Abstract
The work discussed in this talk falls into the emerging area of Population Genomics. I will first introduce the area and then talk about specific problems and combinatorial algorithms involved in the inference of recombination from population data.
A phylogenetic network (or Ancestral Recombination Graph) is a generalization of a tree, allowing structural properties that are not tree-like. With the growth of genomic and population data (coming for example from the HAPMAP project) much of which does not fit ideal tree models, and the increasing appreciation of the genomic role of such phenomena as recombination (crossing-over and gene-conversion), recurrent and back mutation, horizontal gene transfer, and mobile genetic elements, there is greater need to understand the algorithmics and combinatorics of phylogenetic networks.
In this talk I will survey a range of our recent algorithmic, mathematical and practical results on phylogenetic networks with recombination and show applications of these results to several issues in Population Genomics.
Various parts of this work are joint work with Satish Eddhu, Chuck Langley, Dean Hickerson, Yun S. Song, Yufeng Wu, V. Bansal, V. Bafna and Z. Ding. All the papers and associated software can be accessed at http://wwwcsif.cs.ucdavis.edu/~gusfield/
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References
Gusfield, D.: Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained recombination. J. Computer and Systems Sciences 70, 381–398 (2005)
Gusfield, D., Bansal, V.: A fundamental decomposition theory for phylogenetic networks and incompatible characters. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3500, pp. 217–232. Springer, Heidelberg (2005)
Gusfield, D., Bansal, V., Bafna, V., Song, Y.S.: a decomposition theory for phylogenetic networks and incompatible characters. J. Computational Biology (December 2007)
Gusfield, D., Eddhu, S., Langley, C.: Optimal efficient Reconstruction of phylogenetic networks with constrained recombination. Journal of Bioinformatics and Computational Biology 2(1), 173–213 (2004)
Gusfield, D., Eddhu, S., Langley, C.: The fine structure of galls in phylogenetic networks. Inf. J. on Computing, Special issue on Computational Biology 16(4), 459–469 (2004)
Gusfield, D., Hickerson, D., Eddhu, S.: A fundamental, efficiently computed lower bound on the number of recombinations needed in a phylogenetic history. Discrete Applied Math Special issue on Computational Biology (2007)
Song, Y., Gusfield, D., Ding, Z., Langley, C., Wu, Y.: Algorithms to distinguish the role of gene-conversion from single-crossover recombination in the derivation of SNP sequences in populations. In: Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2006. LNCS (LNBI), vol. 3909, pp. 231–245. Springer, Heidelberg (2006)
Song, Y., Wu, Y., Gusfield, D.: Efficient computation of close lower and upper bounds on the minimum number of needed recombinations in the evolution of biological sequences. In: Bioinformatics, Proceedings of the ISMB 2005 Conference, vol. 21, pp. 413–422 (2005)
Wu, Y.: Association mapping of complex diseases with ancestral recombination graphs: models and efficient algorithms. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), vol. 4453, pp. 488–502. Springer, Heidelberg (2007)
Wu, Y., Gusfield, D.: A new recombination lower bound and the minimum perfect phylogenetic forest problem. In: Proceedings of the 13th Annual International Conference on Combinatorics and Computing, pp. 16–26 (2007)
Wu, Y., Gusfield, D.: Improved algorithms for inferring the minimum mosaic of a set of recombinants. In: Ma, B., Zhang, K. (eds.) CPM 2007. LNCS, vol. 4580, pp. 150–161. Springer, Heidelberg (2007)
Wu, Y., Gusfield, D.: Efficient computation of minimum recombination with genotypes (not haplotypes). In: Proceedings of The Computational Systems Biology Conference (2006)
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Gusfield, D. (2008). ReCombinatorics: Combinatorial Algorithms for Studying the History of Recombination in Populations. In: Ferragina, P., Landau, G.M. (eds) Combinatorial Pattern Matching. CPM 2008. Lecture Notes in Computer Science, vol 5029. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69068-9_1
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