Hugues Richard

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

The paper reannotates the zebra finch genome using transcriptome data, revealing new transcriptional units and refining gene models.

decOM improves microbial source tracking in ancient oral metagenomes by using k-mer matrices, outperforming existing methods in accuracy.

The paper introduces ASPRING, a method to detect alternatively spliced protein repeats across species, identifies over 5,000 conserved repeats, and maps them to 3D structures to study their role in protein interactions.

The paper develops evolutionary splicing graphs to assess alternative splicing conservation across species and identifies genes where alternative splicing affects pseudo-repeats.

CovRadar provides a platform for tracking and filtering SARS-CoV-2 mutations in the spike gene, enabling users to analyze and visualize mutational changes and spatio-temporal distributions.

The paper reconstructs the evolutionary history of JNK family transcripts and models their protein structures to understand how alternative splicing and transcription sites contribute to functional diversity.

PureCLIP improves crosslink site detection in CLIP-seq data by modeling truncation patterns and non-specific biases, outperforming existing methods in accuracy and replicate consistency.