James Robert White

Reference-free microsatellite instability detection from tumor sequencing using intrasample variability modeling

PROMIS detects microsatellite instability in tumor sequencing without reference data or matched normals, achieving high accuracy across multiple cancer types and sample types.

Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer

Multi-probe imaging and 16S rRNA profiling of Malaysian colorectal cancers show that Fusobacterium nucleatum, dominated by subspecies animalis clade 2, is enriched specifically within mucus-invasive tumor biofilms.

Cognate Antigen Engagement Induces HIV-1 Expression In CD4+ T Cells From People On Long-Term ART

The paper shows that cognate antigen engagement in CD4+ T cells on long-term ART increases HIV-1 transcription through T cell activation, suggesting a role in viral rebound.

Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer

This study tracks ctDNA and immune cell changes in lung cancer patients on immunotherapy to identify molecular responses and immune-related toxicities.

Batch effects removal for microbiome data via conditional quantile regression (ConQuR)

This paper introduces ConQuR, a method to remove batch effects in microbiome data by using conditional quantile regression, demonstrating its effectiveness in preserving signals and improving analysis.

Incorporation of data from multiple hypervariable regions when analyzing bacterial 16S rRNA sequencing data

The paper presents an analysis pipeline for integrating data from multiple hypervariable regions in 16S rRNA sequencing and applies it to a clinical cohort.