• High-dimensional microbiome interactions shape host fitness
    Alison Gould, Vivian Zhang, Lisa Lamberti, Eric Jones, Benjamin Obadia, Nikolaos Korasidis, Alex Gavryushkin, Jean Carlson, Niko Beerenwinkel, and Will Ludington
    PNAS 2018

  • The geometry of partial fitness orders and an efficient method for detecting genetic interactions
    Caitlin Lienkaemper, Lisa Lamberti, James Drain, Niko Beerenwinkel, and Alex Gavryushkin
    Journal of Mathematical Biology, 77(4), 951–970, 2018

  • Inferring genetic interactions from comparative fitness data
    Kristina Crona, Alex Gavryushkin, Devin Greene, and Niko Beerenwinkel
    eLife 2017;6:e28629

  • The combinatorics of discrete time-trees: theory and open problems
    Alex Gavryushkin, Chris Whidden, and Erick Matsen
    Journal of Mathematical Biology, 76(5), 1101–1121, 2017
    blog post by Erick

  • The space of ultrametric phylogenetic trees
    Alex Gavryushkin and Alexei Drummond
    Journal of Theoretical Biology, 403, 197–208, 2016