Maxwell Murphy

The paper introduces a standardized format for storing phased targeted sequencing data and provides tools to create and manipulate this format.

This paper introduces a Bayesian framework for inferring transmission networks from polyclonal infections, demonstrating its application to Plasmodium falciparum with high precision and recall in simulations.

The paper introduces Aster, a statistical framework for accurately classifying antimalarial drug efficacy outcomes by accounting for complexity of infection and genotyping limitations.

MOIRE, a Bayesian R package, jointly infers allele frequencies, multiplicity of infection (MOI) and within-host relatedness from SNP or polyallelic malaria genotypes, yielding a panel-portable effective MOI.

The paper develops a method to sequence microhaplotypes from Plasmodium falciparum heterozygomes, achieving high coverage, specificity, and sensitivity for detecting polyclonal infections.

The paper characterizes Plasmodium falciparum genetic diversity in Eswatini, finding high diversity despite low transmission, with no added value of diversity metrics in classifying imported vs. local infections.