Recursive algorithms for phylogenetic tree counting. - Alexandra Gavryushkina; David Welch 003; Alexei J. Drummond (Algorithms Mol. Biol., 2013)

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration. - Alexandra Gavryushkina; David Welch 003; Tanja Stadler; Alexei J. Drummond (PLoS Comput. Biol., 2014)

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. - Remco R. Bouckaert; Timothy G. Vaughan; Joëlle Barido-Sottani; Sebastián Duchêne; Mathieu Fourment; Alexandra Gavryushkina; Joseph Heled; Graham Jones; Denise Kühnert; Nicola De Maio; Michael Matschiner; Fábio K. Mendes; et al. (PLoS Comput. Biol., 2019)

ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls. - Harry Biggs; Padmini Parthasarathy; Alexandra Gavryushkina; Paul P. Gardner (Database J. Biol. Databases Curation, 2020)

Filtering for Highly Variable Genes and High-Quality Spots Improves Phylogenetic Analysis of Cancer Spatial Transcriptomics Visium Data. - Alexandra Gavryushkina; Holly R. Pinkney; Sarah D. Diermeier; Alex Gavryushkin (J. Comput. Biol., 2025)