L. A. Huuki

Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics

This study compares simple and complex substitution models for divergence time estimation, finding that simple models can produce similar results to complex ones in many datasets.

A new method for inferring timetrees from temporally sampled molecular sequences

This paper introduces RTDT, a new method for inferring timetrees from temporally sampled molecular sequences, which is more accurate and computationally efficient than existing Bayesian methods.

Predicting clone genotypes from tumor bulk sequencing of multiple samples

The paper evaluates nine computational methods for inferring clone genotypes from bulk tumor sequencing data, finding that most perform poorly on datasets with mixed clonal lineages.

Computational enhancement of single-cell sequences for inferring tumor evolution

This paper introduces BEAM, a Bayesian method for improving single-cell tumor sequencing data by leveraging evolutionary information, showing it outperforms existing methods in imputing missing bases and correcting false positives/negatives.