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For: Zhu SJ, Hendry JA, Almagro-Garcia J, Pearson RD, Amato R, Miles A, Weiss DJ, Lucas TC, Nguyen M, Gething PW, Kwiatkowski D, McVean G. The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria. eLife 2019;8:e40845. [PMID: 31298657 PMCID: PMC6684230 DOI: 10.7554/elife.40845] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 07/10/2019] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Mehra S, Neafsey DE, White M, Taylor AR. Systematic bias in malaria parasite relatedness estimation. G3 (BETHESDA, MD.) 2025;15:jkaf018. [PMID: 39883524 PMCID: PMC12060250 DOI: 10.1093/g3journal/jkaf018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Accepted: 11/22/2024] [Indexed: 01/31/2025]
2
Guo B, Rowley E, O'Connor TD, Takala-Harrison S. Potential and pitfalls of using identity-by-descent for malaria genomic surveillance. Trends Parasitol 2025;41:387-400. [PMID: 40263027 PMCID: PMC12070291 DOI: 10.1016/j.pt.2025.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2025] [Revised: 03/24/2025] [Accepted: 03/25/2025] [Indexed: 04/24/2025]
3
Dwivedi A, Scalsky RJ, Harris DG, Stabler TC, Shrestha B, Joshi S, Gandhi C, Munro JB, Ifeonu OO, Ouedraogo A, Tiono AB, Coulibaly D, Ouattara A, Richie TL, Sim BKL, Plowe CV, Lyke KE, Takala-Harrison S, Hoffman SL, Thera MA, Sirima SB, Laurens MB, Silva JC. Protective targets of PfSPZ vaccines identified from whole-genome sieve analysis of isolates from malaria vaccine efficacy trials in West Africa. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.03.04.25323352. [PMID: 40093207 PMCID: PMC11908318 DOI: 10.1101/2025.03.04.25323352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
4
Stewart LB, Escolar EL, Philpott J, Cox-Singh J, Singh B, Conway DJ. Intrinsic multiplication rate variation of Plasmodium falciparum in clinical isolates prior to elimination in Malaysia. Int J Parasitol 2025:S0020-7519(25)00038-4. [PMID: 40043895 DOI: 10.1016/j.ijpara.2025.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 12/11/2024] [Accepted: 02/27/2025] [Indexed: 03/21/2025]
5
Westaway JAF, Diez Benavente E, Auburn S, Kucharski M, Aranciaga N, Nayak S, William T, Rajahram GS, Piera KA, Braima K, Tan AF, Alaza DA, Barber BE, Drakeley C, Amato R, Sutanto E, Trimarsanto H, Jelip J, Anstey NM, Bozdech Z, Field M, Grigg MJ. Genomic epidemiology of Plasmodium knowlesi reveals putative genetic drivers of adaptation in Malaysia. PLoS Negl Trop Dis 2025;19:e0012885. [PMID: 40072967 PMCID: PMC11932472 DOI: 10.1371/journal.pntd.0012885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 03/24/2025] [Accepted: 02/03/2025] [Indexed: 03/14/2025]  Open
6
Taylor AR, Neubauer Vickers E, Greenhouse B. Review of MrsFreqPhase methods: methods designed to estimate statistically malaria parasite multiplicity of infection, relatedness, frequency and phase. Malar J 2024;23:308. [PMID: 39407242 PMCID: PMC11481338 DOI: 10.1186/s12936-024-05119-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 09/28/2024] [Indexed: 10/19/2024]  Open
7
Murphy M, Greenhouse B. MOIRE: a software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data. Bioinformatics 2024;40:btae619. [PMID: 39423091 PMCID: PMC11524891 DOI: 10.1093/bioinformatics/btae619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 10/08/2024] [Accepted: 10/17/2024] [Indexed: 10/21/2024]  Open
8
Murphy M, Greenhouse B. MOIRE: A software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.03.560769. [PMID: 37873322 PMCID: PMC10592951 DOI: 10.1101/2023.10.03.560769] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
9
Kwiatkowski D. Modelling transmission dynamics and genomic diversity in a recombining parasite population. Wellcome Open Res 2024;9:215. [PMID: 39554245 PMCID: PMC11569386 DOI: 10.12688/wellcomeopenres.19092.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 11/19/2024]  Open
10
Khan A, Alves-Ferreira EVC, Vogel H, Botchie S, Ayi I, Pawlowic MC, Robinson G, Chalmers RM, Lorenzi H, Grigg ME. Phylogenomic reconstruction of Cryptosporidium spp. captured directly from clinical samples reveals extensive genetic diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589752. [PMID: 38659886 PMCID: PMC11042339 DOI: 10.1101/2024.04.17.589752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
11
Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia. COMMUNICATIONS MEDICINE 2024;4:67. [PMID: 38582941 PMCID: PMC10998850 DOI: 10.1038/s43856-024-00498-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024]  Open
12
Guo B, Borda V, Laboulaye R, Spring MD, Wojnarski M, Vesely BA, Silva JC, Waters NC, O'Connor TD, Takala-Harrison S. Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum. Nat Commun 2024;15:2499. [PMID: 38509066 PMCID: PMC10954658 DOI: 10.1038/s41467-024-46659-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]  Open
13
Letcher B, Maciuca S, Iqbal Z. Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum. PLoS Biol 2024;22:e3002507. [PMID: 38451924 PMCID: PMC10919680 DOI: 10.1371/journal.pbio.3002507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/19/2024] [Indexed: 03/09/2024]  Open
14
Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.09.24302570. [PMID: 38370674 PMCID: PMC10871455 DOI: 10.1101/2024.02.09.24302570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
15
Kebede AM, Sutanto E, Trimarsanto H, Benavente ED, Barnes M, Pearson RD, Siegel SV, Erko B, Assefa A, Getachew S, Aseffa A, Petros B, Lo E, Mohammed R, Yilma D, Rumaseb A, Nosten F, Noviyanti R, Rayner JC, Kwiatkowski DP, Price RN, Golassa L, Auburn S. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia. Sci Rep 2023;13:20788. [PMID: 38012191 PMCID: PMC10682486 DOI: 10.1038/s41598-023-47889-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023]  Open
16
Sutanto E, Pava Z, Echeverry DF, Lopera-Mesa TM, Montenegro LM, Yasnot-Acosta MF, Benavente ED, Pearson RD, Herrera S, Arévalo-Herrera M, Trimarsanto H, Rumaseb A, Noviyanti R, Kwiatkowski DP, Price RN, Auburn S. Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas. Sci Rep 2023;13:19779. [PMID: 37957271 PMCID: PMC10643449 DOI: 10.1038/s41598-023-46076-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]  Open
17
Guo B, Borda V, Laboulaye R, Spring MD, Wojnarski M, Vesely BA, Silva JC, Waters NC, O'Connor TD, Takala-Harrison S. Strong Positive Selection Biases Identity-By-Descent-Based Inferences of Recent Demography and Population Structure in Plasmodium falciparum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549114. [PMID: 37502843 PMCID: PMC10370022 DOI: 10.1101/2023.07.14.549114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
18
Argyropoulos DC, Tan MH, Adobor C, Mensah B, Labbé F, Tiedje KE, Koram KA, Ghansah A, Day KP. Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa. Front Genet 2023;14:1071896. [PMID: 37323661 PMCID: PMC10267394 DOI: 10.3389/fgene.2023.1071896] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/17/2023] [Indexed: 06/17/2023]  Open
19
Paschalidis A, Watson OJ, Aydemir O, Verity R, Bailey JA. coiaf: Directly estimating complexity of infection with allele frequencies. PLoS Comput Biol 2023;19:e1010247. [PMID: 37294835 PMCID: PMC10310041 DOI: 10.1371/journal.pcbi.1010247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/29/2023] [Accepted: 05/01/2023] [Indexed: 06/11/2023]  Open
20
Ghansah A, Tiedje KE, Argyropoulos DC, Onwona CO, Deed SL, Labbé F, Oduro AR, Koram KA, Pascual M, Day KP. Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high transmission. FRONTIERS IN PARASITOLOGY 2023;2:1067966. [PMID: 38031549 PMCID: PMC10686283 DOI: 10.3389/fpara.2023.1067966] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/14/2023] [Indexed: 12/01/2023]
21
Camponovo F, Buckee CO, Taylor AR. Measurably recombining malaria parasites. Trends Parasitol 2023;39:17-25. [PMID: 36435688 PMCID: PMC9893849 DOI: 10.1016/j.pt.2022.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/24/2022]
22
Schneider KA, Salas CJ. Evolutionary genetics of malaria. Front Genet 2022;13:1030463. [PMID: 36406132 PMCID: PMC9669584 DOI: 10.3389/fgene.2022.1030463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 09/08/2024]  Open
23
Tsoungui Obama HCJ, Schneider KA. A maximum-likelihood method to estimate haplotype frequencies and prevalence alongside multiplicity of infection from SNP data. FRONTIERS IN EPIDEMIOLOGY 2022;2:943625. [PMID: 38455338 PMCID: PMC10911023 DOI: 10.3389/fepid.2022.943625] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/26/2022] [Indexed: 03/09/2024]
24
Wong W, Volkman S, Daniels R, Schaffner S, Sy M, Ndiaye YD, Badiane AS, Deme AB, Diallo MA, Gomis J, Sy N, Ndiaye D, Wirth DF, Hartl DL. R H: a genetic metric for measuring intrahost Plasmodium falciparum relatedness and distinguishing cotransmission from superinfection. PNAS NEXUS 2022;1:pgac187. [PMID: 36246152 PMCID: PMC9552330 DOI: 10.1093/pnasnexus/pgac187] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/08/2022] [Indexed: 01/29/2023]
25
Gerlovina I, Gerlovin B, Rodríguez-Barraquer I, Greenhouse B. Dcifer: an IBD-based method to calculate genetic distance between polyclonal infections. Genetics 2022;222:6674513. [PMID: 36000888 PMCID: PMC9526043 DOI: 10.1093/genetics/iyac126] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022]  Open
26
Carpi G, Gorenstein L, Harkins TT, Samadi M, Vats P. A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study. Brief Bioinform 2022;23:6658853. [PMID: 35945154 PMCID: PMC9487672 DOI: 10.1093/bib/bbac314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/03/2022] [Accepted: 07/12/2022] [Indexed: 11/15/2022]  Open
27
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, Rayner JC, Corredor V, James K, Cox H, Early AM, MacInnis BL, Neafsey DE. Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study. Mol Ecol Resour 2022;22:2285-2303. [PMID: 35437908 PMCID: PMC9288814 DOI: 10.1111/1755-0998.13622] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/05/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022]
28
Liu Y, Liang X, Li J, Chen J, Huang H, Zheng Y, He J, Ehapo CS, Eyi UM, Yang P, Lin L, Chen W, Sun G, Liu X, Zha G, Wang J, Wang C, Wei H, Lin M. Molecular Surveillance of Artemisinin-Based Combination Therapies Resistance in Plasmodium falciparum Parasites from Bioko Island, Equatorial Guinea. Microbiol Spectr 2022;10:e0041322. [PMID: 35670601 PMCID: PMC9241599 DOI: 10.1128/spectrum.00413-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
29
Ndiaye YD, Hartl DL, McGregor D, Badiane A, Fall FB, Daniels RF, Wirth DF, Ndiaye D, Volkman SK. Genetic surveillance for monitoring the impact of drug use on Plasmodium falciparum populations. Int J Parasitol Drugs Drug Resist 2021;17:12-22. [PMID: 34333350 PMCID: PMC8342550 DOI: 10.1016/j.ijpddr.2021.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 11/23/2022]
30
Dia A, Jett C, Trevino SG, Chu CS, Sriprawat K, Anderson TJC, Nosten F, Cheeseman IH. Single-genome sequencing reveals within-host evolution of human malaria parasites. Cell Host Microbe 2021;29:1496-1506.e3. [PMID: 34492224 DOI: 10.1016/j.chom.2021.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 06/17/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023]
31
Dia A, Cheeseman IH. Single-cell genome sequencing of protozoan parasites. Trends Parasitol 2021;37:803-814. [PMID: 34172399 PMCID: PMC8364489 DOI: 10.1016/j.pt.2021.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/27/2022]
32
Hendry JA, Kwiatkowski D, McVean G. Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria. PLoS Comput Biol 2021;17:e1009287. [PMID: 34411093 PMCID: PMC8407561 DOI: 10.1371/journal.pcbi.1009287] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 08/31/2021] [Accepted: 07/19/2021] [Indexed: 12/05/2022]  Open
33
MalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, et alMalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021;6:42. [PMID: 33824913 PMCID: PMC8008441 DOI: 10.12688/wellcomeopenres.16168.1] [Show More Authors] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 02/02/2023]  Open
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MalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, et alMalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021;6:42. [PMID: 33824913 PMCID: PMC8008441.2 DOI: 10.12688/wellcomeopenres.16168.2] [Show More Authors] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2021] [Indexed: 02/02/2023]  Open
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Ippolito MM, Moser KA, Kabuya JBB, Cunningham C, Juliano JJ. Antimalarial Drug Resistance and Implications for the WHO Global Technical Strategy. CURR EPIDEMIOL REP 2021;8:46-62. [PMID: 33747712 PMCID: PMC7955901 DOI: 10.1007/s40471-021-00266-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 12/28/2022]
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Shi SM, Shi TQ, Chen SB, Cui YB, Kassegne K, Okpeku M, Chen JH, Shen HM. Genome-Wide Scans for Ghanaian Plasmodium falciparum Genes Under Selection From Local and Chinese Host Populations. Front Cell Infect Microbiol 2021;11:630797. [PMID: 33718278 PMCID: PMC7947188 DOI: 10.3389/fcimb.2021.630797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/07/2021] [Indexed: 01/02/2023]  Open
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Watson OJ, Okell LC, Hellewell J, Slater HC, Unwin HJT, Omedo I, Bejon P, Snow RW, Noor AM, Rockett K, Hubbart C, Nankabirwa JI, Greenhouse B, Chang HH, Ghani AC, Verity R. Evaluating the Performance of Malaria Genetics for Inferring Changes in Transmission Intensity Using Transmission Modeling. Mol Biol Evol 2021;38:274-289. [PMID: 32898225 PMCID: PMC7783189 DOI: 10.1093/molbev/msaa225] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
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He X, Xia L, Tumas KC, Wu J, Su XZ. Type I Interferons and Malaria: A Double-Edge Sword Against a Complex Parasitic Disease. Front Cell Infect Microbiol 2020;10:594621. [PMID: 33344264 PMCID: PMC7738626 DOI: 10.3389/fcimb.2020.594621] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/30/2020] [Indexed: 12/12/2022]  Open
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Siegel SV, Rayner JC. Single cell sequencing shines a light on malaria parasite relatedness in complex infections. Trends Parasitol 2020;36:83-85. [PMID: 31883706 DOI: 10.1016/j.pt.2019.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 10/25/2022]
40
Intrinsic multiplication rate variation and plasticity of human blood stage malaria parasites. Commun Biol 2020;3:624. [PMID: 33116247 PMCID: PMC7595149 DOI: 10.1038/s42003-020-01349-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/01/2020] [Indexed: 12/27/2022]  Open
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Su XZ, Zhang C, Joy DA. Host-Malaria Parasite Interactions and Impacts on Mutual Evolution. Front Cell Infect Microbiol 2020;10:587933. [PMID: 33194831 PMCID: PMC7652737 DOI: 10.3389/fcimb.2020.587933] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022]  Open
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Watson JA, Taylor AR, Ashley EA, Dondorp A, Buckee CO, White NJ, Holmes CC. A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices. PLoS Genet 2020;16:e1009037. [PMID: 33035220 PMCID: PMC7577480 DOI: 10.1371/journal.pgen.1009037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/21/2020] [Accepted: 08/08/2020] [Indexed: 11/20/2022]  Open
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Battey CJ, Ralph PL, Kern AD. Predicting geographic location from genetic variation with deep neural networks. eLife 2020;9:e54507. [PMID: 32511092 PMCID: PMC7324158 DOI: 10.7554/elife.54507] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/03/2020] [Indexed: 12/12/2022]  Open
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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;9:51015. [PMID: 32394893 PMCID: PMC7217694 DOI: 10.7554/elife.51015] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 03/25/2020] [Indexed: 12/15/2022]  Open
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Morgan AP, Brazeau NF, Ngasala B, Mhamilawa LE, Denton M, Msellem M, Morris U, Filer DL, Aydemir O, Bailey JA, Parr JB, Mårtensson A, Bjorkman A, Juliano JJ. Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago. Malar J 2020;19:47. [PMID: 31992305 PMCID: PMC6988337 DOI: 10.1186/s12936-020-3137-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022]  Open
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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;10:5595. [PMID: 31811128 PMCID: PMC6898227 DOI: 10.1038/s41467-019-13412-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 10/29/2019] [Indexed: 11/23/2022]  Open
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Auburn S, Getachew S, Pearson RD, Amato R, Miotto O, Trimarsanto H, Zhu SJ, Rumaseb A, Marfurt J, Noviyanti R, Grigg MJ, Barber B, William T, Goncalves SM, Drury E, Sriprawat K, Anstey NM, Nosten F, Petros B, Aseffa A, McVean G, Kwiatkowski DP, Price RN. Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms. J Infect Dis 2019;220:1738-1749. [PMID: 30668735 PMCID: PMC6804337 DOI: 10.1093/infdis/jiz016] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/18/2019] [Indexed: 01/12/2023]  Open
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Li X, Kumar S, McDew-White M, Haile M, Cheeseman IH, Emrich S, Button-Simons K, Nosten F, Kappe SHI, Ferdig MT, Anderson TJC, Vaughan AM. Genetic mapping of fitness determinants across the malaria parasite Plasmodium falciparum life cycle. PLoS Genet 2019;15:e1008453. [PMID: 31609965 PMCID: PMC6821138 DOI: 10.1371/journal.pgen.1008453] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/30/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022]  Open
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Tessema SK, Raman J, Duffy CW, Ishengoma DS, Amambua-Ngwa A, Greenhouse B. Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa. Malar J 2019;18:268. [PMID: 31477139 PMCID: PMC6720407 DOI: 10.1186/s12936-019-2880-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/11/2019] [Indexed: 01/13/2023]  Open
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Taylor AR, Jacob PE, Neafsey DE, Buckee CO. Estimating Relatedness Between Malaria Parasites. Genetics 2019;212:1337-1351. [PMID: 31209105 PMCID: PMC6707449 DOI: 10.1534/genetics.119.302120] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/03/2019] [Indexed: 11/18/2022]  Open
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