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Daniel Edward Neafsey, Ph.D.

Title
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Title
Institution
Department

Biography
Loyola University ChicagoBA6/1998Biology
Harvard UniversityPh.D.6/2004Biology

Overview

Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01AI141544 (NEAFSEY, DANIEL E) Sep 25, 2018 - Aug 31, 2023
    NIH/NIAID
    Exploring the roles of acquired immunity and functional constraint in sculpting malaria antigenic diversity in a longitudinal cohort
    Role: Principal Investigator
  2. U19AI110818 (BIRREN, BRUCE W.) Apr 10, 2014 - Mar 31, 2024
    NIH/NIAID
    Advancing Genomic Technologies to Combat Infectious Disease: Mapping Dynamics within Single Cells, Individual Hosts, and Global Populations
    Role: Co-Principal Investigator

Bibliographic
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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Mathieu LC, Cox H, Early AM, Mok S, Lazrek Y, Paquet JC, Ade MP, Lucchi NW, Grant Q, Udhayakumar V, Alexandre JS, Demar M, Ringwald P, Neafsey DE, Fidock DA, Musset L. Local emergence in Amazonia of Plasmodium falciparum k13 C580Y mutants associated with in vitro artemisinin resistance. Elife. 2020 May 12; 9. PMID: 32394893.
    Citations:    
  2. Gaye A, Sy M, Ndiaye T, Siddle KJ, Park DJ, Deme AB, Mbaye A, Dieye B, Ndiaye YD, Neafsey DE, Early A, Farrell T, Yade MS, Diallo MA, Diongue K, Bei A, Ndiaye IM, Volkman SK, Badiane AS, Ndiaye D. Amplicon deep sequencing of kelch13 in Plasmodium falciparum isolates from Senegal. Malar J. 2020 Mar 30; 19(1):134. PMID: 32228566.
    Citations:    
  3. Redmond SN, Sharma A, Sharakhov I, Tu Z, Sharakhova M, Neafsey DE. Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti. BMC Biol. 2020 03 12; 18(1):26. PMID: 32164699.
    Citations:    
  4. Taylor AR, Watson JA, Chu CS, Puaprasert K, Duanguppama J, Day NPJ, Nosten F, Neafsey DE, Buckee CO, Imwong M, White NJ. Resolving the cause of recurrent Plasmodium vivax malaria probabilistically. Nat Commun. 2019 12 06; 10(1):5595. PMID: 31811128.
    Citations:    
  5. Edelman NB, Frandsen PB, Miyagi M, Clavijo B, Davey J, Dikow RB, García-Accinelli G, Van Belleghem SM, Patterson N, Neafsey DE, Challis R, Kumar S, Moreira GRP, Salazar C, Chouteau M, Counterman BA, Papa R, Blaxter M, Reed RD, Dasmahapatra KK, Kronforst M, Joron M, Jiggins CD, McMillan WO, Di Palma F, Blumberg AJ, Wakeley J, Jaffe D, Mallet J. Genomic architecture and introgression shape a butterfly radiation. Science. 2019 11 01; 366(6465):594-599. PMID: 31672890.
    Citations:    
  6. Early AM, Daniels RF, Farrell TM, Grimsby J, Volkman SK, Wirth DF, MacInnis BL, Neafsey DE. Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing. Malar J. 2019 Jul 01; 18(1):219. PMID: 31262308.
    Citations:    
  7. Taylor AR, Jacob PE, Neafsey DE, Buckee CO. Estimating Relatedness Between Malaria Parasites. Genetics. 2019 08; 212(4):1337-1351. PMID: 31209105.
    Citations:    
  8. Dantzler KW, Ma S, Ngotho P, Stone WJR, Tao D, Rijpma S, De Niz M, Nilsson Bark SK, Jore MM, Raaijmakers TK, Early AM, Ubaida-Mohien C, Lemgruber L, Campo JJ, Teng AA, Le TQ, Walker CL, Hermand P, Deterre P, Davies DH, Felgner P, Morlais I, Wirth DF, Neafsey DE, Dinglasan RR, Laufer M, Huttenhower C, Seydel K, Taylor T, Bousema T, Marti M. Naturally acquired immunity against immature Plasmodium falciparum gametocytes. Sci Transl Med. 2019 06 05; 11(495). PMID: 31167926.
    Citations:    
  9. Wesolowski A, Taylor AR, Chang HH, Verity R, Tessema S, Bailey JA, Alex Perkins T, Neafsey DE, Greenhouse B, Buckee CO. Correction to: Mapping malaria by combining parasite genomic and epidemiologic data. BMC Med. 2018 12 28; 16(1):241. PMID: 30591060.
    Citations:    Fields:    
  10. Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipovic I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašic G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature. 2018 11; 563(7732):501-507. PMID: 30429615.
    Citations:    Fields:    
  11. Demas AR, Sharma AI, Wong W, Early AM, Redmond S, Bopp S, Neafsey DE, Volkman SK, Hartl DL, Wirth DF. Mutations in Plasmodium falciparum actin-binding protein coronin confer reduced artemisinin susceptibility. Proc Natl Acad Sci U S A. 2018 12 11; 115(50):12799-12804. PMID: 30420498.
    Citations:    Fields:    Translation:HumansAnimalsCells
  12. Wesolowski A, Taylor AR, Chang HH, Verity R, Tessema S, Bailey JA, Alex Perkins T, Neafsey DE, Greenhouse B, Buckee CO. Mapping malaria by combining parasite genomic and epidemiologic data. BMC Med. 2018 10 18; 16(1):190. PMID: 30333020.
    Citations:    Fields:    
  13. Redmond SN, MacInnis BM, Bopp S, Bei AK, Ndiaye D, Hartl DL, Wirth DF, Volkman SK, Neafsey DE. De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria. Mol Biol Evol. 2018 07 01; 35(7):1678-1689. PMID: 29722884.
    Citations:    Fields:    
  14. Brancucci NMB, De Niz M, Straub TJ, Ravel D, Sollelis L, Birren BW, Voss TS, Neafsey DE, Marti M. Probing Plasmodium falciparum sexual commitment at the single-cell level. Wellcome Open Res. 2018; 3:70. PMID: 30320226.
    Citations:    
  15. Schaffner SF, Taylor AR, Wong W, Wirth DF, Neafsey DE. hmmIBD: software to infer pairwise identity by descent between haploid genotypes. Malar J. 2018 May 15; 17(1):196. PMID: 29764422.
    Citations: 2     Fields:    Translation:Animals
  16. Grignard L, Gonçalves BP, Early AM, Daniels RF, Tiono AB, Guelbéogo WM, Ouédraogo A, van Veen EM, Lanke K, Diarra A, Nebie I, Sirima SB, Targett GA, Volkman SK, Neafsey DE, Wirth DF, Bousema T, Drakeley C. Transmission of molecularly undetectable circulating parasite clones leads to high infection complexity in mosquitoes post feeding. Int J Parasitol. 2018 07; 48(8):671-677. PMID: 29738740.
    Citations:    Fields:    
  17. Early AM, Lievens M, MacInnis BL, Ockenhouse CF, Volkman SK, Adjei S, Agbenyega T, Ansong D, Gondi S, Greenwood B, Hamel M, Odero C, Otieno K, Otieno W, Owusu-Agyei S, Asante KP, Sorgho H, Tina L, Tinto H, Valea I, Wirth DF, Neafsey DE. Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections. Nat Commun. 2018 04 11; 9(1):1381. PMID: 29643376.
    Citations:    Fields:    Translation:HumansAnimals
  18. Weetman D, Wilding CS, Neafsey DE, Müller P, Ochomo E, Isaacs AT, Steen K, Rippon EJ, Morgan JC, Mawejje HD, Rigden DJ, Okedi LM, Donnelly MJ. Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae. Sci Rep. 2018 02 13; 8(1):2920. PMID: 29440767.
    Citations: 3     Fields:    
  19. Nilsson Bark SK, Ahmad R, Dantzler K, Lukens AK, De Niz M, Szucs MJ, Jin X, Cotton J, Hoffmann D, Bric-Furlong E, Oomen R, Parrington M, Milner D, Neafsey DE, Carr SA, Wirth DF, Marti M. Quantitative Proteomic Profiling Reveals Novel Plasmodium falciparum Surface Antigens and Possible Vaccine Candidates. Mol Cell Proteomics. 2018 01; 17(1):43-60. PMID: 29162636.
    Citations:    Fields:    Translation:AnimalsCells
  20. Taylor AR, Schaffner SF, Cerqueira GC, Nkhoma SC, Anderson TJC, Sriprawat K, Pyae Phyo A, Nosten F, Neafsey DE, Buckee CO. Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent. PLoS Genet. 2017 Oct; 13(10):e1007065. PMID: 29077712.
    Citations: 2     Fields:    Translation:HumansAnimals
  21. Neafsey DE, Volkman SK. Malaria Genomics in the Era of Eradication. Cold Spring Harb Perspect Med. 2017 Aug 01; 7(8). PMID: 28389516.
    Citations:    Fields:    Translation:HumansAnimalsPHPublic Health
  22. Cerqueira GC, Cheeseman IH, Schaffner SF, Nair S, McDew-White M, Phyo AP, Ashley EA, Melnikov A, Rogov P, Birren BW, Nosten F, Anderson TJC, Neafsey DE. Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance. Genome Biol. 2017 04 28; 18(1):78. PMID: 28454557.
    Citations: 7     Fields:    Translation:AnimalsCells
  23. Chang HH, Worby CJ, Yeka A, Nankabirwa J, Kamya MR, Staedke SG, Dorsey G, Murphy M, Neafsey DE, Jeffreys AE, Hubbart C, Rockett KA, Amato R, Kwiatkowski DP, Buckee CO, Greenhouse B. THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites. PLoS Comput Biol. 2017 01; 13(1):e1005348. PMID: 28125584.
    Citations: 8     Fields:    Translation:HumansAnimalsPHPublic Health
  24. Wong W, Griggs AD, Daniels RF, Schaffner SF, Ndiaye D, Bei AK, Deme AB, MacInnis B, Volkman SK, Hartl DL, Neafsey DE, Wirth DF. Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal. Genome Med. 2017 01 24; 9(1):5. PMID: 28118860.
    Citations: 5     Fields:    Translation:HumansAnimals
  25. Molina-Cruz A, Zilversmit MM, Neafsey DE, Hartl DL, Barillas-Mury C. Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria. Annu Rev Genet. 2016 Nov 23; 50:447-465. PMID: 27732796.
    Citations: 6     Fields:    Translation:HumansAnimals
  26. Kato N, Comer E, Sakata-Kato T, Sharma A, Sharma M, Maetani M, Bastien J, Brancucci NM, Bittker JA, Corey V, Clarke D, Derbyshire ER, Dornan GL, Duffy S, Eckley S, Itoe MA, Koolen KM, Lewis TA, Lui PS, Lukens AK, Lund E, March S, Meibalan E, Meier BC, McPhail JA, Mitasev B, Moss EL, Sayes M, Van Gessel Y, Wawer MJ, Yoshinaga T, Zeeman AM, Avery VM, Bhatia SN, Burke JE, Catteruccia F, Clardy JC, Clemons PA, Dechering KJ, Duvall JR, Foley MA, Gusovsky F, Kocken CH, Marti M, Morningstar ML, Munoz B, Neafsey DE, Sharma A, Winzeler EA, Wirth DF, Scherer CA, Schreiber SL. Diversity-oriented synthesis yields novel multistage antimalarial inhibitors. Nature. 2016 Oct 20; 538(7625):344-349. PMID: 27602946.
    Citations: 22     Fields:    Translation:AnimalsCells
  27. Hupalo DN, Luo Z, Melnikov A, Sutton PL, Rogov P, Escalante A, Vallejo AF, Herrera S, Arévalo-Herrera M, Fan Q, Wang Y, Cui L, Lucas CM, Durand S, Sanchez JF, Baldeviano GC, Lescano AG, Laman M, Barnadas C, Barry A, Mueller I, Kazura JW, Eapen A, Kanagaraj D, Valecha N, Ferreira MU, Roobsoong W, Nguitragool W, Sattabonkot J, Gamboa D, Kosek M, Vinetz JM, González-Cerón L, Birren BW, Neafsey DE, Carlton JM. Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax. Nat Genet. 2016 08; 48(8):953-8. PMID: 27348298.
    Citations: 35     Fields:    Translation:HumansAnimalsCells
  28. Redmond SN, Neafsey DE. Genomic Dark Matter Illuminated: Anopheles Y Chromosomes. Trends Parasitol. 2016 08; 32(8):585-587. PMID: 27263828.
    Citations:    Fields:    Translation:AnimalsCells
  29. Gunalan K, Lo E, Hostetler JB, Yewhalaw D, Mu J, Neafsey DE, Yan G, Miller LH. Role of Plasmodium vivax Duffy-binding protein 1 in invasion of Duffy-null Africans. Proc Natl Acad Sci U S A. 2016 May 31; 113(22):6271-6. PMID: 27190089.
    Citations: 13     Fields:    Translation:HumansAnimalsCells
  30. Love RR, Weisenfeld NI, Jaffe DB, Besansky NJ, Neafsey DE. Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly. BMC Genomics. 2016 Mar 05; 17:187. PMID: 26944054.
    Citations: 5     Fields:    Translation:Animals
  31. Neafsey DE, Juraska M, Bedford T, Benkeser D, Valim C, Griggs A, Lievens M, Abdulla S, Adjei S, Agbenyega T, Agnandji ST, Aide P, Anderson S, Ansong D, Aponte JJ, Asante KP, Bejon P, Birkett AJ, Bruls M, Connolly KM, D'Alessandro U, Dobaño C, Gesase S, Greenwood B, Grimsby J, Tinto H, Hamel MJ, Hoffman I, Kamthunzi P, Kariuki S, Kremsner PG, Leach A, Lell B, Lennon NJ, Lusingu J, Marsh K, Martinson F, Molel JT, Moss EL, Njuguna P, Ockenhouse CF, Ogutu BR, Otieno W, Otieno L, Otieno K, Owusu-Agyei S, Park DJ, Pellé K, Robbins D, Russ C, Ryan EM, Sacarlal J, Sogoloff B, Sorgho H, Tanner M, Theander T, Valea I, Volkman SK, Yu Q, Lapierre D, Birren BW, Gilbert PB, Wirth DF. Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine. N Engl J Med. 2015 Nov 19; 373(21):2025-2037. PMID: 26488565.
    Citations: 52     Fields:    Translation:HumansAnimalsCTClinical Trials
  32. Assefa S, Lim C, Preston MD, Duffy CW, Nair MB, Adroub SA, Kadir KA, Goldberg JM, Neafsey DE, Divis P, Clark TG, Duraisingh MT, Conway DJ, Pain A, Singh B. Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi. Proc Natl Acad Sci U S A. 2015 Oct 20; 112(42):13027-32. PMID: 26438871.
    Citations: 15     Fields:    Translation:Animals
  33. 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 Sep 15; 112(37):11672-7. PMID: 26261345.
    Citations: 13     Fields:    Translation:HumansAnimals
  34. Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo J, Cihlár J, Flegontov P, Gornik SG, Hajdušková E, Horák A, Janouškovec J, Katris NJ, Mast FD, Miranda-Saavedra D, Mourier T, Naeem R, Nair M, Panigrahi AK, Rawlings ND, Padron-Regalado E, Ramaprasad A, Samad N, Tomcala A, Wilkes J, Neafsey DE, Doerig C, Bowler C, Keeling PJ, Roos DS, Dacks JB, Templeton TJ, Waller RF, Lukeš J, Oborník M, Pain A. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. Elife. 2015 Jul 15; 4:e06974. PMID: 26175406.
    Citations: 34     Fields:    Translation:Animals
  35. Chuquiyauri R, Molina DM, Moss EL, Wang R, Gardner MJ, Brouwer KC, Torres S, Gilman RH, Llanos-Cuentas A, Neafsey DE, Felgner P, Liang X, Vinetz JM. Genome-Scale Protein Microarray Comparison of Human Antibody Responses in Plasmodium vivax Relapse and Reinfection. Am J Trop Med Hyg. 2015 Oct; 93(4):801-9. PMID: 26149860.
    Citations: 10     Fields:    Translation:HumansAnimals
  36. Daniels RF, Schaffner SF, Wenger EA, Proctor JL, Chang HH, Wong W, Baro N, Ndiaye D, Fall FB, Ndiop M, Ba M, Milner DA, Taylor TE, Neafsey DE, Volkman SK, Eckhoff PA, Hartl DL, Wirth DF. Modeling malaria genomics reveals transmission decline and rebound in Senegal. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):7067-72. PMID: 25941365.
    Citations: 38     Fields:    Translation:HumansAnimals
  37. Baniecki ML, Faust AL, Schaffner SF, Park DJ, Galinsky K, Daniels RF, Hamilton E, Ferreira MU, Karunaweera ND, Serre D, Zimmerman PA, Sá JM, Wellems TE, Musset L, Legrand E, Melnikov A, Neafsey DE, Volkman SK, Wirth DF, Sabeti PC. Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. PLoS Negl Trop Dis. 2015 Mar; 9(3):e0003539. PMID: 25781890.
    Citations: 22     Fields:    Translation:HumansAnimalsCells
  38. 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. PMID: 25599890.
    Citations: 16     Fields:    Translation:HumansAnimals
  39. Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science. 2015 Jan 02; 347(6217):1258522. PMID: 25554792.
    Citations: 98     Fields:    Translation:HumansAnimalsCells
  40. 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 02; 347(6217):1258524. PMID: 25431491.
    Citations: 60     Fields:    Translation:HumansAnimalsCells
  41. Torres KJ, Castrillon CE, Moss EL, Saito M, Tenorio R, Molina DM, Davies H, Neafsey DE, Felgner P, Vinetz JM, Gamboa D. Genome-level determination of Plasmodium falciparum blood-stage targets of malarial clinical immunity in the Peruvian Amazon. J Infect Dis. 2015 Apr 15; 211(8):1342-51. PMID: 25381370.
    Citations: 7     Fields:    Translation:HumansAnimals
  42. Bei AK, Diouf A, Miura K, Larremore DB, Ribacke U, Tullo G, Moss EL, Neafsey DE, Daniels RF, Zeituni AE, Nosamiefan I, Volkman SK, Ahouidi AD, Ndiaye D, Dieye T, Mboup S, Buckee CO, Long CA, Wirth DF. Immune characterization of Plasmodium falciparum parasites with a shared genetic signature in a region of decreasing transmission. Infect Immun. 2015 Jan; 83(1):276-85. PMID: 25368109.
    Citations: 2     Fields:    Translation:HumansAnimals
  43. Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014; 9(6):e99979. PMID: 24936976.
    Citations: 9     Fields:    Translation:HumansAnimals
  44. Stathopoulos S, Neafsey DE, Lawniczak MK, Muskavitch MA, Christophides GK. Genetic dissection of Anopheles gambiae gut epithelial responses to Serratia marcescens. PLoS Pathog. 2014 Mar; 10(3):e1003897. PMID: 24603764.
    Citations: 13     Fields:    Translation:AnimalsCells
  45. Herman JD, Rice DP, Ribacke U, Silterra J, Deik AA, Moss EL, Broadbent KM, Neafsey DE, Desai MM, Clish CB, Mazitschek R, Wirth DF. A genomic and evolutionary approach reveals non-genetic drug resistance in malaria. Genome Biol. 2014; 15(11):511. PMID: 25395010.
    Citations: 6     Fields:    Translation:HumansAnimals
  46. 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. PMID: 24259712.
    Citations: 14     Fields:    Translation:Animals
  47. 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. PMID: 23936092.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  48. 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 Jul 08; 3(7):1191-4. PMID: 23708298.
    Citations: 21     Fields:    Translation:HumansAnimalsCells
  49. Neafsey DE. Genome sequencing sheds light on emerging drug resistance in malaria parasites. Nat Genet. 2013 Jun; 45(6):589-90. PMID: 23715326.
    Citations: 2     Fields:    Translation:HumansAnimals
  50. 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 05; 288(27):19429-40. PMID: 23720749.
    Citations: 23     Fields:    Translation:HumansAnimals
  51. 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. PMID: 23593309.
    Citations: 33     Fields:    Translation:HumansAnimalsPHPublic Health
  52. 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. PMID: 23335339.
    Citations: 12     Fields:    Translation:AnimalsCells
  53. Neafsey DE. ‘Big data’ from shrinking pathogen populations. Mol Ecol. 2013 Jan; 22(2):271-2. PMID: 23409287.
    Citations:    Fields:    Translation:Animals
  54. 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. PMID: 22863733.
    Citations: 96     Fields:    Translation:HumansAnimalsCells
  55. 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 07; 109(32):13052-7. PMID: 22826220.
    Citations: 43     Fields:    Translation:AnimalsCells
  56. 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. PMID: 22734050.
    Citations: 22     Fields:    Translation:HumansAnimals
  57. 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. PMID: 22688945.
    Citations: 14     Fields:    Translation:Animals
  58. 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. PMID: 22495435.
    Citations: 27     Fields:    Translation:HumansAnimals
  59. 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 Feb 07; 11:35. PMID: 22314206.
    Citations: 7     Fields:    Translation:HumansAnimals
  60. 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; 4(12):1202-12. PMID: 23132896.
    Citations: 19     Fields:    Translation:Animals
  61. 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. PMID: 22182668.
    Citations: 8     Fields:    Translation:HumansAnimalsPHPublic Health
  62. 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. PMID: 21835008.
    Citations: 39     Fields:    Translation:HumansAnimalsCells
  63. 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. PMID: 21533027.
    Citations: 39     Fields:    Translation:Animals
  64. Neafsey DE, Haas BJ. 'Next-generation' sequencing becomes 'now-generation'. Genome Biol. 2011; 12(3):303. PMID: 21457529.
    Citations: 3     Fields:    Translation:Humans
  65. Neafsey DE, Lawniczak MKN, 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 MAT. SNP genotyping defines complex gene-flow boundaries among African malaria vector mosquitoes. Science. 2010 Oct 22; 330(6003):514-517. PMID: 20966254.
    Citations: 54     Fields:    Translation:Animals
  66. 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. PMID: 20516208.
    Citations: 45     Fields:    Translation:AnimalsCells
  67. 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. PMID: 19931645.
    Citations: 10     Fields:    Translation:HumansAnimals
  68. 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. PMID: 19745111.
    Citations: 11     Fields:    Translation:AnimalsCells
  69. 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. PMID: 19717792.
    Citations: 84     Fields:    Translation:HumansAnimals
  70. 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. PMID: 19587242.
    Citations: 74     Fields:    Translation:Animals
  71. 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. PMID: 19514854.
    Citations: 50     Fields:    Translation:AnimalsCells
  72. 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. PMID: 19077304.
    Citations: 44     Fields:    Translation:Animals
  73. 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 Oct 29; 7:223. PMID: 18959790.
    Citations: 71     Fields:    Translation:Animals
  74. Carlton JM, Escalante AA, Neafsey D, Volkman SK. Comparative evolutionary genomics of human malaria parasites. Trends Parasitol. 2008 Dec; 24(12):545-50. PMID: 18938107.
    Citations: 27     Fields:    Translation:HumansAnimals
  75. McGuire AM, Pearson MD, Neafsey DE, Galagan JE. Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol. 2008; 9(3):R50. PMID: 18321378.
    Citations: 49     Fields:    Translation:AnimalsCells
  76. Sharpton TJ, Neafsey DE, Galagan JE, Taylor JW. Mechanisms of intron gain and loss in Cryptococcus. Genome Biol. 2008 Jan 30; 9(1):R24. PMID: 18234113.
    Citations: 33     Fields:    Translation:AnimalsCells
  77. Hughes SS, Buckley CO, Neafsey DE. Complex selection on intron size in Cryptococcus neoformans. Mol Biol Evol. 2008 Feb; 25(2):247-53. PMID: 18171915.
    Citations: 8     Fields:    Translation:Animals
  78. Neafsey DE, Galagan JE. Positive selection for unpreferred codon usage in eukaryotic genomes. BMC Evol Biol. 2007 Jul 18; 7:119. PMID: 17640368.
    Citations: 13     Fields:    Translation:AnimalsCells
  79. Neafsey DE, Galagan JE. Dual modes of natural selection on upstream open reading frames. Mol Biol Evol. 2007 Aug; 24(8):1744-51. PMID: 17494029.
    Citations: 20     Fields:    Translation:AnimalsCells
  80. Roy SW, Penny D, Neafsey DE. Evolutionary conservation of UTR intron boundaries in Cryptococcus. Mol Biol Evol. 2007 May; 24(5):1140-8. PMID: 17374879.
    Citations: 9     Fields:    Translation:AnimalsCells
  81. 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. PMID: 17244598.
    Citations: 21     Fields:    Translation:HumansAnimalsCells
  82. 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. PMID: 17159979.
    Citations: 130     Fields:    Translation:HumansAnimals
  83. 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. PMID: 15858207.
    Citations: 11     Fields:    Translation:AnimalsCells
  84. 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 09; 350(2):161-71. PMID: 15820147.
    Citations: 7     Fields:    Translation:AnimalsCells
  85. 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. PMID: 15342795.
    Citations: 11     Fields:    Translation:AnimalsCells
  86. 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. PMID: 12727902.
    Citations: 14     Fields:    Translation:AnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.