Paolo Piazza

Multi-omics reveals a monocyte-macrophage-fibroblast axis in post-COVID-19 fibroinflammatory lung remodelling

This study identifies a monocyte-macrophage-fibroblast axis in post-COVID-19 lung fibrosis using multi-omic profiling and shows its potential as a therapeutic target.

Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data

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

Pan-genotypic probe-based enrichment to improve efficiency of Hepatitis B virus sequencing

This paper introduces a pan-genotypic probe-based enrichment method to enhance HBV sequencing efficiency, showing significant increases in HBV read counts and viral load correlation.

Viral burdens are associated with age and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection related sampling bias.

This study adjusts for sampling bias in SARS-CoV-2 Ct values and finds that viral variant and age affect within-host viral burdens, with variant effects varying by vaccination status.

Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)

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.

Single cell RNA-seq reveals profound transcriptional similarity between Barretts esophagus and esophageal glands

The paper uses single-cell RNA-seq to compare Barretts esophagus with normal esophageal tissues, finding transcriptional similarities with esophageal cells but not with gastric or duodenal cells.

Interferon lambda 4 impacts broadly on hepatitis C virus diversity.

The paper examines the impact of IFN-lambda4 on HCV diversity using host and viral genetic data from 485 patients, finding that IFN-lambda4 variants influence viral amino acid diversity and load.

Insights into platypus population structure and history from whole-genome sequencing

This study uses whole-genome sequencing of platypuses to reveal strong population structure, recent bottlenecks, and genetic relationships across their range.

A high throughput screen for active human transposable elements

This paper introduces TE-NGS, a targeted sequencing protocol and computational pipeline to identify polymorphic and novel transposable element insertions in human genomes, demonstrating high sensitivity and precision.

A practical solution for preserving single cells for RNA sequencing

This paper describes a method using DSP fixation to preserve single cells for RNA sequencing, showing it maintains RNA complexity and reduces technical variability.

Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis.

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