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Daniel Neafsey

Visiting Scientist

Department of Immunology and Infectious Diseases

Department of Immunology and Infectious Diseases

665 Huntington Avenue
Building 1, Room 703
Boston, Massachusetts 02115

Research Interests

Dan Neafsey’s work focuses on the population genomics of malaria parasites and their Anopheline mosquito vectors. In his primary role as Group Leader of Malaria Genome Sequencing and Analysis at the Broad Institute, he plans and executes genome sequencing and high-throughput genotyping projects related to malaria and coordinates analysis of the data. He applies analyses and tools from the fields of population genetics and molecular evolution to investigate questions such as the role of natural selection in Plasmodium and Anopheles genomes, the structure of parasite and vector populations, and the mechanisms by which resistance to drugs and insecticides evolves in parasites and vectors. He also coordinates efforts to adapt parasite genome sequencing to the constraints imposed by the small quantity and often poor quality of samples from clinical field studies of malaria.


B.A., 1988, Loyola University, Chicago, IL
Ph.D., 2004, Harvard University, Cambridge, MA


1. Ahouidi, A.D., Bei, A.K., Neafsey, D.E., Sarr, O., Volkman, S., Milner, D., Cox-Singh, J., Ferreira, M.U., Ndir, O., Premji, Z., Mboup, S., and M. Duraisingh. 2009. Population genetic analysis of large scale sequence polymorphisms in Plasmodium falciparum blood-stage antigens. Infect. Genet. Evol. No. 10(2): 200-6. PMCID: PMC2829370

2. Sharpton, T.J., Stajich, J.E., Rounsley, S.D., Gardner, M.J., Wortman, J.R., Jordar, V.S., Maiti, R., Kodira, C.D., Neafsey, D.E., Zeng, Q., Hung, C.Y., McMahan, C., Muszewska, A., Grynberg, M., Mandel, M.A., Kellner, E.M., Barker, B.M., Galgiani, J.N., Orbach, M.J., Kirkland, T.N., Cole, G.T., Henn, M.R., Birren, B.W., and J.T. Taylor. 2009. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research. 19(10): 1722-31. PMCID: PMC2765278.

3. Lozovsky, E.R., Chookajorn, T., Brown, K.M., Imwong, M., Shaw, P.J., Kamchonwongpaisan, S., Neafsey, D.E., Weinreich, D.M., and D.L. Hartl. 2009. Stepwise acquisition of pyrimethamine resistance in the malaria parasite. P.N.A.S. 106(29): 12025-30. PMCID: PMC2715478.

4. Neafsey, D.E., Schaffner, S.F., Volkman, S.K., Park, D., Montgomery, P., Milner, D.A. Jr., Lukens, A., Rosen, D., Daniels, R., Houde, N., Cortese, J.F., Tyndall, E., Gates, C., Stange-Thomann, N., Sarr, O., Ndiaye, D., Ndir, O., Mboup, S., Ferreira, M.U., Moraes, S.D., Dash, A.P., Chitnis, C.E., Wiegand, R.C., Hartl, D.L., Birren, B.W., Lander, E.S., Sabeti, P.C., and D.F. Wirth. 2008. Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence. Genome Biol. 9: R171. PMCID: PMC2646275.

5. Daniels, R., Volkman, S.K., Milner, D.A., Mahesh, N., Neafsey, D.E., Park, D.J., Rosen, D.R., Angelino, E., Sabeti, P.C., Wirth, D.F., and R.C. Wiegand. 2008. A general SNP-based molecular barcode for P. falciparum identification and tracking. Malaria J. 7:233. PMCID: PMC2584654.

6. Carleton, J.M., Escalante, A.A., Neafsey, D.E., and S.K. Volkman. 2008. Comparative evolutionary genomics of human malaria parasites. Trends in Parasitol. 24: 545-50.

7. McGuire, A.M., Pearson, M., Neafsey, D.E., and J.E. Galagan. 2008. Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol. Mar 5;9(3):R50. PMCID: PMC2397502.

8. Neafsey, D.E. and J.E. Galagan. Positive selection for unpreferred codon usage in eukaryotic genomes. 2007. BMC Evol. Biol. Jul 18;7(1):119.

9. Neafsey, D.E. and J.E. Galagan. 2007. Dual modes of natural selection on upstream open reading frames (uORFs). Mol. Biol. Evol. 24:1744-51. PMCID: PMC1936986.

10. Roy, S.W.,  Penny, D. Neafsey, D.E. 2007. Evolutionary conservation of UTR intron boundaries in Cryptococcus. Mol. Biol. Evol. 24: 1140-1148.

11. Gunasekera, A.M., Wickramarachchi T., Neafsey, D.E., Gangul, I., Perera, L., Premaratne, P. H., Hartl, D.L., Handunnetti, S.M., Udagama-Randeniya, P.V., and D.F. Wirth. 2007. Genetic diversity and selection at the Plasmodium vivax apical membrane antigen-1 (pvAMA-1) locus in a Sri Lankan population. Mol. Biol. Evol. 24: 939-947.

12. Volkman, S.K. Sabeti, S.P., Decaprio, D., Neafsey, D.E., et al. 2007. A genome-wide map of diversity in Plasmodium falciparum. Nature Genetics. 39: 113-119.

13. Neafsey, D.E., Hartl, D.L., and M. Berriman. 2005. Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes.  Mol. Biol. Evol. 7: 1621-1626.