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Articles in journals or magazines
- D. Gusfield, V. Bansal, V. Bafna, and Y. S. Song, "A Decomposition Theory for Phylogenetic Networks and Incompatible Characters," J. Comput. Biol., vol. 14, pp. 1247-1272, 2007.
- Y. S. Song and M. Slatkin, "A Graphical Approach to Multi-Locus Match Probability Computation: Revisiting the Product Rule," Theoretical Population Biology, vol. 72, no. 1, pp. 96-110, Aug. 2007.
- Y. S. Song and J. S. Song, "Analytic Computation of the Expectation of the Linkage Disequilibrium Coefficient r^2," Theoretical Population Biology, vol. 71, no. 1, pp. 49-60, Feb. 2007.
- J. Li and Y. S. Song, "Open String Instantons and Relative Stable Morphisms," Geometry and Topology Monographs, vol. 8, pp. 49-72, 2006.
- Y. S. Song, R. Lyngoe, and J. Hein, "Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 3, pp. 239-251, July 2006.
- Y. S. Song, "Properties of Subtree-Prune-and-Regraft Operations on Totally-Ordered Phylogenetic Trees," Annals of Combinatorics, vol. 10, no. 1, pp. 129-146, June 2006.
- W. Stephan, Y. S. Song, and C. H. Langley, "The Hitchhiking Effect on Linkage Disequilibrium between Linked Neutral Loci," Genetics, vol. 172, pp. 2647-2663, April 2006.
- Y. S. Song, "A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 2, pp. 186-191, April 2006.
- Y. S. Song, Y. Wu, and D. Gusfield, "Efficient Computation of Close Lower and Upper Bounds on the Minimum Number of Recombinations in Biological Sequence Evolution," Bioinformatics, vol. 21, pp. i413-i422, 2005.
- Y. S. Song and J. Hein, "Constructing Minimal Ancestral Recombination Graphs," J. Comput. Biol., vol. 12, no. 2, pp. 147-169, 2005.
- J. S. Song and Y. S. Song, "On a Conjecture of Givental," Journal of Mathematical Physics, vol. 45, no. 12, pp. 4539-4550, Dec. 2004.
- S. Monni, J. S. Song, and Y. S. Song, "The Hurwitz Enumeration Problem of Branched Covers and Hodge Integrals," Journal of Geometry and Physics, vol. 50, pp. 223-256, April 2004.
- G. Lunter, I. Miklos, Y. S. Song, and J. Hein, "An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees," J. Comput. Biol, vol. 10, no. 6, pp. 869-889, 2003.
- Y. S. Song, "On the Combinatorics of Rooted Binary Phylogenetic Trees," Annals of Combinatorics, vol. 7, no. 3, pp. 365-379, Dec. 2003.
Articles in conference proceedings
- R. Lyngsoe, Y. S. Song, and J. Hein, "Accurate Computation of Likelihoods in the Coalescent with Recombination via Parsimony," in Proc. 12th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB 2008), 2008.
- Y. S. Song, Z. Ding, D. Gusfield, C. H. Langley, and Y. Wu, "Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations," in Proc. 10th Annual Intl. Conf. on Research in Computational Molecular Biology, Berlin: Springer, 2006, pp. 231-245.
- R. Lyngsoe, Y. S. Song, and J. Hein, " Minimum Recombination Histories by Branch and Bound," in Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, R. Casadio and G. Myers, Eds., Berlin: Springer, 2005, pp. 239-250.
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