Jacob E. Lemieux

The paper assesses subtype-specific neutralization resistance of RSV-A and RSV-B isolates to mAbs and vaccines, finding RSV-A more resistant and bivalent vaccines more effective.

This study examines immune responses in adults with COVID-19 who received or did not receive nirmatrelvir-ritonavir, finding no differences in immune markers between those with and without virologic rebound.

This paper develops a CRISPR-based assay for rapid detection of cefixime resistance in Neisseria gonorrhoeae by analyzing penA gene mosaicism.

The paper models SARS-CoV-2 evolution during the pandemic, finding that immune escape became more important than infectivity as variants evolved.

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

The paper uses E. coli surface display to study Borrelia burgdorferi Elp proteins, revealing their conserved complement inhibition and novel interaction with perlecan.

The paper designs SARS-CoV-2 Spike proteins with novel mutations to evaluate vaccine effectiveness against future viral variants using a deep learning model.

Delphy provides a fast, scalable Bayesian phylogenetic analysis tool for outbreak tracking, achieving 1,000x speedups while maintaining state-of-the-art accuracy.

The paper models viral rebound after nirmatrelvir-ritonavir treatment, finding that target cell preservation and incomplete viral clearance drive rebound, with extended treatment reducing this risk.

This study uses long-read assemblies to show that genetic modules across multiple plasmids organize Borrelia burgdorferi strain variation and influence virulence in Lyme disease.

This study analyzes the Borreliaceae pangenome to reveal conserved genomic architecture across phylogenetic scales, showing lineage-specific expansions in accessory genomes, particularly among lipoproteins.

This paper introduces BVAS, a Bayesian method to infer fitness-associated mutations in SARS-CoV-2 using 6.9 million genomes, identifying key mutations and epistatic interactions.

This study uses metagenomic sequencing to detect pathogens in CNS infections, identifying novel pathogens and improving detection methods.

The paper introduces DNA spike-ins to detect contamination in SARS-CoV-2 amplicon-based sequencing and demonstrates their utility in a real-world outbreak investigation.