I am a statistician and computational biologist at the Chan-Zuckerberg Biohub. My current work is in genomic epidemiology, and involves phylogenetics, assembly, time series analysis, and Bayesian graphical models. Previously, I have also worked in population genetics, coalescent theory, and ancient DNA. My Ph.D. advisor was Yun Song and postdoc advisor was Richard Durbin.

Preprints

  • Efficiently inferring the demographic history of many populations with allele count data. Kamm, J.A., Terhorst, J., Durbin, R, and Song, Y.S. {Preprint} {Software: momi2}

  • Inference of complex population histories using whole-genome sequences from multiple populations. Steinrücken, M., Kamm, J.A., and Song, Y.S. {Preprint} {Software: diCal2}

Publications

  • Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans. Steinrücken, M., Spence, J.P., Kamm, J.A., Wieczorek, E., and Song, Y.S. Molecular Ecology, in press. {Preprint}

  • Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Moreno-Mayar, J.V., Potter, B.A., Vinner, L, Steinrücken, M. Rasmussen, S., Terhorst, J., Kamm, J.A., Albrechtsen, A., Malaspinas, A.-S., Sikora, M., Reuther, J.D., Irish, J.D., Malhi, R.S., Orlando, L., Song, Y.S., Nielsen, R., Meltzer, D.J., and Willerslev, E. Nature, Vol. 553 (2018) 203-207. {Journal}

  • Robust and scalable inference of population history from hundreds of unphased whole genomes. Terhorst, J., Kamm, J.A., and Song, Y.S. Nature Genetics, Vol. 49 (2017) 303-309. {Journal} {Software: SMC++}

  • Efficient computation of the joint sample frequency spectra for multiple populations. Kamm, J.A., Terhorst, J., and Song, Y.S. Journal of Computational and Graphical Statistics, Vol. 26, No. 1 (2017) 182-194. {Journal} {Preprint} {Software: momi}

  • Two-Locus Likelihoods under Variable Population Size and Fine-Scale Recombination Rate Estimation. Kamm, J.A.*, Spence, J.P.*, Chan, J., and Song, Y.S. (*contributed equally) Genetics, Vol. 203 No. 3 (2016) 1381-1399 2016. {Journal} {Preprint} {Software: LDpop}

  • The site frequency spectrum for general coalescents. Spence, J.*, Kamm, J.A.*, and Song, Y.S. (*contributed equally) Genetics, Vol. 202 No. 4 (2016) 1549-1561. {Journal} {Preprint}

  • Decoding coalescent hidden Markov models in linear time. Harris, K., Sheehan, S., Kamm, J.A., Song, Y.S. Proc. 18th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB), LNBI Vol. 8394, (2014), pp 100-114. {Journal} {Preprint}

  • Approximate sampling formulae for general finite-alleles models of mutation. Bhaskar, A., Kamm, J.A., and Song, Y.S. Advances in Applied Probability, 44 (2012) 408-428. {Journal} {Preprint}

Ph.D. Thesis

  • One and Two Locus Likelihoods Under Complex Demography.
    Statistics, UC Berkeley, December 2015. {pdf}

Posters

  • Learning history from the SFS of low- and high-coverage ancient DNA.
    PopGroup @ University of Bristol, 2018. {pdf}
  • LDpop: 2-locus likelihoods for recombination map estimation under variable population size.
    Probabilistic Modeling in Genomics @ Oxford, 2016. {pdf}
  • momi: a new method for computing the multipopulation sample frequency spectrum.
    Probabilistic Modeling in Genomics @ Cold Spring Harbor, 2015. {pdf}