Ian H. Cheeseman

The paper investigates the bimodal piperaquine response in Plasmodium falciparum by analyzing metabolic, transcriptional, and molecular dynamics data to identify the role of plasmepsin II/III copy number and pfcrt mutations.

The paper tracks malaria parasite lineages using de novo mutations in Plasmodium falciparum genomes from community infections in The Gambia, identifying recent mutations and transmission patterns.

The paper investigates the fitness consequences of selfing and outcrossing in malaria parasites using fluorescent-labelled clones and finds an outcrossing advantage linked to faster sporozoite maturation and increased recombination.

The paper shows that targeted breeding strategies in rhesus macaques reduced SIV-refractory MHC haplotypes without decreasing genetic diversity.

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

This study uses genotype-by-sequencing on hair follicle DNA to genetically characterize a captive marmoset colony, revealing low inbreeding and identifying clinically significant SNVs.

This study uses a genetic cross of Plasmodium falciparum isolates to analyze the roles of pfcrt and pm2/3 in piperaquine resistance and fitness traits.

This study establishes methods to generate marmoset primordial germ cell-like cells from iPSCs, revealing a primate-specific germline transcriptional network and potential for in vitro gametogenesis modeling.

This study identifies pfaat1 as a key gene in chloroquine resistance evolution in malaria parasites, showing it modulates resistance and fitness through amino acid transport.

This study optimizes bulk segregant analysis for identifying drug resistance loci in Plasmodium falciparum using genetic crosses in humanized mice, confirming the kelch13 locus and demonstrating the utility of cryopreserved pools.

The paper examines inter-individual variability in human alveolar macrophage responses to Mycobacterium tuberculosis by analyzing gene and protein expression over time.

This paper develops a method to efficiently profile the transcriptome of the malaria parasite Plasmodium falciparum across its erythrocytic cycle using flow sorting.

The paper uses bulk segregant analysis to identify genetic loci affecting malaria parasite growth in different media, finding EBA-140 as a key gene involved in media-dependent fitness.

The paper tracks genomic diversity in Plasmodium falciparum during in vitro cultivation, showing increased growth rate and clonal interference over 84 asexual cycles.

The paper reports two new genetic crosses of Plasmodium falciparum in humanized mice, showing significant variation in marker segregation and demonstrating improved power for genetic mapping of malaria traits.

This study uses single-cell sequencing to analyze within-host diversity of Plasmodium falciparum in malaria patients, revealing up to seventeen unique lineages per patient and suggesting co-transmission from a single mosquito is more common than superinfection.

This paper develops a single-cell genomics protocol to reconstruct haplotypes of Plasmodium falciparum parasites and analyzes 48 cells from a malaria infection to estimate clonality and haplotype relatedness.

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.