Distance and Similarity Measures in Comparative Genomics

  • Diego P. Rubert UFMS
  • Jens Stoye Bielefeld University
  • Fábio H. V. Martinez UFMS


Research in comparative genomics supports the investigation of important questions in molecular biology, genetics and biomedicine. A central question in this field is the elucidation of similarities and differences between genomes by means of different measures. This summary, submitted to CTD 2020, briefly describes the main contributions, originality and impact possibilities of the thesis entitled "Distance and Similarity Measures in Comparative Genomics", by Diego P. Rubert.

Palavras-chave: Double-cut-and-join (DCJ), Genome rearrangements, Comparative genomics, Approximation algorithms, Heuristics, Integer linear programming, Local genome rearrangements, Ancestral genome reconstruction


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Rubert, D. P., Feijao, P., Braga, M. D. V., Stoye, J., and Martinez, F. H. V. (2017a). Approximating the DCJ distance of balanced genomes in linear time. Algorithms for Molecular Biology, 12(1):3.

Rubert, D. P., Feijao, P., Braga, M. D. V., Stoye, J., and Martinez, F. V. (2016). A linear time approximation ̃algorithm for the DCJ distance for genomes with bounded number of duplicates. In Proc. of the 16th International Workshop on Algorithms in Bioinformatics (WABI 2016), pages 293-306.

Rubert, D. P., Hoshino, E. A., Braga, M. D. V., Stoye, J., and Martinez, F. V. (2018). Computing the family-free DCJ similarity. BMC Bioinformatics, 19(6):152.

Rubert, D. P., Martinez, F. V., Stoye, J., and Doerr, D. (2020). Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants. BMC Genomics, 21(S2):273. (Proc. of the 17th RECOMB Comparative Genomics Satellite International Workshop RECOMB-CG 2019).

Rubert, D. P., Medeiros, G. L., Hoshino, E. A., Braga, M. D. V., Stoye, J., and Martinez, F. V. (2017b). Algorithms for computing the family-free genomic similarity under DCJ. In Proc. of the 15th RECOMB Comparative Genomics Satellite International Workshop (RECOMB-CG 2017), pages 76-100.

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RUBERT, Diego P.; STOYE, Jens; MARTINEZ, Fábio H. V.. Distance and Similarity Measures in Comparative Genomics. In: CONCURSO DE TESES E DISSERTAÇÕES (CTD), 33. , 2020, Cuiabá. Anais [...]. Porto Alegre: Sociedade Brasileira de Computação, 2020 . p. 7-12. ISSN 2763-8820. DOI: https://doi.org/10.5753/ctd.2020.11361.