Bastien Boussau

The paper shows that horizontal gene transfers can reveal information about extinct and unsampled lineages in species trees through gene tree analysis.

This paper improves ancestral genome reconstruction by incorporating gene-content grammar, leading to more accurate and consistent reconstructions across different methods.

The paper introduces a phylogenetic method to detect protein sites associated with continuous traits, showing improved recall but higher computational cost, and applies it to mammalian longevity data.

This paper develops a deep learning model to identify selective pressures on protein sites, showing it outperforms likelihood-based methods on similar data but is less effective on divergent datasets.

Phyloformer uses deep learning to quickly and accurately reconstruct phylogenetic trees from protein sequences, outperforming existing methods on simulated and real data.

This paper shows that horizontal gene transfer methods can detect ghost lineages in phylogenies, revealing hidden diversity despite lack of genomic data.

This study identifies convergent transcriptomic and genomic changes in xeric rodents, showing increased convergence with adaptation age and species relatedness.

This study evaluates the realism of sequence evolution simulations by testing how well supervised learning can distinguish simulated from empirical MSAs.

The paper investigates the link between endoparasitoid lifestyle and the endogenization and domestication of dsDNA viruses in Hymenoptera genomes.

The paper introduces PoMos, a polymorphism-aware method for species tree estimation and evolutionary force analysis using RevBayes, finding mutation and selection biases in grasshopper phylogeny.

Treerecs is a phylogenetic software that performs duplication-loss reconciliation to root gene trees and correct alignment uncertainties.

This paper clarifies how convergent adaptive evolution manifests in coding sequences, reviews detection methods, and evaluates their power through simulations.

MaxTiC ranks a species tree by maximizing time consistency with lateral gene transfer constraints, achieving accurate results on simulated and biological datasets.

The paper reanalyzes data from Nelson-Sathi et al. to show that gene acquisitions in archaea do not correspond to major clade origins, challenging the hypothesis of bacterial HGT-driven diversification.