Paul Bastide

phyloDS: phylogeny-aware differential splicing across species, beyond reference annotations

phyloDS identifies differentially used orthologous splice junctions across species by improving orthology definition, statistical testing, and sequence-level validation.

Trait evolution with incomplete lineage sorting and gene flow: the Gaussian Coalescent model

The paper introduces the Gaussian Coalescent model to account for incomplete lineage sorting and gene flow in trait evolution, showing improved accuracy over standard models.

Interspecies Differential Gene Expression Analysis with Regularized Phylogenetic Linear Models

This paper introduces phyloDE, a method for interspecies differential gene expression analysis that controls FDR and identifies more DE genes with consistent cis-regulatory changes.

Reconciling fast Hepatitis B evolutionary rates with ancient co-divergence

This study uses a Bayesian mixed-effects molecular clock model to analyze HBV genomic data, revealing declining evolutionary rates and linking viral spread to human migration patterns.

Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: an historical and phylogeographical retrospective

This study traces the historical and phylogeographical spread of Rice yellow mottle virus (RYMV) in East Africa, linking its dispersal to rice cultivation, trade, and human activities.

How fast are viruses spreading in the wild?

This study evaluates dispersal metrics for viruses using simulation and compares their spread in animal populations, finding robustness to sampling effort and human-mediated dispersal signatures.

Modeling the velocity of evolving lineages and predicting dispersal patterns

This paper introduces PIV models to estimate dispersal velocity of evolving lineages and shows improved accuracy in predicting pathogen spread using West Nile virus data.

Benchmark of Differential Gene Expression Analysis Methods for Inter-species RNA-Seq Data using a Phylogenetic Simulation Framework

This paper benchmarks differential gene expression analysis methods for inter-species RNA-Seq data using a phylogenetic simulation framework to evaluate their performance across species.