Distance and Similarity Measures in Comparative Genomics

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

Resumo


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

Referências

Badouin, H. et al. (2017). The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature, 546(7656):148-52.

Braga, M. D. V., Chauve, C., Dorr, D., Jahn, K., Stoye, J., Th ̈ evenin, A., and Wittler, R. (2013). The ́potential of family-free genome comparison. In Chauve, C., El-Mabrouk, N., and Tannier, E., editors, Models and Algorithms for Genome Evolution, chapter 13.

Doerr, D., Thevenin, A., and Stoye, J. (2012). Gene family assignment-free comparative genomics. ́ BMC Bioinformatics, 13(Suppl 19):S3.

Jahn, K. (2011). Efficient computation of approximate gene clusters based on reference occurrences. Journal of Computational Biology, 18(9):1255-1274.

Jiang, H., Zheng, C., Sankoff, D., and Zhu, B. (2010). Scaffold filling under the breakpoint distance. In Proc. of the 8th RECOMB Comparative Genomics Satellite International Workshop (RECOMB-CG 2010), volume 6398 of LNB, pages 83-92.

Kolman, P. and Walen, T. (2007). Reversal distance for strings with duplicates: Linear time approximation using hitting set. The Electronic Journal of Combinatorics, 14.

Martinez, F. V., Feijao, P., Braga, M. D. V., and Stoye, J. (2015). On the family-free DCJ distance and similarity. Algorithms for Molecular Biology, 10:13.

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.

Salse, J. (2016). Ancestors of modern plant crops. Current Opinion in Plant Biology, 30:134-42.

Shao, M., Lin, Y., and Moret, B. (2015). An exact algorithm to compute the double-cut-and-join distance for genomes with duplicate genes. Journal of Computational Biology, 22(5):425-435.

Winter, S., Jahn, K., Wehner, S., Kuchenbecker, L., Marz, M., Stoye, J., and Bocker, S. (2016). Finding approximate gene clusters with GECKO 3. Nucleic Acids Res., 44.

Yancopoulos, S., Attie, O., and Friedberg, R. (2005). Efficient sorting of genomic permutations by translocation, inversion and block interchanges. Bioinformatics, 21(16):3340-3346.
Publicado
30/06/2020
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.