Luca Denti

VESPA-SS detects somatic structural variants from long-read sequencing data without requiring read mapping or a high-quality germline reference, achieving high F1 scores on cancer cell lines.

This study evaluates structural variant callers using long-read sequencing data, showing performance variation based on ground truth, reference genome, and genomic regions.

PanSpace is a convolutional neural network-based tool for fast and scalable indexing of bacterial genome databases, reducing disk space and improving query speed.

This paper introduces an assembly-free method to augment pangenome graphs using long reads from new samples, without aligning to a reference or calling variants.

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 pantas, a pangenomic method for detecting and differentially quantifying alternative splicing events using RNA-Seq data, showing competitive accuracy compared to linear reference-based approaches.

This paper introduces a method to construct pangenome graphs by solving an exact cover problem on blocks, showing how different objectives affect graph properties.

The paper investigates how somatic Transformer and sex chromosome karyotype pathways regulate gene expression during Drosophila gonad development, showing their combined and exclusive effects on germ cell development.

ESGq quantifies alternative splicing events across conditions using event splicing graphs, showing consistent results compared to existing tools.

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

SVDSS improves structural variant discovery in hard-to-call regions using long-read sequencing by combining multiple methodologies, outperforming existing methods in repetitive genomic regions.

The paper introduces a method to identify sample-specific strings in long-read sequencing data for comparative genome analysis without read mapping.

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

The paper introduces MP3, a similarity measure for tumor phylogenies that handles multiple mutations, and shows it correctly classifies trees on simulated and real data.

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

MALVA is a mapping-free genotyping method that efficiently handles multi-allelic SNPs, indels, and high-density variants with high accuracy and speed.

ASGAL aligns RNA-Seq data to a splicing graph to detect novel alternative splicing events, outperforming methods that align to a reference genome.