Yun Song, Ph.D.

Yun Song

Professor of Computer Science and Statistics
Director of the Center for Computational Biology

Yun Song, Ph.D. is a professor in electrical engineering and computer sciences and statistics at UC Berkeley. He received B.S. degrees in mathematics and physics from MIT, and a Ph.D. in physics from Stanford University. His research centers around computational and mathematical biology. He is generally interested in developing computational tools and statistical methods to facilitate the research of the broad biomedical community, while also getting deeply involved in data analysis and interpretation. He is also interested in machine learning, combinatorial optimization, algorithms and Monte Carlo methods. He is also a core member of the Center for Computational Biology at UC Berkeley.

Education and Degree(s)
  • B.S., Physics, Massachusetts Institute of Technology
  • B.S., Mathematics, Massachusetts Institute of Technology
  • Ph.D., Physics, Stanford University
Honors and Awards
  • Chan Zuckerberg Biohub Investigator Award
  • Math+X Chair, Simons Foundation
  • Jim and Donna Gray Faculty Award for Excellence in Undergraduate Teaching Computer Science Division, UC Berkeley
  • NSF CAREER Award
Publications
  • Ye, C., Benegas, G., Albors, C., Li, J.C., Prillo, S., Fields, P.D., Clarke, B., Song, Y.S. Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models.
  • Ralph, D.K., Bakis, A.G., Galloway, J., Vora, A.A., Araki, T., Victora, G.D., Song, Y.S., DeWitt, W.S., Matsen IV, F.A. Inference of germinal center evolutionary dynamics via simulation-based deep learning.
  • Bakis, A.G., Vora, A.A., Araki, T., Jia, T., Galloway, J.G., Jennings-Shaffer, C., Victora, G.D., Song, Y.S., DeWitt, W.S., Matsen IV, F.A., Minin, V.M. Bayesian inference of antibody evolutionary dynamics using multitype branching processes.
  • DeWitt, W.S., Vora, A.A., Araki, T., Galloway, J.G., Alkutkar, T., Bortolatto, J., Castro, T.B.R., Dumm, W., Jennings-Shaffer, C., Jia, T., Mesin, L., Ozorowski, G., Pae, J., Ralph, D.K., Bloom, J.D., Nourmohammad, A., Song, Y.S., Ward, A.B., Starr, T.N., Matsen IV, F.A., Victora, G.D. Replaying germinal center evolution on a quantified affinity landscape.
  • Deng, Y., DeWitt, W.S., Song, Y.S., Nielsen, R., A general framework for branch length estimation in ancestral recombination graphs.

Tags

Computational Health