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ReCombinatorics: Combinatorial Algorithms for Studying the History of Recombination in Populations

  • Dan Gusfield
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5029)

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/

Keywords

Horizontal Gene Transfer Computational Biology Mobile Genetic Element HAPMAP Project Phylogenetic Network 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

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    Gusfield, D.: Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained recombination. J. Computer and Systems Sciences 70, 381–398 (2005)zbMATHCrossRefMathSciNetGoogle Scholar
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    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)Google Scholar
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    Gusfield, D., Bansal, V., Bafna, V., Song, Y.S.: a decomposition theory for phylogenetic networks and incompatible characters. J. Computational Biology (December 2007)Google Scholar
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    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)CrossRefGoogle Scholar
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    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)MathSciNetGoogle Scholar
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    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)Google Scholar
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    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)CrossRefGoogle Scholar
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    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)Google Scholar
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    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)CrossRefGoogle Scholar
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    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)Google Scholar
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    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)CrossRefGoogle Scholar
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    Wu, Y., Gusfield, D.: Efficient computation of minimum recombination with genotypes (not haplotypes). In: Proceedings of The Computational Systems Biology Conference (2006)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Dan Gusfield
    • 1
  1. 1.Department of Computer ScienceUniversity of CaliforniaDavisUSA

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