Roger D. Kouyos

Developmental and molecular features shaping broad and synergistic actions of human autoantibodies targeting interferon-α

This study tracks the development of human autoantibodies against interferons over time, revealing their maturation, specificity, and synergistic effects in blocking IFN signaling.

Cross-scale effect of microbiota dynamics on resistance

This paper develops a cross-scale model to study how gut microbiota dynamics influence antimicrobial resistance persistence and transmission across hospital and community settings.

Screening clinical Candida albicans isolates for invasiveness by mimicking the human environment

The paper screens Candida albicans isolates for invasiveness by assessing filamentation patterns under simulated host conditions.

Rare twin cysteine residues in the HIV-1 envelope variable region 1 link to neutralization escape and breadth development

The paper identifies rare twin cysteine residues in HIV-1 Env V1 linked to neutralization escape and breadth development.

Assessing the role of bacterial innate and adaptive immunity as barriers to conjugative plasmids

This study models how bacterial innate and adaptive immunity affect plasmid spread, finding that immunity suppresses costly plasmids but not beneficial ones.

The XbnAb Cohort: 305 people with broadly neutralizing antibody activity to HIV-1

The paper introduces the XbnAb cohort, a large cohort of 305 people with HIV-1 broadly neutralizing antibody activity, to support HIV vaccine research.

Comparative Evaluation of Bioinformatic Pipelines for Full-Length Viral Genome Assembly

This study evaluates four bioinformatic pipelines for assembling full-length viral genomes, finding that reference sequence similarity affects performance and that runtime and usability vary between tools.

A phylogeny-aware GWAS framework to correct for heritable pathogen effects on infectious disease traits

This paper introduces a phylogeny-aware GWAS framework to correct for heritable pathogen effects on infectious disease traits, showing improved detection of host genetic variants in simulations and applied to HIV-1 data.

Increased CHIP Prevalence Amongst People Living with HIV

The paper investigates the prevalence of clonal hematopoiesis of indeterminate potential (CHIP) in people living with HIV and finds a higher prevalence compared to controls.

The influence of human genetic variation on Epstein-Barr virus sequence diversity

The paper investigates how human genetic variation influences Epstein-Barr virus (EBV) sequence diversity by analyzing paired viral and human genomic data from HIV-coinfected individuals.

ColTapp, an automated image analysis application for efficient microbial colony growth dynamics quantification

ColTapp quantifies bacterial colony growth dynamics from images, enabling analysis of persister cell behavior and improving antibiotic therapy diagnostics.

Easy and Accurate Reconstruction of Whole HIV Genomes from Short-Read Sequence Data

The paper develops a tool to accurately reconstruct whole HIV genomes from short-read data by using tailored references, showing improved accuracy over standard references.