Daniel E. Neafsey, Ph.D. - Publications

Harvard University, Cambridge, MA, United States 
evolutionary biology, molecular genetics

106 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Daron J, Bouafou L, Tennessen JA, Rahola N, Makanga B, Akone-Ella O, Ngangue MF, Longo Pendy NM, Paupy C, Neafsey DE, Fontaine MC, Ayala D. Genomic Signatures of Microgeographic Adaptation in Along an Anthropogenic Gradient in Gabon. Biorxiv : the Preprint Server For Biology. PMID 38798379 DOI: 10.1101/2024.05.16.594472  0.369
2024 Vanhove M, Schwabl P, Clementson C, Early AM, Laws M, Anthony F, Florimond C, Mathieu L, James K, Knox C, Singh N, Buckee CO, Musset L, Cox H, Niles-Robin R, ... Neafsey DE, et al. Temporal and spatial dynamics of clonal lineages in Guyana. Biorxiv : the Preprint Server For Biology. PMID 38352461 DOI: 10.1101/2024.01.31.578156  0.357
2023 Florimond C, de Laval F, Early AM, Sauthier S, Lazrek Y, Pelleau S, Monteiro WM, Agranier M, Taudon N, Morin F, Magris M, Lacerda MVG, Viana GMR, Herrera S, Adhin MR, ... ... Neafsey DE, et al. Impact of piperaquine resistance in Plasmodium falciparum on malaria treatment effectiveness in French Guiana: a descriptive epidemiological study. The Lancet. Infectious Diseases. PMID 37858325 DOI: 10.1016/S1473-3099(23)00502-9  0.321
2022 Carrasquilla M, Early AM, Taylor AR, Knudson Ospina A, Echeverry DF, Anderson TJC, Mancilla E, Aponte S, Cárdenas P, Buckee CO, Rayner JC, Sáenz FE, Neafsey DE, Corredor V. Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis. Plos Pathogens. 18: e1010993. PMID 36542676 DOI: 10.1371/journal.ppat.1010993  0.399
2022 Early AM, Camponovo F, Pelleau S, Cerqueira GC, Lazrek Y, Volney B, Carrasquilla M, de Thoisy B, Buckee CO, Childs LM, Musset L, Neafsey DE. Declines in prevalence alter the optimal level of sexual investment for the malaria parasite . Proceedings of the National Academy of Sciences of the United States of America. 119: e2122165119. PMID 35867831 DOI: 10.1073/pnas.2122165119  0.312
2022 LaVerriere E, Schwabl P, Carrasquilla M, Taylor AR, Johnson ZM, Shieh M, Panchal R, Straub TJ, Kuzma R, Watson S, Buckee CO, Andrade CM, Portugal S, Crompton PD, Traore B, ... ... Neafsey DE, et al. Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: a malaria case study. Molecular Ecology Resources. PMID 35437908 DOI: 10.1111/1755-0998.13622  0.383
2021 Ingham VA, Tennessen JA, Lucas ER, Elg S, Yates HC, Carson J, Guelbeogo WM, Sagnon N, Hughes GL, Heinz E, Neafsey DE, Ranson H. Integration of whole genome sequencing and transcriptomics reveals a complex picture of the reestablishment of insecticide resistance in the major malaria vector Anopheles coluzzii. Plos Genetics. 17: e1009970. PMID 34941884 DOI: 10.1371/journal.pgen.1009970  0.355
2021 Schwabl P, Neafsey DE. Molecular surveillance of malaria scales up. Trends in Parasitology. 37: 1020-1021. PMID 34625343 DOI: 10.1016/j.pt.2021.09.010  0.327
2021 de Oliveira TC, Rodrigues PT, Early AM, Duarte AMRC, Buery JC, Bueno MG, Catão-Dias JL, Cerutti C, Rona LDP, Neafsey DE, Ferreira MU. Plasmodium simium: population genomics reveals the origin of a reverse zoonosis. The Journal of Infectious Diseases. PMID 33870436 DOI: 10.1093/infdis/jiab214  0.351
2021 Neafsey DE, Taylor AR, MacInnis BL. Advances and opportunities in malaria population genomics. Nature Reviews. Genetics. PMID 33833443 DOI: 10.1038/s41576-021-00349-5  0.434
2020 Buyon LE, Santamaria AM, Early AM, Quijada M, Barahona I, Lasso J, Avila M, Volkman SK, Marti M, Neafsey DE, Obaldia Iii N. Population genomics of Plasmodium vivax in Panama to assess the risk of case importation on malaria elimination. Plos Neglected Tropical Diseases. 14: e0008962. PMID 33315861 DOI: 10.1371/journal.pntd.0008962  0.345
2020 Small ST, Labbé F, Lobo NF, Koekemoer LL, Sikaala CH, Neafsey DE, Hahn MW, Fontaine MC, Besansky NJ. Radiation with reticulation marks the origin of a major malaria vector. Proceedings of the National Academy of Sciences of the United States of America. PMID 33262284 DOI: 10.1073/pnas.2018142117  0.322
2020 Tennessen JA, Ingham VA, Toé KH, Guelbéogo WM, Sagnon N, Kuzma R, Ranson H, Neafsey DE. A population genomic unveiling of a new cryptic mosquito taxon within the malaria-transmitting Anopheles gambiae complex. Molecular Ecology. PMID 33253481 DOI: 10.1111/mec.15756  0.405
2020 Taylor AR, Echeverry DF, Anderson TJC, Neafsey DE, Buckee CO. Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast. Plos Genetics. 16: e1009101. PMID 33196661 DOI: 10.1371/journal.pgen.1009101  0.333
2020 de Oliveira TC, Corder RM, Early A, Rodrigues PT, Ladeia-Andrade S, Alves JMP, Neafsey DE, Ferreira MU. Population genomics reveals the expansion of highly inbred Plasmodium vivax lineages in the main malaria hotspot of Brazil. Plos Neglected Tropical Diseases. 14: e0008808. PMID 33112884 DOI: 10.1371/journal.pntd.0008808  0.421
2020 Dewasurendra RL, Baniecki ML, Schaffner S, Siriwardena Y, Moon J, Doshi R, Gunawardena S, Daniels RF, Neafsey D, Volkman S, Chandrasekharan NV, Wirth DF, Karunaweera ND. Use of a Plasmodium vivax genetic barcode for genomic surveillance and parasite tracking in Sri Lanka. Malaria Journal. 19: 342. PMID 32958025 DOI: 10.1186/S12936-020-03386-3  0.491
2020 Straub TJ, Shaw WR, Marcenac P, Sawadogo SP, Dabiré RK, Diabaté A, Catteruccia F, Neafsey DE. The Anopheles coluzzii microbiome and its interaction with the intracellular parasite Wolbachia. Scientific Reports. 10: 13847. PMID 32796890 DOI: 10.1038/S41598-020-70745-0  0.407
2020 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, et al. Local emergence in Amazonia of C580Y mutants associated with artemisinin resistance. Elife. 9. PMID 32394893 DOI: 10.7554/Elife.51015  0.467
2020 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, et al. Amplicon deep sequencing of kelch13 in Plasmodium falciparum isolates from Senegal. Malaria Journal. 19: 134. PMID 32228566 DOI: 10.1186/S12936-020-03193-W  0.47
2020 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 Biology. 18: 26. PMID 32164699 DOI: 10.1186/S12915-020-0757-Y  0.377
2019 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. Nature Communications. 10: 5595. PMID 31811128 DOI: 10.1038/S41467-019-13412-X  0.364
2019 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, et al. Genomic architecture and introgression shape a butterfly radiation. Science (New York, N.Y.). 366: 594-599. PMID 31672890 DOI: 10.1126/Science.Aaw2090  0.414
2019 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. Malaria Journal. 18: 219. PMID 31262308 DOI: 10.1186/S12936-019-2856-1  0.418
2019 Taylor AR, Jacob PE, Neafsey DE, Buckee CO. Estimating Relatedness Between Malaria Parasites. Genetics. PMID 31209105 DOI: 10.1534/Genetics.119.302120  0.446
2019 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, ... ... Neafsey DE, et al. Naturally acquired immunity against immature gametocytes. Science Translational Medicine. 11. PMID 31167926 DOI: 10.1126/Scitranslmed.Aav3963  0.364
2018 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 Medicine. 16: 241. PMID 30591060 DOI: 10.1186/S12916-018-1232-2  0.34
2018 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, ... ... Neafsey DE, et al. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature. PMID 30429615 DOI: 10.1038/S41586-018-0692-Z  0.476
2018 Demas AR, Sharma AI, Wong W, Early AM, Redmond S, Bopp S, Neafsey DE, Volkman SK, Hartl DL, Wirth DF. Mutations in actin-binding protein coronin confer reduced artemisinin susceptibility. Proceedings of the National Academy of Sciences of the United States of America. PMID 30420498 DOI: 10.1073/Pnas.1812317115  0.588
2018 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 Medicine. 16: 190. PMID 30333020 DOI: 10.1186/S12916-018-1181-9  0.403
2018 Schaffner SF, Taylor AR, Wong W, Wirth DF, Neafsey DE. hmmIBD: software to infer pairwise identity by descent between haploid genotypes. Malaria Journal. 17: 196. PMID 29764422 DOI: 10.1186/S12936-018-2349-7  0.45
2018 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, et al. Transmission of molecularly undetectable circulating parasite clones leads to high infection complexity in mosquitoes post feeding. International Journal For Parasitology. PMID 29738740 DOI: 10.1016/J.Ijpara.2018.02.005  0.407
2018 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. Molecular Biology and Evolution. PMID 29722884 DOI: 10.1093/Molbev/Msy059  0.603
2018 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, ... ... Neafsey DE, et al. Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections. Nature Communications. 9: 1381. PMID 29643376 DOI: 10.1038/S41467-018-03807-7  0.458
2018 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. Scientific Reports. 8: 2920. PMID 29440767 DOI: 10.1038/S41598-018-21265-5  0.423
2017 Miles A, Harding NJ, Bottà G, Clarkson CS, Antão T, Kozak K, Schrider DR, Kern AD, Redmond S, Sharakhov I, Pearson RD, Bergey C, Fontaine MC, Donnelly MJ, Lawniczak MKN, ... ... Neafsey DE, et al. Genetic diversity of the African malaria vector Anopheles gambiae. Nature. 552: 96-100. PMID 29186111 DOI: 10.1038/Nature24995  0.525
2017 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, et al. Quantitative proteomic profiling reveals novel Plasmodium falciparum surface antigens and possible vaccine candidates. Molecular & Cellular Proteomics : McP. PMID 29162636 DOI: 10.1074/Mcp.Ra117.000076  0.399
2017 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 Genetics. 13: e1007065. PMID 29077712 DOI: 10.1371/Journal.Pgen.1007065  0.483
2017 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 Biology. 18: 78. PMID 28454557 DOI: 10.1186/S13059-017-1204-4  0.5
2017 Neafsey DE, Volkman SK. Malaria Genomics in the Era of Eradication. Cold Spring Harbor Perspectives in Medicine. PMID 28389516 DOI: 10.1101/Cshperspect.A025544  0.482
2017 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 C, et al. THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites. Plos Computational Biology. 13: e1005348. PMID 28125584 DOI: 10.1371/Journal.Pcbi.1005348  0.403
2017 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 Medicine. 9: 5. PMID 28118860 DOI: 10.1186/S13073-017-0398-0  0.574
2016 Molina-Cruz A, Zilversmit MM, Neafsey DE, Hartl DL, Barillas-Mury C. Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria. Annual Review of Genetics. PMID 27732796 DOI: 10.1146/Annurev-Genet-120215-035211  0.613
2016 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 G, Duffy S, Eckley S, ... ... Neafsey DE, et al. Diversity-oriented synthesis yields novel multistage antimalarial inhibitors. Nature. PMID 27602946 DOI: 10.1038/Nature19804  0.317
2016 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, ... ... Neafsey DE, et al. Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax. Nature Genetics. PMID 27348298 DOI: 10.1038/Ng.3588  0.506
2016 Redmond SN, Neafsey DE. Genomic Dark Matter Illuminated: Anopheles Y Chromosomes. Trends in Parasitology. PMID 27263828 DOI: 10.1016/J.Pt.2016.05.008  0.327
2016 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 27190089 DOI: 10.1073/Pnas.1606113113  0.364
2016 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. 17: 187. PMID 26944054 DOI: 10.1186/S12864-016-2531-7  0.343
2015 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, et al. Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine. The New England Journal of Medicine. PMID 26488565 DOI: 10.1056/Nejmoa1505819  0.574
2015 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 26438871 DOI: 10.1073/Pnas.1509534112  0.484
2015 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. Proceedings of the National Academy of Sciences of the United States of America. 112: 11672-7. PMID 26261345 DOI: 10.1073/Pnas.1507142112  0.471
2015 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, Cihlář J, Flegontov P, ... ... Neafsey DE, et al. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. Elife. 4: e06974. PMID 26175406 DOI: 10.7554/Elife.06974  0.445
2015 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. The American Journal of Tropical Medicine and Hygiene. PMID 26149860 DOI: 10.4269/Ajtmh.15-0232  0.377
2015 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, et al. Modeling malaria genomics reveals transmission decline and rebound in Senegal. Proceedings of the National Academy of Sciences of the United States of America. 112: 7067-72. PMID 25941365 DOI: 10.1073/Pnas.1505691112  0.643
2015 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, ... ... Neafsey DE, et al. Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. Plos Neglected Tropical Diseases. 9: e0003539. PMID 25781890 DOI: 10.1371/Journal.Pntd.0003539  0.494
2015 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. Malaria Journal. 14: 4. PMID 25599890 DOI: 10.1186/1475-2875-14-4  0.54
2015 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, et al. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science (New York, N.Y.). 347: 1258522. PMID 25554792 DOI: 10.1126/Science.1258522  0.483
2015 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, et al. Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science (New York, N.Y.). 347: 1258524. PMID 25431491 DOI: 10.1126/Science.1258524  0.425
2015 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. The Journal of Infectious Diseases. 211: 1342-51. PMID 25381370 DOI: 10.1093/Infdis/Jiu614  0.369
2015 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, et al. Immune characterization of Plasmodium falciparum parasites with a shared genetic signature in a region of decreasing transmission. Infection and Immunity. 83: 276-85. PMID 25368109 DOI: 10.1128/Iai.01979-14  0.45
2015 Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, Campo Jd, Cihlář J, Flegontov P, ... ... Neafsey DE, et al. Author response: Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites Elife. DOI: 10.7554/Elife.06974.033  0.426
2015 Volkman S, Daniels R, Chang H, Park D, Neafsey D, Schaffner S, Lukens A, Mboup S, Sabeti P, Wirth D, Hartl D. Genotyping malaria parasites to understand malaria transmission Annals of Global Health. 81: 82. DOI: 10.1016/J.Aogh.2015.02.694  0.582
2014 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 Biology. 15: 511. PMID 25395010 DOI: 10.1186/S13059-014-0511-2  0.461
2014 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, ... ... Neafsey DE, et al. Standardized metadata for human pathogen/vector genomic sequences. Plos One. 9: e99979. PMID 24936976 DOI: 10.1371/Journal.Pone.0099979  0.421
2014 Stathopoulos S, Neafsey DE, Lawniczak MK, Muskavitch MA, Christophides GK. Genetic dissection of Anopheles gambiae gut epithelial responses to Serratia marcescens. Plos Pathogens. 10: e1003897. PMID 24603764 DOI: 10.1371/Journal.Ppat.1003897  0.402
2013 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. Proceedings of the National Academy of Sciences of the United States of America. 110: 20129-34. PMID 24259712 DOI: 10.1073/Pnas.1319857110  0.606
2013 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. 8: e69753. PMID 23936092 DOI: 10.1371/Journal.Pone.0069753  0.442
2013 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. The Journal of Biological Chemistry. 288: 19429-40. PMID 23720749 DOI: 10.1074/Jbc.M113.468371  0.411
2013 Neafsey DE. Genome sequencing sheds light on emerging drug resistance in malaria parasites. Nature Genetics. 45: 589-90. PMID 23715326 DOI: 10.1038/Ng.2648  0.499
2013 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, Md.). 3: 1191-4. PMID 23708298 DOI: 10.1534/G3.113.006247  0.425
2013 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. 8: e60780. PMID 23593309 DOI: 10.1371/Journal.Pone.0060780  0.601
2013 Neafsey DE. ‘Big data’ from shrinking pathogen populations. Molecular Ecology. 22: 271-2. PMID 23409287 DOI: 10.1111/Mec.12175  0.438
2013 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. 193: 1221-31. PMID 23335339 DOI: 10.1534/Genetics.112.148718  0.365
2013 Volkman SK, Neafsey DE, Schaffner SF, Sabeti PC, Wirth DF. From Population Genomics to Elucidated Traits in Plasmodium Falciparum: Population Genomics, Genetic Diversity, and Association in Malaria Evolution of Virulence in Eukaryotic Microbes. 111-123. DOI: 10.1002/9781118308165.ch6  0.372
2012 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 Biology and Evolution. 4: 1202-12. PMID 23132896 DOI: 10.1093/Gbe/Evs095  0.398
2012 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, et al. The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nature Genetics. 44: 1046-50. PMID 22863733 DOI: 10.1038/Ng.2373  0.521
2012 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, et al. Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite. Proceedings of the National Academy of Sciences of the United States of America. 109: 13052-7. PMID 22826220 DOI: 10.1073/Pnas.1210585109  0.656
2012 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. Molecular Biology and Evolution. 29: 3427-39. PMID 22734050 DOI: 10.1093/Molbev/Mss161  0.648
2012 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. Molecular Biology and Evolution. 29: 3249-53. PMID 22688945 DOI: 10.1093/Molbev/Mss151  0.519
2012 Volkman SK, Neafsey DE, Schaffner SF, Park DJ, Wirth DF. Harnessing genomics and genome biology to understand malaria biology. Nature Reviews. Genetics. 13: 315-28. PMID 22495435 DOI: 10.1038/Nrg3187  0.525
2012 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, et al. Human cerebral malaria and Plasmodium falciparum genotypes in Malawi. Malaria Journal. 11: 35. PMID 22314206 DOI: 10.1186/1475-2875-11-35  0.41
2012 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 Tropica. 121: 324-32. PMID 22182668 DOI: 10.1016/J.Actatropica.2011.12.002  0.63
2011 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, ... ... Neafsey DE, et al. Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biology. 12: R73. PMID 21835008 DOI: 10.1186/Gb-2011-12-8-R73  0.429
2011 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, et al. Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum. Plos Genetics. 7: e1001383. PMID 21533027 DOI: 10.1371/Journal.Pgen.1001383  0.664
2011 Neafsey DE, Haas BJ. 'Next-generation' sequencing becomes 'now-generation'. Genome Biology. 12: 303. PMID 21457529 DOI: 10.1186/Gb-2011-12-3-303  0.362
2010 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, et al. SNP genotyping defines complex gene-flow boundaries among African malaria vector mosquitoes. Science (New York, N.Y.). 330: 514-7. PMID 20966254 DOI: 10.1126/Science.1193036  0.496
2010 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, et al. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research. 20: 938-46. PMID 20516208 DOI: 10.1101/Gr.103911.109  0.472
2010 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. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 10: 200-6. PMID 19931645 DOI: 10.1016/J.Meegid.2009.11.008  0.44
2009 Irimia M, Roy SW, Neafsey DE, Abril JF, Garcia-Fernandez J, Koonin EV. Complex selection on 5' splice sites in intron-rich organisms. Genome Research. 19: 2021-7. PMID 19745111 DOI: 10.1101/Gr.089276.108  0.388
2009 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, et al. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research. 19: 1722-31. PMID 19717792 DOI: 10.1101/Gr.087551.108  0.404
2009 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. Proceedings of the National Academy of Sciences of the United States of America. 106: 12025-30. PMID 19587242 DOI: 10.1073/Pnas.0905922106  0.724
2009 Neafsey DE. Malaria genomics: New tools to fight an old disease The Biochemist. 31: 12-15. DOI: 10.1042/bio03104012  0.327
2008 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, et al. Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence. Genome Biology. 9: R171. PMID 19077304 DOI: 10.1186/Gb-2008-9-12-R171  0.619
2008 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. Malaria Journal. 7: 223. PMID 18959790 DOI: 10.1186/1475-2875-7-223  0.412
2008 Carlton JM, Escalante AA, Neafsey D, Volkman SK. Comparative evolutionary genomics of human malaria parasites. Trends in Parasitology. 24: 545-50. PMID 18938107 DOI: 10.1016/J.Pt.2008.09.003  0.497
2008 Sharpton TJ, Neafsey DE, Galagan JE, Taylor JW. Mechanisms of intron gain and loss in Cryptococcus. Genome Biology. 9: R24. PMID 18234113 DOI: 10.1186/Gb-2008-9-1-R24  0.372
2008 Hughes SS, Buckley CO, Neafsey DE. Complex selection on intron size in Cryptococcus neoformans. Molecular Biology and Evolution. 25: 247-53. PMID 18171915 DOI: 10.1093/Molbev/Msm220  0.386
2007 Neafsey DE, Galagan JE. Positive selection for unpreferred codon usage in eukaryotic genomes. Bmc Evolutionary Biology. 7: 119. PMID 17640368 DOI: 10.1186/1471-2148-7-119  0.392
2007 Neafsey DE, Galagan JE. Dual modes of natural selection on upstream open reading frames. Molecular Biology and Evolution. 24: 1744-51. PMID 17494029 DOI: 10.1093/Molbev/Msm093  0.387
2007 Roy SW, Penny D, Neafsey DE. Evolutionary conservation of UTR intron boundaries in Cryptococcus. Molecular Biology and Evolution. 24: 1140-8. PMID 17374879 DOI: 10.1093/Molbev/Msm045  0.337
2007 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. Molecular Biology and Evolution. 24: 939-47. PMID 17244598 DOI: 10.1093/Molbev/Msm013  0.561
2007 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, et al. A genome-wide map of diversity in Plasmodium falciparum. Nature Genetics. 39: 113-9. PMID 17159979 DOI: 10.1038/Ng1930  0.677
2006 Neafsey DE, Hartl DL. Erratum to “Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineages” [Gene 350 (2005) 161–171] Gene. 370: 125. DOI: 10.1016/J.Gene.2006.01.002  0.474
2005 Neafsey DE, Hartl DL, Berriman M. Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes. Molecular Biology and Evolution. 22: 1621-6. PMID 15858207 DOI: 10.1093/Molbev/Msi154  0.571
2005 Neafsey DE, Hartl DL. Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineages. Gene. 350: 161-71. PMID 15820147 DOI: 10.1016/J.Gene.2005.02.011  0.564
2004 Neafsey DE, Blumenstiel JP, Hartl DL. Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies. Molecular Biology and Evolution. 21: 2310-8. PMID 15342795 DOI: 10.1093/Molbev/Msh243  0.742
2003 Neafsey DE, Palumbi SR. Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes. Genome Research. 13: 821-30. PMID 12727902 DOI: 10.1101/Gr.841703  0.374
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