Daniel E. Neafsey

The paper analyzes parasite genotypes in sympatric mosquito species to show divergent selection on Plasmodium falciparum mediated by different vectors.

The paper argues that low diversity in pathogen proteins does not necessarily indicate evolutionary constraint and introduces a tool to explore diversity and divergence in Plasmodium falciparum proteins.

This study uses untargeted sequencing to analyze population genetics and pathogen surveillance in timber rattlesnakes, finding genetic distinctness and a color variation locus linked to ALDH4A1.

The paper shows that additional blood meals increase Plasmodium falciparum sporozoite infectivity to hepatocytes by altering their transcriptional profiles.

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

This study identifies genomic signatures of local adaptation in Anopheles coluzzii across urban, rural, and sylvatic sites in Gabon, revealing distinct genetic responses to human-driven selection pressures and environmental heterogeneity.

This study analyzes whole genomes of 1094 Anopheles darlingi mosquitoes from six South American countries, revealing geographic structure, genetic diversity, and selection signals on cytochrome P450 genes.

The paper examines how evolutionary forces differ across life stages of Plasmodium falciparum, finding reduced selection efficacy in genes expressed in sporozoites.

This study evaluates antibody responses to mosquitoes and arboviruses using a multiplexed phage display library to identify epitopes and antigens associated with exposure.

The paper analyzes temporal changes in haplotypic and allelic diversity in Plasmodium falciparum to understand how drug selection pressures shape genetic adaptation.

The paper develops DINEMITES, a statistical method to distinguish new from persistent infections using longitudinal genotyping data, showing improved accuracy over simple rules.

This paper identifies systematic biases in malaria parasite relatedness estimation and proposes practical tools to address them.

The paper analyzes clonal dynamics of Plasmodium falciparum in Guyana using whole genome sequencing, finding that stochastic factors drive clonality rather than deterministic selection for drug resistance mutations.

This study integrates whole genome sequencing and transcriptomics to identify multiple factors contributing to insecticide resistance in Anopheles coluzzii.

The paper estimates IBD-relatedness with uncertainty between Plasmodium falciparum populations and finds connectivity between Buenaventura and Tumaco is higher than expected under isolation-by-distance.

This paper compares relatedness measures in malaria parasites using identity-by-state and identity-by-descent, recommending identity-by-descent for portability and providing marker requirements for reliable estimates.

The paper presents an improved Aedes aegypti genome assembly, AaegL5, which enhances biological understanding and vector control efforts by resolving key genomic features and identifying new targets for intervention.

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 detects de novo mutations in Plasmodium falciparum to reconstruct disease transmission pathways and identify clade expansions not detectable with previous methods.

The paper sequences genomes of 765 malaria vector mosquitoes to study genetic diversity and insecticide resistance.

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.