Philippe Veber

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.

Cluefish identifies gene clusters and biological functions in transcriptomic data series using over-representation analysis and prior knowledge, revealing retinoid signaling disruption as a sensitive pathway in zebrafish exposed to dibutyl phthalate.

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 study performs a meta-analysis of lncRNA associations with hepatocellular carcinoma, finding limited reproducibility and frequent conflicts in reported roles and expression patterns.

This study quantifies the species-specific impact of transposable elements on gene expression and histone marks in Drosophila melanogaster and Drosophila simulans using transcriptomic and epigenomic data.

The paper introduces SEISM, a selective inference method to test the association between sequence motifs extracted from neural networks and phenotypes, improving analysis in regulatory genomics and GWAS.

GOntact uses chromatin contact data to predict CRE target genes and their Gene Ontology enrichments, showing more specific functional annotations than genomic proximity.

The paper introduces Pantagruel, a software pipeline for analyzing bacterial pangenome data to reconstruct gene evolution and identify co-evolved gene modules.

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.