Joseph Hughes

The paper introduces Flu Mutation Explorer, a web tool that integrates IAV genomic data with mutation annotations to help interpret host adaptation mutations.

This study evaluates how protein language models capture mutational processes and fitness landscapes, finding that explicit mutational accessibility improves predictions while historical biases degrade performance.

The paper investigates the emergence of the influenza A/H3N2 K subclade, finding limited antigenic change and age-dependent vaccine responses, suggesting non-antigenic selection pressures.

CD8scape predicts viral escape from CD8+ T cell response using HLA genotype and within-host sequence variation to identify immune escape potential.

This study shows that H5N1 viruses' ability to adapt to bovine cells varies across genotypes and time, with key mutations in PB2 playing a role.

Viro3D predicts and curates protein structures for 4,400 viruses, expanding structural coverage 30-fold and enabling functional and evolutionary analysis of viral proteins.

This study identifies NSm as a critical protein for bunyavirus transmission between vertebrate and arthropod hosts, showing its necessity for midgut infection and spread.

This study expands the known diversity of human anelloviruses by analyzing 829 genomes from microbiome datasets and identifies new clades and recombination patterns.

The paper shows that XRN1-mediated RNA decay provides nucleotides for alphavirus replication by recycling monophosphate nucleotides through the salvage pathway.

This paper shows that protein language models can assess mutation effects in SARS-CoV-2 spike protein without multiple sequence alignments, capturing evolutionary constraints and variant properties.

The paper introduces a database-integrated genome screening approach to explore the dark genome, identifying over 1.1 million endogenous viral elements across 874 vertebrate species.

The paper develops an interactive 3D tool to explain SARS-CoV-2 spike protein mutations and variants, showing it improves public understanding compared to existing resources.

The paper quantifies unknown sequences in human microbiomes, finding 2% on average are taxonomically undefined, with higher rates in skin and oral microbiomes.

The paper introduces a new metric, Synonymous Dinucleotide Usage (SDU), to quantify dinucleotide representation in viral genomes and demonstrates its application on flaviviruses and rhabdoviruses.

DisCVR rapidly detects human viruses in clinical samples using HTS data with high sensitivity and specificity, and is accessible on low-resource computers.

GLUE is a flexible software system for organizing and processing virus sequence data, demonstrated with a hepatitis C virus case study.

This study investigates the origins and spread of small ruminant lentiviruses using genomic data, finding no clear evidence that the Fertile Crescent was the pandemic origin but suggesting historical breed exports may have contributed to disease emergence.

The paper introduces a computational framework called DIGS for systematically screening genomes using sequence similarity search tools and a relational database, demonstrating its application in identifying novel endogenous viral elements in mammalian genomes.