Remco Bouckaert

BREATH simultaneously infers phylogenetic and transmission trees for outbreaks using sequence data, improving resolution and origin timing estimates in a tuberculosis outbreak.

This paper introduces KRegCCD, a new Bayesian phylogenetic model that improves posterior tree estimation and enables topology testing by providing full support over tree space.

DensiTree 3 is an interactive tool for comparing pairs of tree sets, providing visualizations and CCDs to assess differences in tree distributions and clade support.

This paper introduces a PhyloPotts model that combines Potts models with phylogenetics to improve ancestral sequence reconstruction, though it does not consistently reduce bias in phylogenetic estimates.

This paper introduces a hierarchical clock-mixture model for Bayesian phylogenetic dating to better handle uncertainty in clock choice and improve timescale estimation.

This paper introduces a regenerative molecular recording system called hypercascade that enables deep lineage reconstruction by maintaining a constant mutation rate over time.

MASCOT-Skyline jointly infers spatial and temporal transmission dynamics of infectious diseases using a structured coalescent skyline approach, revealing biases in existing phylogeographic methods.

The paper develops substitution models that account for changes in the coding alphabet size over time, finding support for a reduced ancient alphabet in old proteins and rejecting it in young ones.

This paper introduces improved MCMC proposal distributions for Bayesian phylodynamic inference, enhancing scalability and reducing convergence time in phylogenetic analysis.

This paper introduces a probabilistic framework to detect evolutionary bursts during branching events, showing evidence in proteins, morphologies, and languages.

This paper introduces a Bayesian method for summarizing phylogenetic tree posteriors using clade probabilities, showing it performs as well or better than existing methods.

This paper describes good practices for validating Bayesian models in computational biology and introduces tools to automate validation protocols.

The paper introduces entropy-based rogue detection algorithms to improve Bayesian phylogenetic analysis by identifying and removing rogue taxa and clades that distort tree distributions.

The paper introduces an automated convergence diagnostic for phylogenetic MCMC analyses, demonstrating high accuracy in detecting convergence issues and enabling real-time evaluation.

This paper introduces the 5rf model, which allows each rate class in a phylogenetic model to have its own base frequencies, showing improved likelihoods but also new challenges in modeling mtDNA and nuclear sequences.

The paper introduces a matrix representation of tree space for Bayesian phylogenetic inference, demonstrating it can recover tree parameters and produce better summary trees than traditional methods.

This paper introduces baseMEMOIR, a method that reconstructs high-resolution cell lineage trees and spatial dynamics using base editing and imaging, achieving 792 bits of memory in embryonic stem cells.

The paper analyzes SARS-CoV-2 genomic data from Colombia to study variant transmission dynamics and the impact of control measures during the first two years of the pandemic.

The paper introduces an online Bayesian phylogenetic inference algorithm for BEAST 2 that allows efficient updates to analyses as data changes, without re-running from scratch.

BICEPS improves Bayesian phylogenetic inference by efficiently estimating coalescent epoch models and demonstrating effectiveness on SARS-CoV-2 data.

StarBeast3 improves Bayesian inference of the multispecies coalescent model with faster computation and parallelization, outperforming previous versions and *BEAST on real and synthetic datasets.

This paper improves the efficiency of Bayesian phylogenetic inference by developing adaptive MCMC operators for relaxed clock models, achieving up to 65x speedup in parameter estimation.

The paper introduces TreeModelAdequacy, a tool to assess phylodynamic model adequacy using posterior predictive simulations, applied to Ebola and H1N1 influenza outbreak data.

StarBEAST2 improves species tree inference speed and accuracy by integrating population size analysis and relaxed clocks for substitution rate estimation.

bModelTest infers and marginalizes site models during Bayesian phylogenetic analysis, eliminating the need for pre-determined models.