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Book chapters or sections
- 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.
Articles in journals or magazines
- A. Bhaskar, J. A. Kamm, and Y. S. Song, "Approximate sampling formulae for general finite-alleles models of mutation," Advances in Applied Probability, vol. 44, no. 2, pp. 408-428, 2012.
- A. Bhaskar and Y. S. Song, "Closed-form asymptotic sampling distributions under the coalescent with recombination for an arbitrary number of loci," Advances in Applied Probability, vol. 44, no. 2, pp. 391-407, 2012.
- P. A. Jenkins and Y. S. Song, "Padé approximants and exact two-locus sampling distributions," Annals of Applied Probability, vol. 22, no. 2, pp. 576-607, 2012.
- A. Chan, P. Jenkins, and Y. S. Song, "Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster," PLoS Genetics, vol. 8, no. 12, Dec. 2012. [abstract]
- J. Paul and Y. S. Song, "Blockwise HMM computation for large-scale population genomic inference," Bioinformatics, vol. 28, no. 15, pp. 2008-2015, Aug. 2012.
- Y. S. Song and M. Steinrücken, "A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection," Genetics, vol. 190, no. 3, pp. 1117-1129, March 2012.
- P. A. Jenkins and Y. S. Song, "The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele," Theoretical Population Biology, vol. 80, no. 2, pp. 158-173, Sep. 2011.
- W. Kao, A. Chan, and Y. S. Song, "ECHO: A reference-free short-read error correction algorithm," Genome Research, vol. 21, pp. 1181-1192, July 2011.
- R. Nielsen, J. Paul, A. Albrechtsen, and Y. S. Song, "Genotype and SNP calling from next-generation sequencing data," Nature Reviews Genetics, vol. 12, pp. 443-451, June 2011.
- J. S. Paul, M. Steinrücken, and Y. S. Song, "An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination," Genetics, vol. 187, pp. 1115-1128, April 2011.
- A. Malaspinas, M. Slatkin, and Y. S. Song, "Match probabilities in a finite, subdivided population," Theoretical Population Biology, vol. 79, pp. 55-63, Jan. 2011.
- Y. S. Song, F. Wang, and M. Slatkin, "General epistatic models of the risk of complex diseases," Genetics, vol. 186, pp. 1467-1473, Dec. 2010.
- J. S. Paul and Y. S. Song, "A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination," Genetics, vol. 186, pp. 321-338, Sep. 2010.
- P. A. Jenkins and Y. S. Song, "An asymptotic sampling formula for the coalescent with recombination," Annals of Applied Probability, vol. 20, no. 3, pp. 1005-1028, June 2010.
- P. A. Jenkins and Y. S. Song, "Closed-form two-locus sampling distributions: accuracy and universality," Genetics, vol. 183, pp. 1087-1103, Nov. 2009.
- W. C. Kao, K. Stevens, and Y. S. Song, "BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing," Genome Research, vol. 19, no. 10, pp. 1884-1895, Oct. 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.
Articles in conference proceedings
- K. Stevens, H. Chen, T. E. Filiba, P. McMahon, and Y. S. Song, "SeqHive: A reconfigurable computer cluster for genome re-sequencing," in IEEE Proceedings of the 20th International Conference on Field Programmable Logic and Applications (FPL 2010), 2010, pp. 442-447.
- F. Lam, C. Langley, and Y. S. Song, "On the genealogy of asexual diploids," in Proc. 14th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB 2010), Lecture Notes in Computer Science, Vol. 6044, 2010, pp. 325-340.
- W. Kao and Y. S. Song, "naiveBayesCall: An efficient model-based base-calling algorithm for high-throughput sequencing," in Proc. 14th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB 2010), Lecture Notes in Computer Science, Vol. 6044, 2010, pp. 233-247.
- 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.
- 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.
Ph.D. Theses
- A. Bouchard-Cote, M. Jordan, D. Klein, T. L. Griffiths, and Y. S. Song, "Probabilistic Models of Evolution and Language Change," EECS Department, University of California, Berkeley, Tech. Rep. UCB/EECS-2010-153, Dec. 2010. [abstract]
- Y. S. Song, "Topological String Theory and Enumerative Geometry," Stanford University, Department of Physics, Aug. 2001.
Masters Reports
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