# Faculty Publications - Yun S. Song

## 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

- M. Steinrücken, A. Bhaskar, and Y. S. Song, "A novel spectral method for inferring general selection from time series genetic data,"
*Annals of Applied Statistics*, vol. 8, no. 4, pp. 2203-2222, 2014. - A. Bhaskar and Y. S. Song, "Descartes' rule of signs and the identifiability of population demographic models from genomic variation data,"
*Annals of Statistics*, vol. 42, no. 6, pp. 2469-2493, Dec. 2014. - A. Bhaskar, A. G. Clark, and Y. S. Song, "Distortion of genealogical properties when the sample is very large,"
*PNAS*, vol. 111, no. 6, pp. 2385-2390, Feb. 2014. - P. A. Jenkins, J. W. Mueller, and Y. S. Song, "General triallelic frequency spectrum under demographic models with variable population size,"
*Genetics*, vol. 196, no. 1, pp. 295-311, Jan. 2014. - M. Steinrücken, J. S. Paul, and Y. S. Song, "A sequentially Markov conditional sampling distribution for structured populations with migration and recombination,"
*Theoretical Population Biology*, vol. 87, pp. 51-61, Aug. 2013. - S. Sheehan, K. Harris, and Y. S. Song, "Estimating variable effective population sizes from multiple genomes: A sequentially Markov conditional sampling distribution approach,"
*Genetics*, vol. 194, no. 3, pp. 647-662, July 2013. - M. Steinrücken, Y. R. Wang, and Y. S. Song, "An explicit transition density expansion for a multi-allelic Wright-Fisher diffusion with general diploid selection,"
*Theoretical Population Biology*, vol. 83, pp. 1-14, Feb. 2013. - 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

- N. Wu, "Preliminary Studies on de novo Assembly with Short Reads," S. Rao and Y. S. Song, Eds., EECS Department, University of California, Berkeley, Tech. Rep. UCB/EECS-2009-172, Dec. 2009. [abstract]