Olivier Gascuel

The paper introduces methods to improve consensus tree resolution using fine-grained dissimilarity measures, showing better performance on datasets with low to moderate phylogenetic signal.

PhyloCNN improves tree representation and neural network architecture for deep learning in phylodynamics and diversification studies, achieving high accuracy with smaller training sets.

This paper investigates overfitting in ML phylogenetic inference using cross-validation and finds no significant overfitting in most tools.

The paper introduces a Bayesian phylogenetic bootstrap method to improve branch support interpretation in phylogenetics, showing higher expected support for correct branches compared to the frequentist Felsenstein bootstrap.

This paper introduces early stopping criteria to accelerate maximum likelihood phylogenetic inference without sacrificing accuracy, achieving faster inference times on empirical and simulated datasets.

This study compares Felsenstein's bootstrap proportions and Transfer Bootstrap Expectation in assessing phylogenetic support under varying taxon sampling and finds TBE more robust in most cases.

TiPS generates trajectories and phylogenetic trees from compartmental models using stochastic simulations and coalescent methods, with an R package for flexible and efficient modeling.

The paper introduces a deep learning method for phylodynamic analysis that outperforms existing approaches on simulated data and applies to HIV outbreak dynamics.

The paper was withdrawn due to duplicate posting and does not provide original research findings.

The paper analyzes CRF19 HIV-1 subtype sequences from Cuba to trace its origin, spread, and transmission patterns, finding early introduction and rapid progression to AIDS.

Gotree/Goalign provides a toolkit and Go API for phylogenetic workflows, offering 120 commands and an API for sequence alignment and tree manipulations.

This study analyzes how global and regional public health interventions affected SARS-CoV-2 transmission clusters using genetic sequence data and phylogenetic analysis.

The paper introduces COVID-Align, a tool for efficiently aligning SARS-CoV-2 genomes using profile HMM, enabling rapid and accurate analysis of large datasets.

This paper introduces an algorithm to compute the transfer index for all branches in a phylogenetic tree efficiently, improving runtime from O(n²) to O(n log³ n).

The paper improves pairwise protein sequence comparison by integrating domain co-occurrence information, increasing BLAST hit sensitivity and proteome coverage.