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.
J. Y. Zou, D. S. Park, E. G. Burchard, D. G. Torgerson, M. Pino-Yanes, Y. S. Song, S. Sankararaman, E. Halperin, and N. Zaitlen, "Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns," PNAS, vol. 112, no. 44, pp. 13621-13626, Nov. 2015.
D. Živković, M. Steinrücken, Y. S. Song, and W. Stephan, "Transition densities and sample frequency spectra of diffusion processes with selection and variable population size," Genetics, vol. 200, no. 2, pp. 601-617, June 2015.
P. A. Jenkins, P. Fearnhead, and Y. S. Song, "Tractable diffusion and coalescent processes for weakly correlated loci," Electronic Journal of Probability, vol. 20, no. 58, pp. 1-26, May 2015.
J. Terhorst, C. Schlötterer, and Y. S. Song, "Multi-locus analysis of genomic time series data from experimental evolution," PLoS Genetics, vol. 11, no. 4, pp. e1005069, April 2015.
A. Talwalkar, J. Liptrap, J. Newcomb, C. Hartl, J. Terhorst, K. Curtis, M. Bresler, Y. S. Song, M. Jordan, and D. A. Patterson, "SMaSH: A benchmarking toolkit for human genome variant calling," Bioinformatics, vol. 30, no. 19, pp. 2787-2795, June 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.
R. Rohlfs, E. Murphy, Y. S. Song, and M. Slatkin, "The influence of relatives on the efficiency and error rate of familial searching," PLoS ONE, vol. 8, no. 8, pp. e70495, Aug. 2013.
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. Malaspinas, M. Slatkin, and Y. S. Song, "Match probabilities in a finite, subdivided population," Theoretical Population Biology, vol. 79, pp. 55-63, Jan. 2011.
N. Bhattacharya, N. Thomas, R. Rao, J. Dauparas, P. K. Koo, D. Baker, Y. S. Song, and S. Ovchinnikov, "Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention," in Pacific Symposium on Biocomputing, Vol. 27, 2022, pp. 34--45.
R. Rao, N. Bhattacharya, N. Thomas, Y. Duan, P. Chen, J. F. Canny, P. Abbeel, and Y. S. Song, "Evaluating protein transfer learning with TAPE," Vol. 32, 2019.
R. Rao, N. Bhattacharya, N. Thomas, Y. Duan, P. Chen, J. F. Canny, P. Abbeel, and Y. S. Song, "Evaluating Protein Transfer Learning with TAPE," in Advances in Neural Information Processing Systems (NeurIPS), Vol. 32, 2019.
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.
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.
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 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.