Yun S. Song

Associate Professor

Research Areas

• Biosystems & Computational Biology (BIO)
• Theory (THY)
• Applied Probability

Biography

Yun S. Song is an associate professor in EECS and Statistics. He received the BS degrees in mathematics and physics from MIT, and a PhD in physics from Stanford University. After his PhD, he spent a year at the Mathematical Institute at the University of Oxford, where he decided to change fields. He became a postdoctoral researcher in the Department of Statistics at Oxford, and started doing research in computational biology and mathematical population genetics. From 2004 to 2007, he was a postdoctoral researcher at UC Davis in the Department of Computer Science, and the Section of Evolution and Ecology. Recent honors and awards include an NIH Pathway to Independence Award K99/R00 (2006), an Alfred P. Sloan Research Fellowship (2008), a Packard Fellowship for Science and Engineering (2008), and an NSF CAREER Award (2009).

Selected Publications

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.