Mariateresa de Cesare

Castanet is a pipeline for analyzing multi-pathogen enrichment sequencing data, providing accurate consensus sequences and metrics for pathogen detection and quantification.

This paper introduces a cost-effective targeted nanopore sequencing approach for P. falciparum genomic surveillance, validated with mock and field samples.

This study analyzes within-host SARS-CoV-2 diversity and transmission patterns using 1390 UK clinical samples, finding low within-host diversity and a narrow transmission bottleneck.

This study evaluates the accuracy of Oxford Nanopore MinION sequencing for whole-genome assembly of Rickettsia typhi in resource-limited settings, finding it insufficient for phylogenetic analysis but useful with error correction.

This paper describes a method to generate full-length HBV genome data using isothermal amplification and sequencing with Nanopore and Illumina, achieving high consensus accuracy and resolving intra-sample variants.

This paper introduces veSEQ-HIV, a cost-effective, high-throughput sequencing method for HIV that recovers complete genomes and quantifies viral load, enabling drug resistance monitoring and transmission analysis.

This paper develops a tool to predict antibiotic resistance in S. aureus and M. tuberculosis from genome sequences with high accuracy and speed.