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Book chapters or sections
- R. B. Lyngso, Y. S. Song, and J. Hein, "Accurate computation of likelihoods in the coalescent with recombination via parsimony," in Research in Computational Molecular Biology: Proc. 12th Annual Intl. Conf. (RECOMB 2008), M. Vingron and L. Wong, Eds., Lecture Notes in Computer Science, Vol. 4955, Berlin, Germany: Springer-Verlag, 2008, pp. 463-477.
- 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 Research in Computational Molecular Biology: Proc. 10th Annual Intl. Conf. (RECOMB 2006), A. Apostolico, C. Guerra, S. Istrail, P. A. Pevzner, and M. S. Waterman, Eds., Lecture Notes in Computer Science, Vol. 3909, Berlin, Germany: Springer-Verlag, 2006, pp. 231-245.
- J. Li and Y. S. Song, "Open string instantons and relative stable morphisms (Invited Reprint)," in The Interaction of Finite-Type and Gromov-Witten Invariants (BIRS 2003), D. Auckly and J. Bryan, Eds., Geometry and Topology Monographs, Vol. 8, Berkeley, CA: Mathematical Sciences Publishers, 2006, pp. 49-72.
- R. B. Lyngso, Y. S. Song, and J. Hein, "Minimum recombination histories by branch and bound," in Algorithms in Bioinformatics: Proc. 5th Intl. Workshop (WABI 2005), R. Casadio and G. Myers, Eds., Lecture Notes in Computer Science::Lecture Notes in Bioinformatics, Vol. 3692, Berlin, Germany: Springer-Verlag, 2005, pp. 239-250.
- Y. S. Song, Y. Wu, and D. Gusfield, "Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event," in Algorithms in Bioinformatics: Proc. 5rd Intl. Workshop (WABI 2005), R. Casadio and G. Myers, Eds., Lecture Notes in Computer Science::Lecture Notes in Bioinformatics, Vol. 3692, Berlin, Germany: Springer-Verlag, 2005, pp. 152-164.
- Y. S. Song and J. Hein, "Parsimonious reconstruction of sequence evolution and haplotype blocks," in Algorithms in Bioinformatics: Proc. 3rd Intl. Workshop (WABI 2003), G. Benson and R. Page, Eds., Lecture Notes in Computer Science:: Lecture Notes in Bioinformatics, Vol. 2812, Berlin, Germany: Springer-Verlag, 2003, pp. 287-302.
Articles in journals or magazines
- P. A. Jenkins and Y. S. Song, "An asymptotic sampling formula for the coalescent with recombination," Annals of Applied Probability (in press), 2009.
- P. A. Jenkins and Y. S. Song, "Closed-form two-locus sampling distributions: accuracy and universality," Genetics, Nov. 2009.
- A. Bhaskar and Y. S. Song, "Multi-locus match probability in a finite population: A fundamental difference between the Moran and Wright-Fisher models," Proceedings of ISMB 2009. Bioinformatics, vol. 25, no. 12, pp. i187-i195, June 2009.
- J. Yin, M. Jordan, and Y. S. Song, "Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data," Proceedings of ISMB 2009. Bioinformatics, vol. 25, no. 12, pp. i231-i239, June 2009.
- Y. S. Song, A. Patil, E. Murphy, and M. Slatkin, "Average probability that a "cold hit" in a DNA database search results in an erroneous attribution," J. Forensic Sciences, vol. 54, pp. 22-27, Jan. 2009.
- Z. Ding, T. Mailund, and Y. S. Song, "Efficient whole-genome association mapping using local phylogenies for unphased genotype data," Bioinformatics, vol. 24, no. 19, pp. 2215-2221, Oct. 2008.
- R. C. Griffiths, P. A. Jenkins, and Y. S. Song, "Importance sampling and the two-locus model with subdivided population structure," Advances in Applied Probability, vol. 40, no. 2, pp. 473-500, June 2008.
- J. A. Anderson, Y. S. Song, and C. H. Langley, "Molecular population genetics of Drosophila subtelomeric DNA," Genetics, vol. 178, pp. 477-487, Jan. 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," J. Computational Biology, vol. 14, no. 10, pp. 1273-1286, Dec. 2007.
- D. Gusfield, V. Bansal, V. Bafna, and Y. S. Song, "A decomposition theory for phylogenetic networks and incompatible characters," J. Computational Biology, vol. 14, no. 10, pp. 1247-1272, Dec. 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.
- 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, 2006.
- Y. S. Song, R. Lyngso, and J. Hein, "Counting all possible ancestral configurations of sample sequences in population genetics," IEEE/ACM Trans. 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. 147-163, June 2006.
- Y. S. Song, "A concise necessary and sufficient condition for the existence of a galled-tree," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 2, pp. 186-191, April 2006.
- Y. S. Song, "A sufficient condition for reducing recursions in hidden Markov models," Mathematical Biology, vol. 68, no. 2, pp. 361-384, Feb. 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, no. Suppl. 1, pp. i413-i422, 2005.
- Y. S. Song and J. Hein, "Constructing minimal ancestral recombination graphs," J. Computational Biology, vol. 12, no. 2, pp. 147-169, March 2005.
- Y. S. Song and J. Hein, "Book Review: Phylogenetics by Charles Semple and Mike Steel," Systematic Biology, vol. 53, no. 6, pp. 1003-1006, Dec. 2004.
- J. S. Song and Y. S. Song, "On a conjecture of Givental," J. 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," J. Geometry and Physics, vol. 50, no. 1-4, pp. 223-256, April 2004.
- Y. S. Song and J. Hein, "On the minimum number of recombination events in the evolutionary history of DNA sequences," J. Mathematical Biology, vol. 48, no. 2, pp. 160-186, Feb. 2004.
- G. A. Lunter, I. Miklos, Y. S. Song, and J. Hein, "An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees," J. Computational Biology, vol. 10, no. 6, pp. 869-889, Dec. 2003.
- Y. S. Song, "On the combinatorics of rooted binary phylogenetic trees," Annals of Combinatorics, vol. 7, no. 3, pp. 365-379, Dec. 2003.
- J. Li and Y. S. Song, "Open string instantons and relative stable morphisms," Advances in Theoretical and Mathematical Physics, vol. 5, no. 1, pp. 67-91, Jan. 2001.
- E. Silverstein and Y. S. Song, "On the critical behavior of D1-brane theories," J. High Energy Physics, vol. 3, no. 029, pp. 21 pg, March 2000.
Ph.D. Theses
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