A. Gavryushkin

The Fossilised Birth-Death Model is Identifiable

The paper proves that time-dependent fossilised birth-death models are identifiable, but shows that adding a removal after sampling parameter makes them unidentifiable.

Ranked Subtree Prune and Regraft

This paper introduces a modified SPR rearrangement for ranked phylogenetic trees and studies its algorithmic properties and implications for time tree inference.

Testing for phylogenetic signal in single-cell RNA-seq data

This study shows that scRNA-seq data can be used for phylogenetic analysis, revealing tumor clonal composition through expression levels and SNVs.

Accounting for errors in data improves timing in single-cell cancer evolution

This study improves timing accuracy in single-cell cancer evolution by modeling errors in single-cell DNA sequencing data using BEAST2, showing that error accounting shifts divergence times forward and reduces overestimation of phylogenetic diversity.

The geometry of partial fitness orders and an efficient method for detecting genetic interactions

This paper introduces an efficient method to detect genetic interactions from partial fitness orders using geometric and graph-theoretic approaches, improving upon previous methods exponentially.

Inferring Genetic Interactions From Comparative Fitness Data

This paper develops quantitative tools to infer genetic interactions from fitness rank orders, demonstrating their application across multiple genetic systems.

The combinatorics of discrete time-trees: theory and open problems

This paper studies discrete approximations of time-trees, analyzing graph-theoretic properties and proposing open problems for phylogenetic applications.