Yun S. Song

Calabi-Simons Visiting Professor of Mathematics and Biology
Lynch 103H
yss@sas.upenn.edu
3-9712
Evolution
Genetics, Epigenetics, Genomics
Computational Biology
Education: 
Ph.D., Physics, Stanford University, 2001
B.S., Mathematics, MIT, 1997
B.S., Physics, MIT, 1996
Research Interests: 

My research interests reside at the interface between biology, computer science, mathematics, and statistics.  In particular, I am interested in developing accurate, efficient statistical methods for population genomic inference.  Other recent interests include computational genomics and immunology.

Selected Publications: 

Raghavan, M., Steinrücken, M., Harris, K., et al. Genomic evidence for the Pleistocene and recent population history of Native Americans.  Science 349, aab3884 (2015). [ Journal ]

Terhorst, J. and Song, Y.S. Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum. Proc. Natl. Acad. Sci. U.S.A., Vol. 112, No. 25 (2015) 7677-7682. [ Journal ]

Jenkins, P.A., Fearnhead, P., and Song, Y.S. Tractable diffusion and coalescent processes for weakly correlated loci. Electronic Journal of Probability, Vol. 20, No. 58 (2015) 1-26. [ Journal ]

Terhorst, J., Schlötterer, C., Song, Y.S. Multi-locus analysis of genomic time series data from experimental evolution.  PLoS Genetics, Vol. 11, No. 4 (2015) e1005069. [ Journal ]

Bhaskar, A., Wang, Y.X.R. and Song, Y.S. Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data. Genome Research, Vol. 25, No. 2 (2015) 268-279. [ Journal ]

Bhaskar, A. and Song, Y.S. Descartes' rule of signs and the identifiability of population demographic models from genomic variation data. Annals of Statistics, Vol. 42, No. 6 (2014) 2469-2493. [ Journal ]

Steinrücken, M., Bhaskar, A. and Song, Y.S. A novel spectral method for inferring general diploid selection from time series genetic data. Annals of Applied Statistics, Vol. 8, No. 4 (2014) 2203-2222. [ Journal ]

Bhaskar, A., Clark, A.G., and Song, Y.S. Distortion of genealogical properties when the sample is very large. Proc. Natl. Acad. Sci. U.S.A., Vol. 111, No. 6 (2014) 2385-2390.  [ Journal ]

Jenkins, P.A., Mueller, J.W, and Song, Y.S. General triallelic frequency spectrum under demographic models with variable population size. Genetics, 196 (2014) 295-311.  [ Journal ]

Steinrücken, M., Paul, J.S., and Song, Y.S. A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. Theoretical Population Biology 87 (2013) 51-61. [ Journal ]

Sheehan, S., Harris, K., Song, Y.S. Estimating variable effective population sizes from multiple genomes: A sequentially Markov conditional sampling distribution approach. Genetics, 194 (2013) 647-662. [ Journal ]

Chan, A.H., Jenkins, P.A., and Song, Y.S. Genome-wide fine-scale recombination rate variation in Drosophila melanogaster. PLoS Genetics, Vol. 8 No. 12 (2012) e1003090. [ Journal ]

Song, Y.S. and Steinrücken, M. A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection. Genetics 190 (2012) 1117-1129. [ Journal ]

Paul, J.S., Steinrücken, M., and Song, Y.S. An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics 187 (2011) 1115-1128. [ Journal ]