Joshua P. Earl

Identification of disease-specific alleles and gene duplications from 1,600 Haemophilus influenzae genomes using predicted protein analyses from an unsupervised language model and clinical metadata

The paper identifies disease-specific alleles and gene duplications in H. influenzae by analyzing protein sequences and clinical metadata from 1,600 genomes.

Development of a long-read high-throughput chromatin conformation capture method for evaluating both cis and trans interactions between integrated Hepatitis B Virus and host genomes.

The paper develops a long-read Hi-C method to study 3D interactions between integrated HBV DNA and host genomes, improving sensitivity and specificity for analyzing these interactions.

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

The paper presents a pipeline using PacBio CCS to sequence full-length 16S rRNA genes for species-level microbiome analysis, showing high accuracy in mock communities and variation in sinonasal microbiomes.

Microbiome-TP53 Gene Interaction in Human Lung Cancer

This study identifies a microbiome-TP53 interaction in squamous cell lung cancer, showing Acidovorax enrichment in smokers with TP53 mutations.