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 primary role is associate director of the Broad Institute’s Genomic Center for Infectious Disease, where he leads a group focusing on the genomics of malaria parasites and mosquito vectors. He is excited by the potential for new technology and information types to turn the tide against diseases like malaria.

Neafsey’s current projects involve the application of comparative genomic and population genetic analyses to Plasmodium malaria parasites and Anopheles mosquitoes to study population structure, natural selection, and genomic factors underlying parasite and vector phenotypes that impact public health. Neafsey’s interests also include the use of pathogen polymorphism data to inform vaccine design and understand vaccine efficacy, analysis of drug resistance mechanisms and evolution, the use of clinical genotyping data to interpret disease transmission dynamics, and the development of new genomic protocols and informatic tools to address key questions in infectious disease and global health.


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

Representative Publications

1: Pelleau S, Moss EL, Dhingra SK, Volney B, Casteras J, Gabryszewski SJ, Volkman SK, Wirth DF, Legrand E, Fidock DA, Neafsey DE, Musset L. Adaptive evolution of malaria parasites in French Guiana: Reversal of chloroquine resistance by acquisition of a mutation in pfcrt. Proc Natl Acad Sci U S A. 2015 Aug 10. pii: 201507142. [Epub ahead of print]

2: Galinsky K, Valim C, Salmier A, de Thoisy B, Musset L, Legrand E, Faust A, Baniecki ML, Ndiaye D, Daniels RF, Hartl DL, Sabeti PC, Wirth DF, Volkman SK, Neafsey DE. COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism data. Malar J. 2015 Jan 19;14:4.

3: Neafsey DE, Waterhouse RM, et al. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science. 2015 Jan 2;347(6217):1258522.

4: Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ. Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science. 2015 Jan 2;347(6217):1258524.

5: Chang HH, Moss EL, Park DJ, Ndiaye D, Mboup S, Volkman SK, Sabeti PC, Wirth DF, Neafsey DE, Hartl DL. Malaria life cycle intensifies both natural selection and random genetic drift. Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20129-34.

6: Neafsey DE, Galinsky K, Jiang RH, Young L, Sykes SM, Saif S, Gujja S, Goldberg JM, Young S, Zeng Q, Chapman SB, Dash AP, Anvikar AR, Sutton PL, Birren BW, Escalante AA, Barnwell JW, Carlton JM. The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat Genet. 2012 Sep;44(9):1046-50.

7: Park DJ, Lukens AK, Neafsey DE, Schaffner SF, Chang HH, Valim C, Ribacke U, Van Tyne D, Galinsky K, Galligan M, Becker JS, Ndiaye D, Mboup S, Wiegand RC, Hartl DL, Sabeti PC, Wirth DF, Volkman SK. Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite. Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):13052-7.

8: Volkman SK, Neafsey DE, Schaffner SF, Park DJ, Wirth DF. Harnessing genomics and genome biology to understand malaria biology. Nat Rev Genet. 2012 Apr 12;13(5):315-28.

9: Melnikov A, Galinsky K, Rogov P, Fennell T, Van Tyne D, Russ C, Daniels R, Barnes KG, Bochicchio J, Ndiaye D, Sene PD, Wirth DF, Nusbaum C, Volkman SK, Birren BW, Gnirke A, Neafsey DE. Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biol. 2011 Aug 11;12(8):R73.

10: Neafsey DE, Lawniczak MK, Park DJ, Redmond SN, Coulibaly MB, Traoré SF, Sagnon N, Costantini C, Johnson C, Wiegand RC, Collins FH, Lander ES, Wirth DF, Kafatos FC, Besansky NJ, Christophides GK, Muskavitch MA. SNP genotyping defines complex gene-flow boundaries among African malaria vector mosquitoes. Science. 2010 Oct 22;330(6003):514-7.