My research program applies genomic, molecular, epidemiological, and computational approaches to understand pathogen transmission, therapeutic response, and the emergence of drug and diagnostic resistance, particularly in East Africa and the Horn of Africa.
A major focus of my work is improving malaria therapeutic efficacy studies (TES) by integrating clinical outcomes with quantitative parasite-clearance measures, parasite genomics, molecular markers, and laboratory phenotyping. I investigate the emergence and spread of antimalarial resistance, including Plasmodium falciparum kelch13 mutations associated with artemisinin partial resistance, partner-drug resistance, and pfhrp2/pfhrp3 deletions that threaten HRP2-based malaria diagnosis. My goal is to identify changes in therapeutic response early and translate molecular and genomic evidence into more effective surveillance strategies.
My research extends beyond P. falciparum to P. vivax and other non-falciparum malaria species, including their genomic diversity, drug resistance, mixed-species infections, and contributions to malaria transmission and disease. I am also expanding this framework to non-malarial febrile illness, using molecular and genomic approaches to improve pathogen detection and better understand undifferentiated fever in malaria-endemic populations.
A complementary focus of my research is the development and optimization of scalable genomic technologies for challenging field samples. I develop and apply highly multiplexed amplicon sequencing and parasite DNA-enrichment approaches, including selective whole-genome amplification (sWGA), random whole-genome amplification (rWGA), and leukocyte-depletion strategies, to improve Plasmodium whole-genome sequencing from low-parasitemia and host-DNA-rich samples. These approaches are designed to make high-resolution genomic surveillance more robust, cost-effective, and accessible in malaria-endemic and resource-limited settings.
Methodologically, my work combines whole-genome sequencing, targeted deep sequencing, molecular inversion probes, parasite DNA enrichment, population genomics, molecular epidemiology, and computational modeling. The overarching strategy of my research is to integrate multidimensional big data → build predictive models → develop actionable surveillance tools. Ultimately, I aim to move genomic surveillance beyond describing pathogen variation toward predicting emerging threats and informing treatment, diagnostic, and public health decisions.
An important component of my research program is strengthening sustainable genomic surveillance capacity through mentorship, training, technology transfer, and equitable international collaborations, particularly with scientists and public health institutions in malaria-endemic countries.
