• Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software
    Paul Gardner, James Paterson, Stephanie McGimpsey, Fatemeh Ashari-Ghomi, Sinan Umu, Aleksandra Pawlik, Alex Gavryushkin, and Michael Black
    bioRxiv 2021

  • A Fast Lasso-based Method for Inferring Pairwise Interactions
    Kieran Elmes, Astra Heywood, Zhiyi Huang, and Alex Gavryushkin
    bioRxiv 2021

  • Cancer phylogenetics using single-cell RNA-seq data
    Jiří Moravec, Rob Lanfear, David Spector, Sarah Diermeier, and Alex Gavryushkin
    bioRxiv 2021

  • The geometry of the space of Discrete Coalescent Trees
    Lena Collienne, Kieran Elmes, Mareike Fischer, David Bryant, and Alex Gavryushkin
    arXiv 2021

  • Learning epistatic gene interactions from perturbation screens
    Kieran Elmes, Fabian Schmich, Ewa Szczurek, Jeremy Jenkins, Niko Beerenwinkel, and Alex Gavryushkin
    PLoS ONE 16(7): e0254491, 2021

  • Computing nearest neighbour interchange distances between ranked phylogenetic trees
    Lena Collienne and Alex Gavryushkin
    Journal of Mathematical Biology, 82(8), 2021

  • Geometry of Ranked Nearest Neighbour Interchange Space of Phylogenetic Trees
    Lena Collienne, Kieran Elmes, Mareike Fischer, David Bryant, and Alex Gavryushkin
    bioRxiv 2019
    blog

  • 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