Publications

Latest publications

15 Jul 2022

Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study

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.
Molecular Ecology Resources 2022 22 2285 DOI: https://doi.org/10.1111/1755-0998.13622
31 May 2022

Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination

Christopher G Jacob, Nguyen Thuy-Nhien, Mayfong Mayxay, Richard J Maude, Huynh Hong Quang, Bouasy Hongvanthong, Viengxay Vanisaveth, Thang Ngo Duc, Huy Rekol, Rob van der Pluijm, Lorenz von Seidlein, Rick Fairhurst, François Nosten, Md Amir Hossain, Naomi Park, Scott Goodwin, Pascal Ringwald, Keobouphaphone Chindavongsa, Paul Newton, Elizabeth Ashley, Sonexay Phalivong, Rapeephan Maude, Rithea Leang, Cheah Huch, Le Thanh Dong, Kim-Tuyen Nguyen, Tran Minh Nhat, Tran Tinh Hien, Hoa Nguyen, Nicole Zdrojewski, Sara Canavati, Abdullah Abu Sayeed, Didar Uddin, Caroline Buckee, Caterina I Fanello, Marie Onyamboko, Thomas Peto, Rupam Tripura, Chanaki Amaratunga, Aung Myint Thu, Gilles Delmas, Jordi Landier, Daniel M Parker, Nguyen Hoang Chau, Dysoley Lek, Seila Suon, James Callery, Podjanee Jittamala, Borimas Hanboonkunupakarn, Sasithon Pukrittayakamee, Aung Pyae Phyo, Frank Smithuis, Khin Lin, Myo Thant, Tin Maung Hlaing, Parthasarathi Satpathi, Sanghamitra Satpathi, Prativa K Behera, Amar Tripura, Subrata Baidya, Neena Valecha, Anupkumar R Anvikar, Akhter Ul Islam, Abul Faiz, Chanon Kunasol, Eleanor Drury, Mihir Kekre, Mozam Ali, Katie Love, Shavanthi Rajatileka, Anna E Jeffreys, Kate Rowlands, Christina S Hubbart, Mehul Dhorda, Ranitha Vongpromek, Namfon Kotanan, Phrutsamon Wongnak, Jacob Almagro Garcia, Richard D Pearson, Cristina V Ariani, Thanat Chookajorn, Cinzia Malangone, T Nguyen, Jim Stalker, Ben Jeffery, Jonathan Keatley, Kimberly J Johnson, Dawn Muddyman, Xin Hui S Chan, John Sillitoe, Roberto Amato, Victoria Simpson, Sonia Gonçalves, Kirk Rockett, Nicholas P Day, Arjen M Dondorp, Dominic P Kwiatkowski, Olivo Miotto
eLife 2021 10 e62997 DOI: https://doi.org/10.7554/eLife.62997
31 May 2022

Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination

Christopher G Jacob, Nguyen Thuy-Nhien, Mayfong Mayxay, Richard J Maude, Huynh Hong Quang, Bouasy Hongvanthong, Viengxay Vanisaveth, Thang Ngo Duc, Huy Rekol, Rob van der Pluijm, Lorenz von Seidlein, Rick Fairhurst, François Nosten, Md Amir Hossain, Naomi Park, Scott Goodwin, Pascal Ringwald, Keobouphaphone Chindavongsa, Paul Newton, Elizabeth Ashley, Sonexay Phalivong, Rapeephan Maude, Rithea Leang, Cheah Huch, Le Thanh Dong, Kim-Tuyen Nguyen, Tran Minh Nhat, Tran Tinh Hien, Hoa Nguyen, Nicole Zdrojewski, Sara Canavati, Abdullah Abu Sayeed, Didar Uddin, Caroline Buckee, Caterina I Fanello, Marie Onyamboko, Thomas Peto, Rupam Tripura, Chanaki Amaratunga, Aung Myint Thu, Gilles Delmas, Jordi Landier, Daniel M Parker, Nguyen Hoang Chau, Dysoley Lek, Seila Suon, James Callery, Podjanee Jittamala, Borimas Hanboonkunupakarn, Sasithon Pukrittayakamee, Aung Pyae Phyo, Frank Smithuis, Khin Lin, Myo Thant, Tin Maung Hlaing, Parthasarathi Satpathi, Sanghamitra Satpathi, Prativa K Behera, Amar Tripura, Subrata Baidya, Neena Valecha, Anupkumar R Anvikar, Akhter Ul Islam, Abul Faiz, Chanon Kunasol, Eleanor Drury, Mihir Kekre, Mozam Ali, Katie Love, Shavanthi Rajatileka, Anna E Jeffreys, Kate Rowlands, Christina S Hubbart, Mehul Dhorda, Ranitha Vongpromek, Namfon Kotanan, Phrutsamon Wongnak, Jacob Almagro Garcia, Richard D Pearson, Cristina V Ariani, Thanat Chookajorn, Cinzia Malangone, T Nguyen, Jim Stalker, Ben Jeffery, Jonathan Keatley, Kimberly J Johnson, Dawn Muddyman, Xin Hui S Chan, John Sillitoe, Roberto Amato, Victoria Simpson, Sonia Gonçalves, Kirk Rockett, Nicholas P Day, Arjen M Dondorp, Dominic P Kwiatkowski, Olivo Miotto
eLife 2021 10 e62997 DOI: https://doi.org/10.7554/eLife.62997
19 Apr 2022

Protective Immunity against Severe Malaria in Children Is Associated with a Limited Repertoire of Antibodies to Conserved PfEMP1 Variants

Tessema SK, Nakajima R, Jasinskas A, Monk SL, Lekieffre L, Lin E, Kiniboro B, Proietti C, Siba P, Felgner PL, Doolan DL, Mueller I, Barry AE.
Cell Host & Microbe 2019 26(5) 579-590.e5 DOI: https://doi.org/10.1016/j.chom.2019.10.012
19 Apr 2022

Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens

Naung MT, Martin E, Munro J, Mehra S, Guy AJ, Laman M, Harrison GLA, Tavul L, Hetzel M, Kwiatkowski D, Mueller I, Bahlo M, Barry AE.
PLoS Computational Biology 2022 18(2) e1009801 DOI: https://doi.org/10.1371/journal.pcbi.1009801
8 Apr 2022

Plasmodium malariae and Plasmodium ovale infections and their association with common red blood cell polymorphisms in a highly endemic area of Uganda

Subissi L, Kanoi BN, Balikagala B, Egwang TG, Oguike M, Verra F, Proietti C, Bousema T, Drakeley CJ, Sepúlveda N
Transactions of The Royal Society of Tropical Medicine and Hygiene 2019 113(7) 370-378 DOI: https://doi.org/10.1093/trstmh/trz015
8 Apr 2022

Influence of infection on malaria-specific antibody dynamics in a cohort exposed to intense malaria transmission in northern Uganda

Proietti C, Verra F, Bretscher MT, Stone W, Kanoi BN, Balikagala B, Egwang TG, Corran P, Ronca R, Arcà B, Riley EM, Crisanti A, Drakeley C, Bousema T
Parasite Immunology 2013 35(5-6) 164-73 DOI: https://doi.org/10.1111/pim.12031
4 Apr 2022

Artemisinin resistance in the malaria parasite, Plasmodium falciparum, originates from its initial transcriptional response

Zhu L, van der Pluijm RW, Kucharski M, Nayak S, Tripathi J, White NJ, Day NPJ, Faiz A, Phyo AP, Amaratunga C, Lek D, Ashley EA, Nosten F, Smithuis F, Ginsburg H, von Seidlein L, Lin K, Imwong M, Chotivanich K, Mayxay M, Dhorda M, Nguyen HC, Nguyen TNT, Miotto O, Newton PN, Jittamala P, Tripura R, Pukrittayakamee S, Peto TJ, Hien TT, Dondorp AM, Bozdech Z.
Communications Biology 2022 5 274 DOI: https://doi.org/10.1038/s42003-022-03215-0
4 Apr 2022

Molecular epidemiology of resistance to antimalarial drugs in the Greater Mekong subregion: an observational study

Imwong M, Dhorda M, Myo Tun K, Thu AM, Phyo AP, Proux S, Suwannasin K, Kunasol C, Srisutham S, Duanguppama J, Vongpromek R, Promnarate C, Saejeng A, Khantikul N, Sugaram R, Thanapongpichat S, Sawangjaroen N, Sutawong K, Han KT, Htut Y, Linn K, Win AA, Hlaing TM, van der Pluijm RW, Mayxay M, Pongvongsa T, Phommasone K, Tripura R, Peto TJ, von Seidlein L, Nguon C, Lek D, Chan XHS, Rekol H, Leang R, Huch C, Kwiatkowski DP, Miotto O, Ashley EA, Kyaw MP, Pukrittayakamee S, Day NPJ, Dondorp AM, Smithuis FM, Nosten FH, White NJ.
The Lancet Infectious Diseases 2020 20(12) 1470-1480 DOI: https://doi.org/10.1016/S1473-3099(20)30228-0
19 Feb 2022

Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis

Carrasquilla M, Early AM, Taylor AR, Knudson A, Echeverry DF, Anderson TJ, Mancilla E, Aponte S, Cárdenas P, Buckee CO, Rayner JC, Sáenz FE, Neafsey DE, Corredor V
bioRxiv 2022 DOI: https://doi.org/10.1101/2022.02.18.480973
9 Dec 2021

The protective effect of sickle cell haemoglobin against severe malaria depends on parasite genotype

Gavin Band, Ellen M. Leffler, Muminatou Jallow, Fatoumatta Sisay-Joof, Carolyne M. Ndila, Alexander W. Macharia, Christina Hubbart, Anna E. Jeffreys, Kate Rowlands, Thuy Nguyen, Sónia Gonçalves, Cristina V. Ariani, Jim Stalker, Richard D. Pearson, Roberto Amato, Eleanor Drury, Giorgio Sirugo, Umberto d’Alessandro, Kalifa A. Bojang, Kevin Marsh, Norbert Peshu, Joseph W. Saelens, Mahamadou Diakité, Steve M. Taylor, David J. Conway, Thomas N. Williams, Kirk A. Rockett & Dominic P. Kwiatkowski
Malaria protection due to sickle haemoglobin depends on parasite genotype 2021 DOI: https://doi.org/10.1038/s41586-021-04288-3
12 Nov 2021

Amin1: Anopheles minimus genome variation data resource

19 Oct 2021

Increase in the proportion of Plasmodium falciparum with kelch13 C580Y mutation and decline in pfcrt and pfmdr1 mutant alleles in Papua New Guinea

Yoshida N, Yamauchi M, Morikawa R, Hombhanje F, Mita T.
Malaria Journal 2021 20 410 DOI: https://doi.org/10.1186/s12936-021-03933-6
10 Aug 2021

Genetic surveillance in the Greater Mekong Subregion and South Asia to support malaria control and elimination: about the data

Jacob CG, Thuy-Nhien N, Mayxay M, et al.
eLife 2021 10:e62997 DOI: 10.7554/eLife.62997
10 Aug 2021

Genetic surveillance in the Greater Mekong Subregion and South Asia to support malaria control and elimination: about the data

Jacob CG, Thuy-Nhien N, Mayxay M, et al.
eLife 2021 10:e62997 DOI: 10.7554/eLife.62997
17 Jun 2021

Mass drug administration for the acceleration of malaria elimination in a region of Myanmar with artemisinin-resistant falciparum malaria: a cluster-randomised trial

McLean ARD, Indrasuta C, Khant ZS, Phyo AK, Maung SM, Heaton J, Aung H, Aung Y, Soe K, Swe MMM, von Seidlein L, Tun NN, Tun KM, Day NPJ, Ashley EA, Hlaing T, Kyaw TT, Dondorp AM, Imwong M, White NJ, Smithuis FM.
The Lancet Infectious Diseases 2021 21 1579 DOI: 10.1016/S1473-3099(20)30997-X
14 Jun 2021

Using deep learning to identify recent positive selection in malaria parasite sequence data

Deelder W, Benavente ED, Phelan J, Manko E, Campino S, Palla L, Clark TG.
Malaria Journal 2021 20(1) 270 DOI: 10.1186/s12936-021-03788-x
7 Jun 2021

Arterolane–piperaquine–mefloquine versus arterolane–piperaquine and artemether–lumefantrine in the treatment of uncomplicated Plasmodium falciparum malaria in Kenyan children: a single-centre, open-label, randomised, non-inferiority trial

Hamaluba M, van der Pluijm RW, Weya J, Njuguna P, Ngama M, Kalume P, Mwambingu G, Ngetsa C, Wambua J, Boga M, Mturi N, Lal AA, Khuroo A, Taylor WRJ, Gonçalves S, Miotto O, Dhorda M, Mutinda B, Mukaka M, Waithira N, Hoglund RM, Imwong M, Tarning J, Day NPJ, White NJ, Bejon P, Dondorp AM
The Lancet Infectious Diseases 2021 20 30929-4 DOI: 10.1016/S1473-3099(20)30929-4
4 Jun 2021

About the Plasmodium falciparum version 7 data

26 May 2021

Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa

Benavente ED, Manko E, Phelan J, Campos M, Nolder D, Fernandez D, Velez-Tobon G, Castaño AT, Dombrowski JG, Marinho CRF, Aguiar ACC, Pereira DB, Sriprawat K, Nosten F, Moon R, Sutherland CJ, Campino S, Clark TG.
Nature Communications 2021 12(1) 3160 DOI: 10.1038/s41467-021-23422-3
25 May 2021

A. Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii.

Wagah MG, Korlević P, Clarkson C, Miles A; Anopheles gambiae 1000 Genomes Consortium, Lawniczak MKN, Makunin A
Malaria Journal 2021 20 234 DOI: 10.1186/s12936-021-03757-4
28 Apr 2021

Population genomic evidence of Plasmodium vivax Southeast Asian origin

Daron J, Boissière A, Boundenga L, Ngoubangoye B, Houze S, Arnathau C, Sidobre C, Trape JF, Durand P, Renaud F, Fontaine MC, Prugnolle F, Rougeron V.
Science Advances 2021 7(18) eabc3713 DOI: 10.1126/sciadv.abc3713
31 Mar 2021

Genomic analysis reveals independent evolution of Plasmodium falciparum populations in Ethiopia

Abera D, Kibet CK, Degefa T, Amenga-Etego L, Bargul JL, Golassa L.
Malaria Journal 2021 20 129 DOI: https://doi.org/10.1186/s12936-021-03660-y
31 Mar 2021

Genomic analysis reveals independent evolution of Plasmodium falciparum populations in Ethiopia

Abera D, Kibet CK, Degefa T, Amenga-Etego L, Bargul JL, Golassa L.
Malaria Journal 2021 20 129 DOI: https://doi.org/10.1186/s12936-021-03660-y
9 Mar 2021

Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning.

Xue AT, Schrider DR, Kern AD; Ag1000g Consortium.
Mol Biol Evol 2021 38 1168-1183 DOI: 10.1093/molbev/msaa259
15 Feb 2021

Novel genotyping approaches to easily detect genomic admixture between the major Afrotropical malaria vector species, Anopheles coluzzii and An. gambiae

Caputo B, Pichler V, Bottà G, De Marco C, Hubbart C, Perugini E, Pinto J, Rockett KA, Miles A, Della Torre A.
Mol Ecol Resour. 2021 DOI: 10.1111/1755-0998.13359
8 Feb 2021

Ag3: The Anopheles gambiae 1000 Genomes Project phase 3 data resource

21 Jan 2021

Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus.

Grau-Bové X, Lucas E, Pipini D, Rippon E, van 't Hof AE, Constant E, Dadzie S, Egyir-Yawson A, Essandoh J, Chabi J, Djogbénou L, Harding NJ, Miles A, Kwiatkowski D, Donnelly MJ, Weetman D; Anopheles gambiae 1000 Genomes Consortium.
PLoS Genetics 2021 17 DOI: 10.1371/journal.pgen.1009253
15 Dec 2020

Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of New Guinea

Miotto O, Sekihara M, Tachibana SI, Yamauchi M, Pearson RD, Amato R, Gonçalves S, Mehra S, Noviyanti R, Marfurt J, Auburn S, Price RN, Mueller I, Ikeda M, Mori T, Hirai M, Tavul L, Hetzel MW, Laman M, Barry AE, Ringwald P, Ohashi J, Hombhanje F, Kwiatkowski DP, Mita T.
PLoS Pathogens 2020 16(12) e1009133 DOI: https://doi.org/10.1371/journal.ppat.1009133
16 Nov 2020

Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast

Taylor AR, Echeverry DF, Anderson TJC, Neafsey DE, Buckee CO.
PLoS Genetics 2020 16(11) e1009101 DOI: 10.1371/journal.pgen.1009101