings in Informatics (LIPIcs): Vol. 242. 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022) Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.WABI.2022.24

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• [23]
  

  2022 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2965398

  Dias Vieira Braga, M., Brockmann, L. R., Klerx, K., & Stoye, J. (2022). A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. In C. Boucher & S. Rahmann (Eds.), Leibniz International Proceedings in Informatics. LIPIcs: Vol. 242. 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022) (pp. 13:1-13:16). Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.WABI.2022.13

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• [22]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2954832

  Rubert, D., Martinez, F. V., & Dias Vieira Braga, M. (2021). Natural family-free genomic distance. Algorithms for molecular biology : AMB, 16(1), 4. https://doi.org/10.1186/s13015-021-00183-8

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• [21]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2959611

  Rubert, D., Doerr, D., & Dias Vieira Braga, M. (2021). The potential of family-free rearrangements towards gene orthology inference. Journal of Bioinformatics and Computational Biology, 19(6), 2140014. https://doi.org/10.1142/S021972002140014X

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• [20]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2942686

  Willing, E., Stoye, J., & Dias Vieira Braga, M. (2021). Computing the Inversion-Indel Distance. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(6), 2314-2326. https://doi.org/10.1109/TCBB.2020.2988950

  PUB | DOI | WoS | PubMed | Europe PMC | arXiv
   
• [19]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2946303

  Bohnenkämper, L., Dias Vieira Braga, M., Dörr, D., & Stoye, J. (2021). Computing the rearrangement distance of natural genomes. Journal of Computational Biology, 28(4), 410-431. https://doi.org/10.1089/cmb.2020.0434

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• [18]
  

  2020 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2965072

  Rubert, D., Martinez, F. V., & Dias Vieira Braga, M. (2020). Natural Family-Free Genomic Distance. In C. Kingsford & N. Pisanti (Eds.), Leibniz International Proceedings in Informatics (LIPIcs): Vol. 172. 20th International Workshop on Algorithms in Bioinformatics (WABI 2020) (pp. 3:1-3:23). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.WABI.2020.3

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• [17]
  

  2020 | Preprint | Veröffentlicht | PUB-ID: 2939861

  Bohnenkämper, L., Dias Vieira Braga, M., Dörr, D., & Stoye, J. (2020). Computing the rearrangement distance of natural genomes. arXiv:2001.02139

  PUB | Download (ext.) | arXiv
   
• [16]
  

  2020 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2939729

  Bohnenkämper, L., Dias Vieira Braga, M., Dörr, D., & Stoye, J. (2020). Computing the rearrangement distance of natural genomes. Proceedings of RECOMB 2020, LNBI, 12074, 3-18. doi:10.1007/978-3-030-45257-5_1

  PUB | DOI
   
• [15]
  

  2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006

  Rubert, D., Hoshino, E. A., Dias Vieira Braga, M., Stoye, J., & Martinez, F. H. V. (2018). Computing the family-free DCJ similarity. BMC Bioinformatics, 19(Suppl. 6), 152. https://doi.org/10.1186/s12859-018-2130-5

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• [14]
  

  2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015

  Rubert, D., Medeiros, G. L., Hoshino, E. A., Dias Vieira Braga, M., Stoye, J., & Martinez, F. H. V. (2017). Algorithms for Computing the Family-Free Genomic Similarity under DCJ. In J. Meidanis & L. Nakhleh (Eds.), Lecture Notes in Bioinformatics: Vol. 10562. Comparative Genomics. RECOMB-CG 2017 (pp. 76-100). Cham: Springer Verlag. https://doi.org/10.1007/978-3-319-67979-2_5

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• [13]
  

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057

  Rubert, D., Feijão, P., Dias Vieira Braga, M., Stoye, J., & Martinez, F. H. V. (2017). Approximating the DCJ distance of balanced genomes in linear time. Algorithms for Molecular Biology, 12(1), 3. https://doi.org/10.1186/s13015-017-0095-y

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• [12]
  

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916552

  da Silva, P. H., Machado, R., Dantas, S., & Dias Vieira Braga, M. (2017). Genomic Distance with High Indel Costs. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14(3), 728-732. doi:10.1109/TCBB.2016.2555301

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• [11]
  

  2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708

  Rubert, D., Feijão, P., Dias Vieira Braga, M., Stoye, J., & Martinez, F. H. V. (2016). A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates. In M. Frith & C. N. Storm Pedersen (Eds.), Lecture Notes in Bioinformatics: Vol. 9838. Algorithms in Bioinformatics. WABI 2016 (pp. 293-306). Cham: Springer. https://doi.org/10.1007/978-3-319-43681-4_24

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• [10]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366

  Viduani Martinez, F. H., Feijão, P., Dias Vieira Braga, M., & Stoye, J. (2015). On the family-free DCJ distance and similarity. Algorithms for Molecular Biology, 10(1), 13. doi:10.1186/s13015-015-0041-9

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• [9]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2677844

  Dias Vieira Braga, M., & Stoye, J. (2015). Sorting linear genomes with rearrangements and indels. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(3), 500-506. doi:10.1109/TCBB.2014.2329297

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• [8]
  

  2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611648

  Dias Vieira Braga, M., Chauve, C., Dörr, D., Jahn, K., Stoye, J., Thévenin, A., & Wittler, R. (2013). The Potential of Family-Free Genome Comparison. In C. Chauve, N. El-Mabrouk, & E. Tannier (Eds.), Computational Biology Series: Vol. 19. Models and Algorithms for Genome Evolution (pp. 287-307). London: Springer Verlag. doi:10.1007/978-1-4471-5298-9_13

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• [7]
  

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091794

  Dias Vieira Braga, M., Willing, E., & Stoye, J. (2011). Double Cut and Join with Insertions and Deletions. Journal of Computational Biology, 18(9), 1167-1184. https://doi.org/10.1089/cmb.2011.0118

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• [6]
  

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091790

  Kovac, J., Warren, R., Dias Vieira Braga, M., & Stoye, J. (2011). Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation. Journal of Computational Biology, 18(9), 1231-1241. https://doi.org/10.1089/cmb.2011.0116

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• [5]
  

  2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919216

  Kovac, J., Dias Vieira Braga, M., & Stoye, J. (2010). The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. Proc. of Recomb-CG 2010, LNBI, 6398, 13-24. https://doi.org/10.1007/978-3-642-16181-0_2

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• [4]
  

  2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898025

  Dias Vieira Braga, M., & Stoye, J. (2010). The Solution Space of Sorting by DCJ. Journal of Computational Biology, 17(9), 1145-1165. https://doi.org/10.1089/cmb.2010.0109

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [3]
  

  2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919215

  Dias Vieira Braga, M., Willing, E., & Stoye, J. (2010). Genomic Distance with DCJ and Indels. Proc. of WABI 2010, LNBI, 6293, 90-101. https://doi.org/10.1007/978-3-642-15294-8_8

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• [2]
  

  2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919206

  Dias Vieira Braga, M., & Stoye, J. (2009). Counting All DCJ Sorting Scenarios. Proc. of Recomb-CG 2009, LNBI, 5817, 36-47. https://doi.org/10.1007/978-3-642-04744-2_4

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• [1]
  

  2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588760

  Dias Vieira Braga, M., Gautier, C., & Sagot, M. - F. (2009). An asymmetric approach to preserve common intervals while sorting by reversals. Algorithms for Molecular Biology, 4(1), 16. https://doi.org/10.1186/1748-7188-4-16

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