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Daniel Edward Neafsey, Ph.D.

TitleVisiting Scientist
InstitutionHarvard School of Public Health
DepartmentImmunology and Infectious Diseases
AddressHarvard School of Public Health
Rm 703
651 Huntington Ave
Boston MA 02115

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. 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.
    View in: PubMed
  2. Rovira-Vallbona E, Monteiro I, Bardají A, Serra-Casas E, Neafsey DE, Quelhas D, Valim C, Alonso P, Dobaño C, Ordi J, Menéndez C, Mayor A. VAR2CSA Signatures of High Plasmodium falciparum Parasitemia in the Placenta. PLoS One. 2013; 8(7):e69753.
    View in: PubMed
  3. Neafsey DE, Christophides GK, Collins FH, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Howell PI, Kafatos FC, Lawson D, Muskavitch MA, Waterhouse RM, Williams LJ, Besansky NJ. The evolution of the anopheles 16 genomes project. G3 (Bethesda). 2013; 3(7):1191-4.
    View in: PubMed
  4. Neafsey DE. Genome sequencing sheds light on emerging drug resistance in malaria parasites. Nat Genet. 2013 May 29; 45(6):589-90.
    View in: PubMed
  5. Sharma P, Wollenberg K, Sellers M, Zainabadi K, Galinsky K, Moss E, Nguitragool W, Neafsey D, Desai SA. An epigenetic antimalarial resistance mechanism involving parasite genes linked to nutrient uptake. J Biol Chem. 2013 Jul 5; 288(27):19429-40.
    View in: PubMed
  6. Daniels R, Chang HH, Séne PD, Park DC, Neafsey DE, Schaffner SF, Hamilton EJ, Lukens AK, Van Tyne D, Mboup S, Sabeti PC, Ndiaye D, Wirth DF, Hartl DL, Volkman SK. Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal. PLoS One. 2013; 8(4):e60780.
    View in: PubMed
  7. Nwakanma DC, Neafsey DE, Jawara M, Adiamoh M, Lund E, Rodrigues A, Loua KM, Konate L, Sy N, Dia I, Awolola TS, Muskavitch MA, Conway DJ. Breakdown in the Process of Incipient Speciation in Anopheles gambiae. Genetics. 2013 Apr; 193(4):1221-31.
    View in: PubMed
  8. Neafsey DE. ‘Big data’ from shrinking pathogen populations. Mol Ecol. 2013 Jan; 22(2):271-2.
    View in: PubMed
  9. 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.
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  10. 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.
    View in: PubMed
  11. Chang HH, Park DJ, Galinsky KJ, Schaffner SF, Ndiaye D, Ndir O, Mboup S, Wiegand RC, Volkman SK, Sabeti PC, Wirth DF, Neafsey DE, Hartl DL. Genomic Sequencing of Plasmodium falciparum Malaria Parasites from Senegal Reveals the Demographic History of the Population. Mol Biol Evol. 2012 Nov; 29(11):3427-39.
    View in: PubMed
  12. Amambua-Ngwa A, Park DJ, Volkman SK, Barnes KG, Bei AK, Lukens AK, Sene P, Van Tyne D, Ndiaye D, Wirth DF, Conway DJ, Neafsey DE, Schaffner SF. SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites. Mol Biol Evol. 2012 Nov; 29(11):3249-53.
    View in: PubMed
  13. Volkman SK, Neafsey DE, Schaffner SF, Park DJ, Wirth DF. Harnessing genomics and genome biology to understand malaria biology. Nat Rev Genet. 2012 May; 13(5):315-28.
    View in: PubMed
  14. Milner DA, Vareta J, Valim C, Montgomery J, Daniels RF, Volkman SK, Neafsey DE, Park DJ, Schaffner SF, Mahesh NC, Barnes KG, Rosen DM, Lukens AK, Van Tyne D, Wiegand RC, Sabeti PC, Seydel KB, Glover SJ, Kamiza S, Molyneux ME, Taylor TE, Wirth DF. Human cerebral malaria and Plasmodium falciparum genotypes in Malawi. Malar J. 2012; 11:35.
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  15. Reidenbach KR, Neafsey DE, Costantini C, Sagnon N, Simard F, Ragland GJ, Egan SP, Feder JL, Muskavitch MA, Besansky NJ. Patterns of Genomic Differentiation between Ecologically Differentiated M and S Forms of Anopheles gambiae in West and Central Africa. Genome Biol Evol. 2012 Jan; 4(12):1202-12.
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  16. Volkman SK, Ndiaye D, Diakite M, Koita OA, Nwakanma D, Daniels RF, Park DJ, Neafsey DE, Muskavitch MA, Krogstad DJ, Sabeti PC, Hartl DL, Wirth DF. Application of genomics to field investigations of malaria by the international centers of excellence for malaria research. Acta Trop. 2012 Mar; 121(3):324-32.
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  17. 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; 12(8):R73.
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  18. Van Tyne D, Park DJ, Schaffner SF, Neafsey DE, Angelino E, Cortese JF, Barnes KG, Rosen DM, Lukens AK, Daniels RF, Milner DA, Johnson CA, Shlyakhter I, Grossman SR, Becker JS, Yamins D, Karlsson EK, Ndiaye D, Sarr O, Mboup S, Happi C, Furlotte NA, Eskin E, Kang HM, Hartl DL, Birren BW, Wiegand RC, Lander ES, Wirth DF, Volkman SK, Sabeti PC. Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum. PLoS Genet. 2011 Apr; 7(4):e1001383.
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  19. Neafsey DE, Haas BJ. 'Next-generation' sequencing becomes 'now-generation'. Genome Biol. 2011; 12(3):303.
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  20. 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.
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  21. Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, Hung CY, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, Bessette D, Brown A, FitzGerald M, Lui A, Macdonald JP, Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, Henn MR, Taylor JW, Rounsley SD. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Res. 2010 Jul; 20(7):938-46.
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  22. Ahouidi AD, Bei AK, Neafsey DE, Sarr O, Volkman S, Milner D, Cox-Singh J, Ferreira MU, Ndir O, Premji Z, Mboup S, Duraisingh MT. Population genetic analysis of large sequence polymorphisms in Plasmodium falciparum blood-stage antigens. Infect Genet Evol. 2010 Mar; 10(2):200-6.
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  23. Irimia M, Roy SW, Neafsey DE, Abril JF, Garcia-Fernandez J, Koonin EV. Complex selection on 5' splice sites in intron-rich organisms. Genome Res. 2009 Nov; 19(11):2021-7.
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  24. Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung CY, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res. 2009 Oct; 19(10):1722-31.
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  25. Lozovsky ER, Chookajorn T, Brown KM, Imwong M, Shaw PJ, Kamchonwongpaisan S, Neafsey DE, Weinreich DM, Hartl DL. Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Natl Acad Sci U S A. 2009 Jul 21; 106(29):12025-30.
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  26. Hood HM, Neafsey DE, Galagan J, Sachs MS. Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. Annu Rev Microbiol. 2009; 63:385-409.
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  27. Neafsey DE, Schaffner SF, Volkman SK, Park D, Montgomery P, Milner DA, Lukens A, Rosen D, Daniels R, Houde N, Cortese JF, Tyndall E, Gates C, Stange-Thomann N, Sarr O, Ndiaye D, Ndir O, Mboup S, Ferreira MU, Moraes Sdo L, Dash AP, Chitnis CE, Wiegand RC, Hartl DL, Birren BW, Lander ES, Sabeti PC, Wirth DF. Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence. Genome Biol. 2008; 9(12):R171.
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  28. Daniels R, Volkman SK, Milner DA, Mahesh N, Neafsey DE, Park DJ, Rosen D, Angelino E, Sabeti PC, Wirth DF, Wiegand RC. A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking. Malar J. 2008; 7:223.
    View in: PubMed
  29. Carlton JM, Escalante AA, Neafsey D, Volkman SK. Comparative evolutionary genomics of human malaria parasites. Trends Parasitol. 2008 Dec; 24(12):545-50.
    View in: PubMed
  30. McGuire AM, Pearson MD, Neafsey DE, Galagan JE. Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol. 2008; 9(3):R50.
    View in: PubMed
  31. Sharpton TJ, Neafsey DE, Galagan JE, Taylor JW. Mechanisms of intron gain and loss in Cryptococcus. Genome Biol. 2008; 9(1):R24.
    View in: PubMed
  32. Hughes SS, Buckley CO, Neafsey DE. Complex selection on intron size in Cryptococcus neoformans. Mol Biol Evol. 2008 Feb; 25(2):247-53.
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  33. Neafsey DE, Galagan JE. Positive selection for unpreferred codon usage in eukaryotic genomes. BMC Evol Biol. 2007; 7:119.
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  34. Neafsey DE, Galagan JE. Dual modes of natural selection on upstream open reading frames. Mol Biol Evol. 2007 Aug; 24(8):1744-51.
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  35. Roy SW, Penny D, Neafsey DE. Evolutionary conservation of UTR intron boundaries in Cryptococcus. Mol Biol Evol. 2007 May; 24(5):1140-8.
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  36. Gunasekera AM, Wickramarachchi T, Neafsey DE, Ganguli I, Perera L, Premaratne PH, Hartl D, Handunnetti SM, Udagama-Randeniya PV, Wirth DF. Genetic diversity and selection at the Plasmodium vivax apical membrane antigen-1 (PvAMA-1) locus in a Sri Lankan population. Mol Biol Evol. 2007 Apr; 24(4):939-47.
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  37. Volkman SK, Sabeti PC, DeCaprio D, Neafsey DE, Schaffner SF, Milner DA, Daily JP, Sarr O, Ndiaye D, Ndir O, Mboup S, Duraisingh MT, Lukens A, Derr A, Stange-Thomann N, Waggoner S, Onofrio R, Ziaugra L, Mauceli E, Gnerre S, Jaffe DB, Zainoun J, Wiegand RC, Birren BW, Hartl DL, Galagan JE, Lander ES, Wirth DF. A genome-wide map of diversity in Plasmodium falciparum. Nat Genet. 2007 Jan; 39(1):113-9.
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  38. Neafsey DE, Hartl DL, Berriman M. Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes. Mol Biol Evol. 2005 Jul; 22(7):1621-6.
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  39. Neafsey DE, Hartl DL. Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineages. Gene. 2005 May 9; 350(2):161-71.
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  40. Neafsey DE, Blumenstiel JP, Hartl DL. Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies. Mol Biol Evol. 2004 Dec; 21(12):2310-8.
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  41. Neafsey DE, Palumbi SR. Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes. Genome Res. 2003 May; 13(5):821-30.
    View in: PubMed
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