Massimiliano Rossi

Scalable and comprehensive mosaic variant calling using DRAGEN

The paper introduces DRAGEN, a scalable mosaic variant caller that detects low VAF variants with high accuracy and efficiency, and presents a benchmark for low-VAF variants.

A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

The paper develops a benchmark for detecting low-frequency mosaic variants in the HG002 reference material using high-coverage sequencing data and validates its utility across multiple technologies.

Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk

The paper introduces a CN caller for KIV-2 repeats using short reads, showing high accuracy and demonstrating its correlation with Lp(a) levels and population-specific CN distributions.

Comprehensive analysis of the genetic variation in the LPA gene from short-read sequencing

The paper analyzes genetic variation in the LPA gene using short-read sequencing to predict LP(a) concentration, finding allele-specific KIV-2 CN provides better prediction than total CN.

Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms

DRAGEN provides fast and accurate genome analysis across 3,202 genomes, outperforming existing methods in variant detection speed and accuracy for various types including SNV, indel, STR, SV, and CNV.

SPUMONI 2: Improved pangenome classification using a compressed index of minimizer digests

SPUMONI 2 improves pangenome classification by using a compressed index of minimizer digests, achieving faster speed, lower memory use, and better performance for short and long reads.

μ-PBWT: Enabling the Storage and Use of UK Biobank Data on a Commodity Laptop

The paper introduces μ-PBWT, a memory-efficient method for haplotype matching, reducing memory usage by up to 25 times and enabling storage of large datasets on a commodity laptop.

Compressed Data Structures for Population-Scale Positional Burrows-Wheeler Transforms

The paper presents efficient data structures for storing and querying the positional Burrows-Wheeler Transform (PBWT) to improve memory usage for large haplotype datasets.

Finding Overlapping Rmaps via Gaussian Mixture Model Clustering

The paper introduces a Gaussian mixture model clustering method to find overlapping Rmaps without quantization, improving precision and efficiency in optical mapping analysis.

MONI: A Pangenomics Index for Finding MEMs

MONI is a pangenomics index that efficiently finds maximal exact matches by combining prefix-free parsing with threshold calculation, outperforming existing tools in speed and memory usage.

Pan-genomic Matching Statistics for Targeted Nanopore Sequencing

SPUMONI enables fast and accurate targeted nanopore sequencing using efficient pangenome indexes, outperforming minimap2 in speed and memory usage.