Samuel M. Nicholls

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.

The paper formalizes and addresses the computational complexity of haplotyping microbial communities using metagenomic data and provides open-source tools for the task.

MAJORA enables decentralized sequencing and integration of SARS-CoV-2 genomic data and metadata across the COG-UK network, supporting rapid genomic surveillance.

This paper introduces a method to recover gene haplotypes from metagenomes and shows it accurately identifies mutation rate differences between core and accessory gene families in rumen microbiomes.

The paper presents ultra-deep, long-read nanopore sequencing datasets from a mock microbial community to evaluate bioinformatics tools and pipelines for long-read metagenomics.

This paper introduces a probabilistic method to recover haplotypes from metagenomic data, achieving 100% accuracy in recovering cryptic gene isoforms from HIV-1 strain mix data.

This paper demonstrates that in-field nanopore sequencing of metagenomes and 16S rRNA gene amplicons accurately characterizes glacier microbiota, matching lab-based sequencing results.