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.