This study identifies retroviral sequences in guinea pig genomes and demonstrates viral RNA expression in lymphomas, suggesting a potential role in neoplasia.

bioRxiv · Jan 13, 2026 · PreprintMicrobiology

Comprehensive hallmark gene sequence, genomic and structural analysis of Picornavirales viruses clarifies new and existing taxa

Richard Mayne, Donald B. Smith, Katherine A. Brown, Yan Ping Chen, Andrew E. Firth, Kazuhiko Katayama, Nick J. Knowles, Peter Simmonds K

The paper genetically classifies 525 Picornavirales genomes and 'picorna-like' viruses using multiple sequence and structural analyses, revealing support for existing families and six novel families, along with 32 new genera.

bioRxiv · Jan 5, 2026 · PreprintMicrobiology

Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterised sequences in public protein databases

Katherine A. Brown, Andrew E. Firth

This study identifies 3,560 uncharacterized protein sequences from public databases likely derived from RNA viral RdRp, including new endogenous viral elements and potential false positives.

Virus Evolution · Jan 1, 2025Peer-reviewedMicrobiology

CIAlign - A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments.

Charlotte Tumescheit, Andrew E. Firth, Katherine A. Brown

CIAlign is a command line tool that cleans, interprets, and visualizes multiple sequence alignments by removing problematic regions and providing visual feedback.

PeerJ · Mar 15, 2022Peer-reviewedBioinformatics

Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus

Chris H. Hill, Georgia M. Cook, Sawsan Napthine, Anuja Kibe, Katherine A. Brown, Neva Caliskan, Andrew E. Firth, Stephen C. Graham, Ian Brierley

This study investigates how the 2A protein of Theilovirus stimulates ribosomal frameshifting by analyzing its interaction with an RNA pseudoknot and using ribosome profiling.

Nucleic Acids Research · Oct 7, 2021Peer-reviewedMolecular Biology

CGAT-core: a python framework for building scalable, reproducible computational biology workflows

Adam P. Cribbs, Sebastián Luna-Valero, Charlotte L. George, Ian M. Sudbery, Antonio J. Berlanga‐Taylor, Stephen Nicholas Sansom, Tom S. Smith, Nicholas Edward Ilott, Jethro S. Johnson, Jakub Scaber, Katherine A. Brown, David Sims, Andreas Heger

CGAT-core is a Python framework for building scalable, reproducible computational biology workflows, demonstrated with an RNAseq analysis pipeline.

F1000Research · Apr 4, 2019Peer-reviewedGenomics