Publications

20 Jan 2023
Genetic Epidemiology Use Cases for Malaria Control Programmes: A Methodology
Olivo Miotto, Principal Investigator, GenRe-Mekong Project
Genetic Epidemiology Use Cases for Malaria Control Programmes: A Methodology, 2023;

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16 Jan 2023
Pf7: An open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
MalariaGEN et. al
Wellcome Open Research, 2023; 8 22
DOI: 10.12688/wellcomeopenres.18681.1

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9 Jan 2023
Unravelling var complexity: Relationship between DBLα types and var genes in Plasmodium falciparum
Tan et al
Front Parasitol, 2023; 1 1006341
DOI: 10.3389/fpara.2022.1006341

2 Jan 2023
Drug Resistant Prediction Based on Plasmodium falciparum DNA-Barcoding using Bidirectional Long Short Term Memory Method
Muflikhah et al
International Journal of Advanced Computer Science and Applications (IJACSA), 2023; 14(7)
DOI: 10.14569/IJACSA.2023.0140747

28 Nov 2022
Population genomics reveal distinct and diverging populations of An. minimus in Cambodia
St. Laurent et al.
Nature Communications Biology, 2022; 28;5(1) 1308
DOI: 10.1038/s42003-022-04259-y

13 Nov 2022
Analysis of the Genetic Variation of the Fruitless Gene within the Anopheles gambiae (Diptera: Culicidae) Complex Populations in Africa
Kientega et al.
Insects, 2022; 13(11) 1048
DOI: 10.3390/insects13111048

1 Oct 2022
Drug resistance and population structure of Plasmodium falciparum and Plasmodium vivax in the Peruvian Amazon
Villena FE et al.
Scientific Reports, 2022; 12(1) 16474
DOI: 10.1038/s41598-022-21028-3

23 Sep 2022
Phenotypic characterization of Ghanaian P. falciparum clinical isolates reveals a homogenous parasite population
Thiam et al
Frontiers Immunology, 2022; 13 1009252
DOI: 10.3389/fimmu.2022.1009252

15 Jul 2022
Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study
LaVerriere E et al.
Molecular Ecology Resources, 2022; 22 2285
DOI: 10.1111/1755-0998.13622

19 Apr 2022
Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens
Naung et al
PLoS Computational Biology, 2022; 18(2) e1009801
DOI: 10.1371/journal.pcbi.1009801

19 Apr 2022
Protective Immunity against Severe Malaria in Children Is Associated with a Limited Repertoire of Antibodies to Conserved PfEMP1 Variants
Tessema et al
Cell Host & Microbe, 2019; 26(5) 579-590.e5
DOI: 10.1016/j.chom.2019.10.012

8 Apr 2022
Influence of infection on malaria-specific antibody dynamics in a cohort exposed to intense malaria transmission in northern Uganda
Proietti et al
Parasite Immunology, 2013; 35(5-6) 164-73
DOI: 10.1111/pim.12031

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 et al
Transactions of The Royal Society of Tropical Medicine and Hygiene, 2019; 113(7) 370-378
DOI: 10.1093/trstmh/trz015

8 Apr 2022
An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
MalariaGEN et. al
Wellcome Open Research, 2022; 7 136
DOI: 10.12688/wellcomeopenres.17795.1

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4 Apr 2022
Molecular epidemiology of resistance to antimalarial drugs in the Greater Mekong subregion: an observational study
Imwong et al
The Lancet Infectious Diseases, 2020; 20(12) 1470-1480
DOI: 10.1016/S1473-3099(20)30228-0

4 Apr 2022
Artemisinin resistance in the malaria parasite, Plasmodium falciparum, originates from its initial transcriptional response
Zhu et al
Communications Biology, 2022; 5 274
DOI: 10.1038/s42003-022-03215-0

19 Feb 2022
Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis
Carrasquilla et al.
bioRxiv, 2022;
DOI: 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: 10.1038/s41586-021-04288-3

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12 Nov 2021
Amin1: Anopheles minimus genome variation data resource

2021;

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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 et al.
Malaria Journal, 2021; 20 410
DOI: 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

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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 et al
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 et al.
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 et al
The Lancet Infectious Diseases, 2021; 21(10) 1395-1406
DOI: 10.1016/S1473-3099(20)30929-4

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 et. al
The Lancet Infectious Diseases, 2021; 20 30929-4
DOI: 10.1016/S1473-3099(20)30929-4

26 May 2021
Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa
Benavente et al.
Nature Communications, 2021; 12(1) 3160
DOI: 10.1038/s41467-021-23422-3

25 May 2021
Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii
Wagah et al.
Malaria Journal, 2021; 20 234
DOI: 10.1186/s12936-021-03757-4

5 May 2021
Contemporary Ne estimation using temporally spaced data with linked loci
Hui et al.
Molecular Ecology Resources, 2021;
DOI: 10.1111/1755-0998.13412

28 Apr 2021
Population genomic evidence of Plasmodium vivax Southeast Asian origin
Daron et al.
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 et al
Malaria Journal, 2021; 20 129
DOI: 10.1186/s12936-021-03660-y

17 Mar 2021
Temporal evolution of sulfadoxine-pyrimethamine resistance genotypes and genetic diversity in response to a decade of increased interventions against Plasmodium falciparum in northern Ghana
Amenga-Etego, L.N. et al
Malaria Journal, 2021; 20(152)
DOI: 10.1186/s12936-021-03693-3

9 Mar 2021
Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning
Xue et al.
Mol Biol Evol, 2021; 38 1168-1183
DOI: 10.1093/molbev/msaa259

24 Feb 2021
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
MalariaGEN et. al
Wellcome Open Research, 2021; 6 42
DOI: 10.12688/wellcomeopenres.16168.1

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16 Feb 2021
The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii
Clarkson et al.
Molecular Ecology, 2021;
DOI: 10.1111/mec.15845

15 Feb 2021
Novel genotyping approaches to easily detect genomic admixture between the major Afrotropical malaria vector species, Anopheles coluzzii and An. gambiae
Caputo et al.
Molecular Ecology Resources, 2021;
DOI: 10.1111/1755-0998.13359

8 Feb 2021
Ag3: The Anopheles gambiae 1000 Genomes Project phase 3 data resource

2021;

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21 Jan 2021
Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus.
Grau-Bové et al.
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 et al
PLoS Pathogens, 2020; 16(12) e1009133
DOI: 10.1371/journal.ppat.1009133

1 Dec 2020
Genomic surveillance of Plasmodium falciparum and Plasmodium vivax cases at the University Hospital in Tegucigalpa, Honduras
Valdivia et al
Scientific Reports, 2020; 10 (1) 20975
DOI: 10.1038/s41598-020-78103-w

16 Nov 2020
Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast
Taylor et al.
PLoS Genetics, 2020; 16(11) e1009101
DOI: 10.1371/journal.pgen.1009101

12 Oct 2020
Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes
Ford et al.
PLoS Neglected Tropical Diseases, 2020; 14(10) e0008234
DOI: 10.1371/journal.pntd.0008234

1 Oct 2020
Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression
Grau-Bové et al.
Mol Biol Evol, 2020; 1 37
DOI: 10.1093/molbev/msaa128

28 Sep 2020
Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
The Anopheles gambiae 1000 Genomes Consortium
Genome Research, 2020; 30 1533-1546
DOI: 10.1101/gr.262790.120

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20 Aug 2020
Antimalarial drug resistance molecular makers of Plasmodium falciparum isolates from Sudan during 2015–2017
Hussien et al.
PLOS ONE, 2020; 15(8) e0235401
DOI: 10.1371/journal.pone.0235401

22 Jul 2020
Occurrence of septuple and elevated Pfdhfr-Pfdhps quintuple mutations in a general population threatens the use of sulfadoxine-pyrimethamine for malaria prevention during pregnancy in eastern coast of Tanzania
Bwire et al
BMC Infectious Diseases, 2020; 20 530
DOI: 10.1186/s12879-020-05253-7

9 Jul 2020
Genetic diversity and neutral selection in Plasmodium vivax erythrocyte binding protein correlates with patient antigenicity
Han et al.
PLoS Neglected Tropical Diseases, 2020; 14(7) e0008202
DOI: 10.1371/journal.pntd.0008202

21 May 2020
Efficacy of dihydroartemisinin/piperaquine and artesunate monotherapy for the treatment of uncomplicated Plasmodium falciparum malaria in Central Vietnam
Rovira-Vallbona E et al.
Journal of Antimicrobial Chemotherapy, 2020; 75 2272
DOI: 10.1093/jac/dkaa172

4 Mar 2020
Mapping the travel patterns of people with malaria in Bangladesh
Sinha et al.
BMC Medicine, 2020; 18(1) 45
DOI: 10.1186/s12916-020-1512-5

1 Mar 2020
Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain
van Dorp et al.
Molecular Biology and Evolution, 2020; 37(3) 773-785
DOI: 10.1093/molbev/msz264

26 Feb 2020
Detection of mutations associated with artemisinin resistance at k13- propeller gene and a near complete return of chloroquine susceptible falciparum malaria in Southeast of Tanzania
Bwire et al
Scientific Reports, 2020; 10 3500
DOI: 10.1038/s41598-020-60549-7

18 Feb 2020
Assessment of Plasmodium falciparum drug resistance molecular markers from the Blue Nile State, Southeast Sudan
Mohamed et al.
Malaria Journal, 2020; 19(1) 78
DOI: 10.1186/s12936-020-03165-0

13 Feb 2020
A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria
Diez Benavente et al.
PLoS Genetics, 2020; 16(2) e1008576
DOI: 10.1371/journal.pgen.1008576

5 Feb 2020
Mass drug administrations with dihydroartemisinin-piperaquine and single low dose primaquine to eliminate Plasmodium falciparum have only a transient impact on Plasmodium vivax: Findings from randomised controlled trials
Phommasone K et al.
PloS One, 2020; 15 e0228190
DOI: 10.1371/journal.pone.0228190

30 Jan 2020
Analysis of Plasmodium falciparum Rh2b deletion polymorphism across different transmission areas
Aniweh et al
Scientific Reports, 2020; 10(1) 1498
DOI: 10.1038/s41598-020-58300-3

18 Dec 2019
Intracluster correlation coefficients in the Greater Mekong Subregion for sample size calculations of cluster randomized malaria trials
Peerawaranun P et al.
Intracluster correlation coefficients in the Greater Mekong Subregion for sample size calculations of cluster randomized malaria trials, 2019; 18 428
DOI: 10.1186/s12936-019-3062-x

16 Dec 2019
Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania
MalariaGEN
Nature Communications, 2019; 10 5732
DOI: 10.1038/s41467-019-13480-z

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24 Sep 2019
A molecular barcode and online tool to identify and map imported infection with Plasmodium vivax
Trimarsanto et al.
bioRxiv, 2019; 776781
DOI: 10.1101/776781

1 Aug 2019
Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes
Lucas et al.
Genome Research, 2019;
DOI: 10.1101/gr.245795.118

9 Apr 2019
Robust Estimation of Recent Effective Population Size from Number of Independent Origins in Soft Sweeps
Khatri and Burt
Molecular Biology and Evolution, 2019;
DOI: 10.1093/molbev/msz081

2 Apr 2019
Mapping imported malaria in Bangladesh using parasite genetic and human mobility data
Chang et al.
eLife, 2019; 8 e43481
DOI: https://doi.org/10.7554/eLife.43481

15 Feb 2019
The impact of targeted malaria elimination with mass drug administrations on falciparum malaria in Southeast Asia: A cluster randomised trial
von Seidlein L et al
PLOS Medicine, 2019; 16 e1002745
DOI: 10.1371/journal.pmed.1002745

24 Jan 2019
Access to and use of preventive intermittent treatment for Malaria during pregnancy: A qualitative study in the Chókwè district, Southern Mozambique
Arnaldo P et al.
PLoS One, 2019; 14 e0203740
DOI: 10.1371/journal.pone.0203740

21 Jan 2019
Genomic analysis of Plasmodium vivax in southern Ethiopia reveals selective pressures in multiple parasite mechanisms.
Auburn et al.
The Journal of Infectious Diseases, 2019; 220 1738-1749
DOI: 10.1093/infdis/jiz016

17 Jan 2019
Tafenoquine versus Primaquine to Prevent Relapse of Plasmodium vivax Malaria
Llanos-Cuentas et al.
New England Journal of Medicine , 2019; 380(3) 229-241
DOI: 10.1056/NEJMoa1802537

17 Jan 2019
Single-Dose Tafenoquine to Prevent Relapse of Plasmodium vivax Malaria
Lacerda et al.
New England Journal of Medicine, 2019; 380(3) 215-228
DOI: 10.1056/NEJMoa1710775

17 Dec 2018
Host genetic polymorphisms and serological response against malaria in a selected population in Sri Lanka
Dewasurendra RL, Jeffreys A, Gunawardena SA, Chandrasekharan NV, Rockett K, Kwiatkowski D, & Karunaweera ND
Malaria Journal, 2018; 17 473
DOI: 10.1186/s12936-018-2622-9

4 Dec 2018
The origins of malaria artemisinin resistance defined by a genetic and transcriptomic background
Zhu l, Tripathi J, Rocamora FM, Miotto O, Van der Pluijm R, Voss TS, Mok S, Kwiatkowski DP, Nosten F, Day NPJ, White NJ, Dondorp AM & Bozdech Z.
Nature Communications, 2018; 9 5158
DOI: 10.1038/s41467-018-07588-x

3 Dec 2018
Prevalence of chloroquine and antifolate drug resistance alleles in Plasmodium falciparum clinical isolates from three areas in Ghana
Abugri et al
AAS Open Research, 2018; 1 1
DOI: 10.12688/aasopenres.12825.2

29 Nov 2018
A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways
Campino S, Marin-Menendez A, Kemp A, Cross N, Drought l, Otto TD, Benavente ED, Ravenhall M, Schwach F, Girling G, Manske M, Theron M, Gould K, Drury E, Clark TG, Kwiatkowski DP, Pance A & Rayner JC.
PLoS Pathogens, 2018; 4(11)
DOI: 10.1371/journal.ppat.1007436

26 Nov 2018
Lack of significant recovery of chloroquine sensitivity in Plasmodium falciparum parasites following discontinuance of chloroquine use in Papua New Guinea
Sekihara M et al.
Malaria Journal, 2018; 17 434
DOI: 10.1186/s12936-018-2585-x

25 Oct 2018
Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development
Duffy CW, Amambua-Ngwa A, Ahouidi AD, Diakite M, Awandare GA, Ba H, Tarr SJ, Murray l, Stewart lB, D'Alessandro U, Otto TD, Kwiatkowski DP & Conway DJ.
Scientific Reports, 2018; 8 15763
DOI: 10.1038/s41598-018-34078-3

23 Jul 2018
Antibodies to Intercellular Adhesion Molecule 1-Binding Plasmodium falciparum Erythrocyte Membrane Protein 1-DBLbeta Are Biomarkers of Protective Immunity to Malaria in a Cohort of Young Children from Papua New Guinea
Tessema et al
Infection and Immunity, 2018; 86 e00485-17
DOI: 10.1128/IAI.00485-17

19 Jul 2018
Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study
Ndila CM, Uyoga S, Macharia AW, Nyutu G, Peshu N, Ojal J, Shebe M, Awuondo KO, Mturi N, Tsofa B, Sepulveda N, Clark TG, Band G, Clarke G, Rowlands K, Hubbart C, Jeffreys A, Kariuki S, Marsh K, Mackinnon M, Maitland K, Kwiatkowski DP, Rockett KA & Williams TN.
The Lancet Haematology, 2018; 5
DOI: 10.1016/S2352-3026(18)30107-8

26 Jun 2018
Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from The Gambia
Amambua-Ngwa A, Jeffries D, Amato R, Worwui A, Karim M, Ceesay S, Nyang H, Nwakanma D, Okebe J, Kwiatkowski D, Conway D & D'Alessandro U.
Scientific Reports, 2018; 8 9687
DOI: 10.1038/s41598-018-28017-5

17 May 2018
Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics
Auburn S, Benavente ED, et al.
Nature Communications, 2018; 9 2585
DOI: 10.1038/s41467-018-04965-4

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12 May 2018
Effect of generalised access to early diagnosis and treatment and targeted mass drug administration on Plasmodium falciparum malaria in Eastern Myanmar: an observational study of a regional elimination programme
Landier et al
The Lancet, 2018; 391(10133) 1916-1926
DOI: 10.1016/S0140-6736(18)30792-X

25 Apr 2018
Two complement receptor one alleles have opposing associations with cerebral malaria and interact with alpha(+)thalassaemia
Opi DH, Swann O, Macharia A, Uyoga S, Band G, Ndila CM, Harrison EM, Thera MA, Kone AK, Diallo DA, Doumbo OK, lyke KE, Plowe CV, Moulds JM, Shebbe M, Mturi N, Peshu N, Maitland K, Raza A, Kwiatkowski DP, Rockett KA, Williams TN & Rowe JA.
eLife, 2018; 7
DOI: 10.7554/eLife.31579

12 Mar 2018
Uptake of intermittent preventive treatment and pregnancy outcomes: health facilities and community surveys in Chókwè district, southern Mozambique
Arnaldo P et al.
Malaria Journal, 2018; 17 109
DOI: 10.1186/s12936-018-2255-z

1 Feb 2018
Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study
Amato et. al
The Lancet Infectious Diseases, 2018; 18 337-345
DOI: 10.1016/S1473-3099(18)30068-9

29 Nov 2017
Genetic diversity of the African malaria vector Anopheles gambiae
The Anopheles gambiae 1000 Genomes Consortium
Nature, 2017;
DOI: 10.1038/nature24995

7 Nov 2017
Molecular markers for artemisinin and partner drug resistance in natural Plasmodium falciparum populations following increased insecticide treated net coverage along the slope of mount Cameroon: cross-sectional study
Apinjoh, Mugri et al.
Infectious Diseases of Poverty, 2017; 6 136
DOI: 10.1186/s40249-017-0350-y

6 Sep 2017
Safety and effectiveness of mass drug administration to accelerate elimination of artemisinin-resistant falciparum malaria: A pilot trial in four villages of Eastern Myanmar
Landier J et al
Wellcome Open Research, 2017; 2 81
DOI: 10.12688/wellcomeopenres.12240.1

22 Aug 2017
Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data
Zhu, Almagro-Garcia, McVean.
Bioinformatics, 2017;
DOI: 10.1093/bioinformatics/btx530

23 Jun 2017
Panoptes: web-based exploration of large scale genome variation data
Vauterin et al.
Bioinformatics, 2017;
DOI: 10.1093/bioinformatics/btx410

7 Jun 2017
Evidence from a natural experiment that malaria parasitemia is pathogenic in retinopathy-negative cerebral malaria
Small, Taylor et al.
eLife, 2017; 6 e2369
DOI: 10.7554/eLife.23699

25 May 2017
Malaria host candidate genes validated by association with current, recent and historic measures of transmission intensity
Sepúlveda, Manjurano et al.
The Journal of Infectious Diseases, 2017;
DOI: 10.1093/infdis/jix250

19 May 2017
Resistance to malaria through structural variation of red blood cell invasion receptors
Leffler, Band et al.
Science, 2017;
DOI: 10.1126/science.aam6393

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11 May 2017
Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure
Diez Benavente et al.
PLoS One, 2017; 12(5) e0177134
DOI: 10.1371/journal.pone.0177134

15 Mar 2017
Population genetic structure and adaptation of malaria parasites on the edge of endemic distribution
Duffy et al.
Molecular Ecology, 2017;
DOI: 10.1111/mec.14066

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26 Jan 2017
THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites
Chang, Worby et al.
PLoS Computational Biology, 2017; 13(1) e1005348
DOI: 10.1371/journal.pcbi.1005348

25 Jan 2017
Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution
Rutledge, Böhme et al.
Nature, 2017;
DOI: 10.1038/nature21038

24 Jan 2017
Culture adaptation of malaria parasites selects for convergent loss-of-function mutants
Claessens, Affara et al.
Scientific Reports, 2017; 7 41303
DOI: 10.1038/srep41303

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9 Jan 2017
Characterisation of the opposing effects of G6PD deficiency on cerebral malaria and severe malarial anaemia
Clarke, Rockett et al.
eLife, 2017; 6 e15085
DOI: 10.7554/eLife.15085

20 Dec 2016
Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification
Oyola et. al.
Malaria Journal, 2016; 15 597
DOI: 10.1186/s12936-016-1641-7

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19 Dec 2016
Extreme mutation bias and high AT content in Plasmodium falciparum
Hamilton, Claessens et al.
Nucleic Acids Research, 2016; pii gkw1259
DOI: 10.1093/nar/gkw1259

15 Nov 2016
A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
Auburn et al.
Wellcome Open Research, 2016; 1 4
DOI: 10.12688/wellcomeopenres.9876.1

3 Nov 2016
Genetic markers associated with dihydroartemisinin–piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype–phenotype association study
Amato, Lim, et al.
The Lancet Infectious Diseases, 2016;
DOI: 10.1016/S1473-3099(16)30409-1

15 Oct 2016
Genomic analysis reveals a common breakpoint in amplifications of the Plasmodium vivax multidrug resistance 1 locus in Thailand
Auburn et al.
The Journal of Infectious Diseases, 2016; 214 1235-1242
DOI: 10.1093/infdis/jiw323

14 Oct 2016
Independent origin and global distribution of distinct Plasmodium vivax Duffy Binding Protein gene duplications
Hostetler et al.
PLoS Neglected Tropical Diseases, 2016; 10(10) e0005091
DOI: 10.1371/journal.pntd.0005091

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16 Aug 2016
Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
Miles et al.
Genome Research, 2016; 26 1288-1299
DOI: 10.1101/gr.203711.115.

27 Jun 2016
Genomic analysis of local variation and recent evolution in Plasmodium vivax
Pearson et al
Nature Genetics, 2016; 48 959-964
DOI: 10.1038/ng.3599

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21 Jun 2016
Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing
Auburn et al.
PLoS One, 2013; 8(1) e53160
DOI: 10.1371/journal.pone.0053160

21 Jun 2016
Admixture into and within sub-Saharan Africa
Busby et al
eLife, 2016; 5:e15266
DOI: 10.7554/eLife.15266

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24 Mar 2016
Persistent Plasmodium falciparum and Plasmodium vivax infections in a western Cambodian population: implications for prevention, treatment and elimination strategies
Tripura R et al.
Persistent Plasmodium falciparum and Plasmodium vivax infections in a western Cambodian population: implications for prevention, treatment and elimination strategies, 2016; 15 181
DOI: 10.1186/s12936-016-1224-7

8 Mar 2016
The ethics of sustainable genomic research in Africa
Parker M, Kwiatkowski DP
Genome Biology, 2016; 17 44
DOI: 10.1186/s13059-016-0914-3

4 Mar 2016
Genomic epidemiology of artemisinin resistant malaria
MalariaGEN P. falciparum Community Project
eLife, 2016; 5 e08714
DOI: 10.7554/eLife.08714

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20 Oct 2015
Artemisinin-resistant Plasmodium falciparum clinical isolates can infect diverse mosquito vectors of Southeast Asia and Africa
St Laurent et al.
Nature Communications, 2015; 6 8614
DOI: 10.1038/ncomms9614

1 Oct 2015
A global reference for human genetic variation
1000 Genomes Project Consortium et al.
Nature, 2015; 526(7571) 68-74
DOI: 10.1038/nature15393

30 Sep 2015
A novel locus of resistance to severe malaria in a region of ancient balancing selection
Malaria Genomic Epidemiology Network
Nature, 2015; 526(7572) 253-257
DOI: 10.1038/nature15390

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28 Aug 2015
Genetic determinants of anti-malarial acquired immunity in a large multi-centre study
Shelton et al.
Malaria Journal, 2015; 14 333
DOI: 10.1186/s12936-015-0833-x

16 Jul 2015
Comparison of genomic signatures of selection on Plasmodium falciparum between different regions of a country with high malaria endemicity
Duffy et al.
BMC Genomics, 2015; 16 527
DOI: 10.1186/s12864-015-1746-3

16 Jun 2015
Understandings of genomic research in developing countries: a qualitative study of the views of MalariaGEN participants in Mali
Traore et al.
BMC Medical Ethics, 2015; 16 42
DOI: 10.1186/s12910-015-0035-7

15 Apr 2015
K13-propeller polymorphisms in Plasmodium falciparum parasites from sub-Saharan Africa
Kamau et al.
Journal of Infectious Diseases, 2015; 211(8) 1352-5
DOI: 10.1093/infdis/jiu608

24 Mar 2015
USP38, FREM3, SDC1, DDC, and LOC727982 Gene Polymorphisms and Differential Susceptibility to Severe Malaria in Tanzania
Manjurano et al.
Journal of Infectious Diseases, 2015; 212(7) 1129-39
DOI: 10.1093/infdis/jiv192

26 Feb 2015
Malaria genomics: tracking a diverse and evolving parasite population
Kwiatkowski
International Health, 2015; 7(2) 82-84
DOI: 10.1093/inthealth/ihv007

23 Feb 2015
Novel Insights Into the Protective Role of Hemoglobin S and C Against Plasmodium falciparum Parasitemia
Mangano et al.
Journal of Infectious Diseases, 2015; 212(4) 626-34
DOI: 10.1093/infdis/jiv098

22 Feb 2015
G6PD gene variants and its association with malaria in a Sri Lankan population
Dewasurendra et al.
Malaria Journal, 2015; 14 93
DOI: 10.1186/s12936-015-0603-9

11 Feb 2015
African glucose-6-phosphate dehydrogenase alleles associated with protection from severe malaria in heterozygous females in Tanzania
Manjurano et al.
PloS Genetics, 2015; 11(2) e1004960
DOI: 10.1371/journal.pgen.1004960

23 Jan 2015
Population transcriptomics of human malaria parasites reveals the mechanism of artemisinin resistance
Mok et al.
Science, 2015; 347(6220) 431-5
DOI: 10.1126/science.1260403

19 Jan 2015
Genetic architecture of artemisinin-resistant Plasmodium falciparum
Miotto et al
Nature Genetics, 2015; 47(3) 226-34
DOI: 10.1038/ng.3189

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15 Dec 2014
Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates
Ocholla et al.
Journal of Infectious Diseases, 2014; 210(12) 1991-2000
DOI: 10.1093/infdis/jiu349

28 Sep 2014
Reappraisal of known malaria resistance loci in a large multi-centre study
Rockett et al.
Nature Genetics, 2014; 46(11) 1197-204
DOI: 10.1038/ng.3107

18 Sep 2014
Optimized whole-genome amplification strategy for extremely AT-biased template
Oyola et al.
DNA Research, 2014; 21(6) 661-71
DOI: 10.1093/dnares/dsu028

12 Sep 2014
Monitoring parasite diversity for malaria elimination in sub-Saharan Africa
Ghansah et al.
Science, 2014; 345(6202) 1297-8
DOI: 10.1126/science.1259423

9 Sep 2014
Genetic determinants of glucose-6-phosphate dehydrogenase activity in Kenya
Shah et al.
BMC Medical Genetics, 2014; 15 93
DOI: 10.1186/s12881-014-0093-6

1 Sep 2014
Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia
Takala-Harrison et al.
Journal of Infectious Diseases, 2014; 211(5) 670-9
DOI: 10.1093/infdis/jiu491

13 Aug 2014
Knowing who to trust: exploring the role of 'ethical metadata' in mediating risk of harm in collaborative genomics research in Africa
de Vries et al.
BMC Medical Ethics, 2014; 15 62
DOI: 10.1186/1472-6939-15-62

31 Jul 2014
Spread of artemisinin resistance in Plasmodium falciparum malaria
Ashley et al.
New England Journal of Medicine, 2014; 371(5) 411-23
DOI: 10.1056/NEJMoa1314981

11 Jul 2014
Glucose-6-phosphate dehydrogenase polymorphisms and susceptibility to mild malaria in Dogon and Fulani, Mali
Maiga et al.
Malaria Journal, 2014; 13 270
DOI: 10.1186/1475-2875-13-270

25 Jun 2014
Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation
Clarkson et al.
Nature Communications, 2014; 5 4248
DOI: 10.1038/ncomms5248

16 Jun 2014
Association of candidate gene polymorphisms and TGF-beta/IL-10 levels with malaria in three regions of Cameroon: a case-control study
Apinjoh et al.
Malaria Journal, 2014; 13 236
DOI: 10.1186/1475-2875-13-236

13 Jun 2014
A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains
Preston et al.
Nature Communications, 2014; 5 4052
DOI: 10.1038/ncomms5052

27 May 2014
Plasmodium falciparum founder populations in western Cambodia have reduced artemisinin sensitivity in vitro
Amaratunga et al.
Antimicrob Agents Chemother, 2014; 58(8) 4935-7
DOI: 10.1128/AAC.03055-14

8 May 2014
A genome wide association study of Plasmodium falciparum susceptibility to 22 antimalarial drugs in Kenya
Wendler et al.
PLoS One, 2014; 9(5) e96486
DOI: 10.1371/journal.pone.0096486

23 Feb 2014
A transcriptional switch underlies commitment to sexual development in malaria parasites
Kafsack et al.
Nature, 2014; 507(7491) 248-52
DOI: 10.1038/nature12920

2 Jan 2014
A molecular marker of artemisinin-resistant Plasmodium falciparum malaria
Ariey et al.
Nature, 2014; 505(7481) 50-5
DOI: 10.1038/nature12876

27 Nov 2013
Association of cytokine and Toll-like receptor gene polymorphisms with severe malaria in three regions of Cameroon
Apinjoh et al.
PLoS One, 2013; 8(11) e81071
DOI: 10.1371/journal.pone.0081071

2 Oct 2013
Human candidate polymorphisms in sympatric ethnic groups differing in malaria susceptibility in Mali
Maiga et al.
PLoS One, 2013; 8(10) e75675
DOI: 10.1371/journal.pone.0075675

12 Aug 2013
Ex vivo susceptibility of Plasmodium falciparum to antimalarial drugs in western, northern, and eastern Cambodia, 2011-2012: association with molecular markers
Lim et al.
Antimicrob Agents Chemother, 2013; 57(11) 5277-83
DOI: 10.1128/AAC.00687-13

23 May 2013
Imputation-based meta-analysis of severe malaria in three African populations
Band et al.
PloS Genetics, 2013; 9(5) e1003509
DOI: 10.1371/journal.pgen.1003509

28 Apr 2013
Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia
Miotto et al
Nature Genetics, 2013; 45(6) 648-55
DOI: 10.1038/ng.2624

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24 Apr 2013
The genetic risk of acute seizures in African children with falciparum malaria
Kariuki et al.
Epilepsia, 2013; 54(6) 990-1001
DOI: 10.1111/epi.12173

2 Jan 2013
Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia
Takala-Harrison et al.
Proc Natl Acad Sci USA, 2013; 110(1) 240-5
DOI: 10.1073/pnas.1211205110

1 Nov 2012
Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites
Amambua-Ngwa et al.
PLoS Genetics, 2012; 8(11) e1002992
DOI: 10.1371/journal.pgen.1002992

29 Oct 2012
Candidate human genetic polymorphisms and severe malaria in a Tanzanian population
Manjurano et al.
PLoS One, 2012; 7(10) e47463
DOI: 10.1371/journal.pone.0047463

5 Sep 2012
Candidate polymorphisms and severe malaria in a Malian population
Toure et al.
PLoS One, 2012; 7(9) e43987
DOI: 10.1371/journal.pone.0043987

4 Sep 2012
Reduced Risk of Plasmodium vivax Malaria in Papua New Guinean Children with Southeast Asian Ovalocytosis in Two Cohorts and a Case-Control Study
Rosanas-Urgell et al.
PLoS Medicine, 2012; 9(9) e1001305
DOI: 10.1371/journal.pmed.1001305

1 Sep 2012
Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese
Dunstan et al.
Genes Immunology, 2012; 13(6) 503-8
DOI: 10.1038/gene.2012.25

20 Aug 2012
Genetic polymorphisms associated with anti-malarial antibody levels in a low and unstable malaria transmission area in southern Sri Lanka
Dewasurendra et al.
Malaria Journal, 2012; 11 281
DOI: doi:10.1186/1475-2875-11-281

19 Jul 2012
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
Manske et al.
Nature, 2012; 487(7407) 375-9
DOI: 10.1038/nature11174

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2 Jul 2012
Seeking consent to genetic and genomic research in a rural Ghanaian setting: a qualitative study of the MalariaGEN experience
Tindana et al.
BMC Medical Ethics, 2012; 13 15
DOI: 10.1186/1472-6939-13-15

24 Jun 2012
Severe and uncomplicated falciparum malaria in children from three regions and three ethnic groups in Cameroon: prospective study
Achidi et al.
Malaria Journal, 2012; 11 215
DOI: 10.1186/1475-2875-11-215

16 Jun 2012
Investigating the potential for ethnic group harm in collaborative genomics research in Africa: is ethnic stigmatisation likely?
de Vries et al.
Social Science & Medicine, 2012; 75(8) 1400-7
DOI: 10.1016/j.socscimed.2012.05.020

7 Jun 2012
Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese
Dunstan SJ et al
Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese, 2012; 13(6) 503-8
DOI: 10.1038/gene.2012.25

29 Feb 2012
Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data
Auburn et al
PLoS One, 2012; 7(2) e32891
DOI: 10.1371/journal.pone.0032891

10 Feb 2012
Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum-infected whole blood samples
Venkatesan et al.
Malaria Journal, 2012; 11 41
DOI: 10.1186/1475-2875-11-41

18 Nov 2011
Ethical issues in human genomics research in developing countries
de Vries et al.
BMC Medical Ethics, 2011; 12 5
DOI: 10.1186/1472-6939-12-5

11 Aug 2011
Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients
Robinson et al.
PLoS One, 2011; 6(8) e23204
DOI: 10.1371/journal.pone.0023204

18 Jul 2011
An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing
Auburn et al.
PLoS One, 2011; 6(7) e22213
DOI: 10.1371/journal.pone.0022213

6 Jun 2011
Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay
Campino S et al.
PLoS One, 2011; 6(6) e20251
DOI: 10.1371/journal.pone.0020251

5 Nov 2010
Measuring the efficacy of anti-malarial drugs in vivo: quantitative PCR measurement of parasite clearance
Beshir et al.
Malaria Journal, 2010; 9 312
DOI: 10.1186/1475-2875-9-312

2 Nov 2010
Global distribution of the sickle cell gene and geographical confirmation of the malaria hypothesis
Piel et al.
Nature Communications, 2010; 1 104
DOI: 10.1038/ncomms1104

1 Feb 2010
Methodological challenges of genome-wide association analysis in Africa
Teo et al.
Nature Reviews Genetics, 2010; 11(2) 149-60
DOI: 10.1038/nrg2731

24 Nov 2009
Ethical data-release in genome-wide association studies in developing countries
Parker et al.
PLoS Medicine, 2009; 6(11) e1000143
DOI: 10.1371/journal.pmed.1000143

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24 May 2009
Genome-wide and fine-resolution association analysis of malaria in West Africa
Jallow et al.
Nature Genetics, 2009; 41(6) 657-65
DOI: 10.1038/ng.388

11 Dec 2008
A global network for investigating the genomic epidemiology of malaria
Malaria Genomic Epidemiology Network
Nature, 2008; 456(7223) 732-7
DOI: 10.1038/nature07632

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24 Apr 2007
Valid consent for genomic epidemiology in developing countries
Chokshi et al.
PLoS Medicine, 2007; 4(4) e95
DOI: DOI: 10.1371/journal.pmed.0040095

23 Mar 2006
Standardized data collection for multi-center clinical studies of severe malaria in African children: establishing the SMAC network
Taylor et al.
Transactions of the Royal Society of Tropical Medicine & Hygiene, 2006; 100(7) 615-22
DOI: doi: 10.1016/j.trstmh.2005.09.021