Andrew E. Firth

The dynamics and strategy of RNA replication in astroviruses

This study investigates RNA replication dynamics in astroviruses using high-throughput sequencing, revealing a conserved premature termination model for subgenomic RNA production.

Flexibility and modulation of translation initiation in enterovirus genomes

This study shows enteroviruses can use two upstream AUGs for translation initiation, with the second AUG providing a competitive advantage in specific host environments.

Molecular architecture and diversity of StopGo/2A translational recoding

The paper investigates the StopGo/2A translational recoding mechanism using cryo-EM and bioinformatics, revealing structural and sequence features that enable this process in viruses.

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

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.

Encephalomyocarditis virus protein 2B* antagonises innate immune signalling by interacting with 14-3-3 protein family members

This paper identifies 2B* as an EMCV protein that antagonizes innate immune signaling by interacting with 14-3-3 proteins, specifically through the RRNSS sequence.

An intra-family conserved high-order RNA structure within the M ORF is important for arterivirus subgenomic RNA accumulation and infectious virus production

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

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.

Programmed ribosomal frameshifting during PLEKHM2 mRNA decoding generates a constitutively active mediator of kinesin-1-dependent lysosome transport

The paper identifies a programmed ribosomal frameshifting event in PLEKHM2 mRNA that generates a constitutively active protein domain essential for lysosome transport and cardiac function.

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

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

A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit

This study identifies a late-stage quality control step in human mitochondrial ribosome large subunit assembly, showing that MRM2 ablation impairs oxidative phosphorylation through defective translation and accumulation of assembly intermediates.

Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch

This paper elucidates the structural basis of how the Cardiovirus 2A protein regulates gene expression by interacting with RNA elements and ribosomes.

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

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

The stem loop 2 motif is a site of vulnerability for SARS-CoV-2

The paper identifies the stem loop 2 motif as a vulnerable site in SARS-CoV-2 that can be targeted by antisense oligonucleotides to inhibit replication and infection.

A putative new SARS-CoV protein, 3a*, encoded in an ORF overlapping ORF3a

The paper identifies a putative new SARS-CoV gene, ORF3a*, overlapping ORF3a in an alternative reading frame, supported by conservation and ribosome profiling data.

A case for a reverse-frame coding sequence in a group of positive-sense RNA viruses

The paper identifies long reverse-frame ORFs in narnaviruses, showing coding capacity on the negative strand of positive-sense RNA viruses.

Upstream translation initiation expands the coding capacity of segmented negative-strand RNA viruses

This study shows segmented negative-strand RNA viruses use upstream translation initiation to expand their coding capacity through non-AUG initiation and host mRNA leader sequence appropriation.

Comparative analysis of gene expression in virulent and attenuated strains of infectious bronchitis virus at sub-codon resolution

This study compares gene expression in virulent and attenuated IBV strains using RNASeq and RiboSeq, revealing differences in transcription, translation, and host response.

Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome

The paper uses retapamulin-assisted ribosome profiling to identify alternative translation start sites in E. coli, revealing new proteins and regulatory roles.