Stephen F. Schaffner

The paper evaluates the impact of drug resistance mutations on antimalarial drug resistance and fitness in Plasmodium falciparum isolates from Senegal using genetic and phenotypic assays.

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

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.

MalKinID identifies malaria parasite genealogical relationships using IBD proportions and segment distributions, showing high accuracy in outcrossed importations but reduced performance in inbreeding scenarios.

The paper identifies three regulatory variants associated with IVD expression and linked to GWAS signals, showing synergistic and opposing effects through functional experiments.

The paper identifies a blood protein biomarker signature to distinguish bacterial from viral/malaria pneumonia in children in a malaria-endemic setting, with high sensitivity and specificity.

This paper develops CRISPR-Cas13a-based diagnostics for real-time detection of Ebola and Lassa viruses in field settings, demonstrating sensitivity and usability in clinical samples.

The paper uses metagenomic sequencing to identify a yellow fever outbreak in Edo State, Nigeria, from undiagnosed fever cases.

The paper analyzes mumps virus circulation in the US using genomic data to show multiple co-circulating lineages and transmission patterns, but finds no evidence of vaccine escape variants.

The paper introduces hmmIBD, a software tool for estimating pairwise identity by descent between haploid genomes, validated using simulated data and applied to Plasmodium falciparum samples.

This study sequenced 110 Zika virus genomes from 10 countries, revealing rapid expansion in Brazil, multiple introductions into other regions, and undetected circulation before confirmed cases.

The paper uses longitudinal genomic data from Plasmodium falciparum isolates in Thailand to identify genetic markers associated with artemisinin resistance, finding significant changes in SNPs beyond kelch13.

Cosi2 simulates coalescent processes with selection, improving speed and supporting gene conversion and complex demographics.