Amy Trebes

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.

An autosomal dominant cardiac arrhythmia syndrome, ST Depression Syndrome, is caused by the de novo creation of a cardiomyocyte enhancer.

The paper identifies a de novo enhancer mutation in KCNB1 causing ST Depression Syndrome, a cardiac arrhythmia, and shows it can be predicted by a deep neural network.

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.

Within-host genomics of SARS-CoV-2

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.

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.