• Filtering for highly variable genes and high quality spots improves phylogenetic analysis of cancer spatial transcriptomics Visium data
    Sasha Gavryushkina, Holly Pinkney, Sarah Diermeier, and Alex Gavryushkin
    bioRxiv 2024

  • Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities
    Lars Berling, Jonathan Klawitter, Remco Bouckaert, Dong Xie, Alex Gavryushkin, and Alexei Drummond
    bioRxiv 2024

  • Online Bayesian analysis with BEAST 2
    Remco Bouckaert, Lena Collienne, and Alex Gavryushkin
    bioRxiv 2022

  • The Fossilised Birth-Death Model is Identifiable
    Kate Truman, Timothy Vaughan, Alex Gavryushkin, and Sasha Gavryushkina
    Systematic Biology 2024

  • Automated convergence diagnostic for phylogenetic MCMC analyses
    Lars Berling, Remco Bouckaert, and Alex Gavryushkin
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 2024

  • Estimating the mean in the space of ranked phylogenetic trees
    Lars Berling, Lena Collienne, and Alex Gavryushkin
    Bioinformatics 2024

  • Ranked subtree prune and regraft
    Lena Collienne, Chris Whidden, and Alex Gavryushkin
    Bulletin of Mathematical Biology 2024

  • Testing for phylogenetic signal in single-cell RNA-seq data
    Jiří Moravec, Rob Lanfear, David Spector, Sarah Diermeier, and Alex Gavryushkin
    Journal of Computational Biology 2023

  • A fast lasso-based method for inferring higher-order interactions
    Kieran Elmes, Astra Heywood, Zhiyi Huang, and Alex Gavryushkin
    PLOS Computational Biology 2022

  • SNVformer: an attention-based deep neural network for GWAS data
    Kieran Elmes, Diana Benavides-Prado, Neset Ozkan Tan, Trung Bao Nguyen, Nicholas Sumpter, Megan Leask, Michael Witbrock, and Alex Gavryushkin
    ICML Workshop on Computational Biology 2022

  • Accounting for errors in data improves timing in single-cell cancer evolution
    Kylie Chen, Jiří Moravec, Alex Gavryushkin, David Welch, and Alexei Drummond
    Molecular Biology and Evolution 2022

  • Tuberous sclerosis complex: a complex case
    Ryan Powell, Sharon Pattison, Jiri Moravec, Basharat Bhat, Nada Guirguis, David Markie, Greg Jones, Jason Copedo, Ian Morison, Alex Gavryushkin, Bronwyn Gray, Lisa Wyeth, Mike Eccles, and Erin Macaulay
    Cold Spring Harbor Molecular Case Studies 2022

  • 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
    Genome Biology 2022

  • Discrete coalescent trees
    Lena Collienne, Kieran Elmes, Mareike Fischer, David Bryant, and Alex Gavryushkin
    Journal of Mathematical Biology 2021

  • Learning epistatic gene interactions from perturbation screens
    Kieran Elmes, Fabian Schmich, Ewa Szczurek, Jeremy Jenkins, Niko Beerenwinkel, and Alex Gavryushkin
    PLOS ONE 2021

  • Computing nearest neighbour interchange distances between ranked phylogenetic trees
    Lena Collienne and Alex Gavryushkin
    Journal of Mathematical Biology 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 2018

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

  • The combinatorics of discrete time-trees: theory and open problems
    Alex Gavryushkin, Chris Whidden, and Erick Matsen
    Journal of Mathematical Biology 2017
    blog post by Erick

  • The space of ultrametric phylogenetic trees
    Alex Gavryushkin and Alexei Drummond
    Journal of Theoretical Biology 2016