Christopher J. R. Illingworth

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 analyzes within-host SARS-CoV-2 evolution in chronic infections, finding variable rates of evolution and evidence of subpopulation structure.

The paper estimates the timeline and parameters of an influenza A(H1N2)v spillover event using likelihood-free rejection sampling with limited data.

This paper evaluates a whole genome sequence report form (SRF) used to change infection prevention behaviors in UK hospitals during the pandemic, finding it supported key theoretical mechanisms and intervention functions.

This study identifies HVR-1 as an autoinhibitory region in HCV E1E2 that suppresses viral entry through conformational entropy, which is released upon receptor binding to enhance entry but reduce antibody resistance.

The paper uses transposon mutagenesis and a hidden Markov model to identify functional elements in the fission yeast genome, finding that 90% of the genome has fitness consequences.

The paper identifies a single major QTL on chromosome V associated with ivermectin resistance in Haemonchus contortus through genome-wide analysis of genetic crosses.

This study applies single-cell RNA-sequencing to malaria parasites, revealing transcriptional variation and novel gene expression patterns in sexual stages.

This paper introduces a method to identify genetic drivers of multiple phenotypes in malaria parasites by combining LGS, sequencing, and mathematical modeling, demonstrating its effectiveness in detecting novel alleles for growth rate and strain-specific immunity.