E. Molloy

Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones

The paper models gene expression adaptation in tumor subclones using stochastic processes and finds non-genetic mechanisms drive subclonal evolution and treatment response.

TREE-QMC: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees

TREE-QMC improves species tree estimation by addressing scalability and accuracy issues in quartet-based methods using a novel graph construction approach.

Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone

This paper evaluates methods for estimating species trees using retroelement insertions, finding that ASTRAL BP and SDPquartets are statistically consistent and accurate, especially in the anomaly zone.

To include or not to include: The impact of gene filtering on species tree estimation methods

This study evaluates how gene filtering affects species tree estimation methods, finding that filtering based on missing data is generally harmful, while filtering based on gene tree error can sometimes improve accuracy under specific conditions.