Yuri Pirola

Pangebin improves plasmid binning in bacterial isolates by using pangenome-assembly graphs to enhance accuracy across different assemblers.

This paper introduces deepSpecas, a deep learning method for differential analysis of alternative splicing events in RNA-seq samples, achieving higher precision with reduced sensitivity.

The paper introduces RecGraph, a tool that extends sequence-to-graph alignment by incorporating recombinations, and evaluates its performance on bacterial pangenome graphs.

Shark removes irrelevant RNA-Seq reads to improve analysis efficiency without affecting results.

MALVIRUS efficiently calls viral variants from sequencing data and generates population SNP catalogs, validated against GISAID data for SARS-CoV-2.