Bruce Rannala

Professor, Department of Evolution and Ecology @ UC Davis.



Welcome to the home page of Bruce Rannala. I develop statistical methods, computer software, and sometimes new theory. I also teach a course on human genetic variation EVE 131 each Fall. My research focuses on statistical genetics, population genetics, and phylogenetics. However, our methods are often applied to real world problems such as pandemics (HIV, COVID19), cancer genetics, conservation biology and disease gene mapping.

Examples of Current Projects

  • Bayesian inference of ages of latent lineages of HIV using sequence data (PhD student Anna Nagel)
  • Bayesian inference of hybrid and backcross individuals using genomic sequences (Postdoc Sneha Chakraborty)
  • New models aimed at early identification of SARS-CoV2 variants of concern using phylogenetic information (Postdoc Mike May)


Dec 18, 2023 Anna Nagel has received her PhD. :sparkles: Congratulations Dr. Nagel! :mortar_board:
Oct 22, 2023 Anna Nagel will present an exit seminar on her PhD work at the Center for Population Biology Seminar Series on November 14, 2023.
Mar 14, 2023 BayesAss (BA3) release with new documentation and homebrew tap!
Feb 16, 2023 Sneha Chakraborty has passed her PhD defense. :sparkles: Congratulations Dr. Chakraborty! :mortar_board:

selected publications

  1. PNAS
    Model misspecification misleads inference of the spatial dynamics of disease outbreaks
    Jiansi Gao, Michael R May, Bruce Rannala, and Brian R Moore
    Proceedings of the National Academy of Sciences, 2023
  2. Bioinformatics
    PrioriTree: a utility for improving phylodynamic analyses in BEAST
    Jiansi Gao, Michael R May, Bruce Rannala, and Brian R Moore
    Bioinformatics, 2023
  3. Genetics
    An efficient exact algorithm for identifying hybrids using population genomic sequences
    Sneha Chakraborty, and Bruce Rannala
    Genetics, 2023
  4. SystBiol
    Estimation of species divergence times in presence of cross-species gene flow
    George P Tiley, Tomás Flouri, Xiyun Jiao, Jelmer W Poelstra, Bo Xu, and 4 more authors
    Systematic Biology, Mar 2023
  5. RSocInterface
    Bayesian phylogenetic inference of HIV latent lineage ages using serial sequences
    Anna A Nagel, and Bruce Rannala
    J. R. Soc. Interface, Mar 2023
  6. PNAS
    Efficient Bayesian inference under the multispecies coalescent with migration
    Tomáš Flouri, Xiyun Jiao, Jun Huang, Bruce Rannala, and Ziheng Yang
    Proceedings of the National Academy of Sciences, Mar 2023