Publications

Latest publications

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 SK, Utama D, Chesnokov O, Hodder AN, Lin CS, Harrison GLA, Jespersen JS, Petersen B, Tavul L, Siba P, Kwiatkowski D, Lavstsen T, Hansen DS, Oleinikov AV, Mueller I & Barry AE.
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, Miotto O, Pearson RD, Amato R, Grigg MJ, Barber B, William T, Handayuni I, Marfurt J, Trimarsanto H, Noviyanti R, Sriprawat K, Nosten F, Campino S, Clark TG, Anstey NA, Kwiatkowski DP, Price RN
Nature Communications 2018 9 2585 DOI: 10.1038/s41467-018-04965-4
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, Rovira-Vallbona E, Langa JS, Salvador C, Guetens P, Chiheb D, Xavier B, Kestens L, Enosse SM, Rosanas-Urgell A.
Malaria Journal 2018 17 109 DOI: 10.1186/s12936-018-2255-z
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 TO, Mugri RN, Miotto O, Chi HF, Tata RB, Anchang-Kimbi JK, Fon EM, Tangoh DA, Nyingchu RV, Jacob C, Amato R, Djimde A, Kwiatkowski D, Achidi EA, Amambua-Ngwa A.
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, Kajeechiwa L, Thwin MM, Parker DM, Chaumeau V, Wiladphaingern J, Imwong M, Miotto O, Patumrat K, Duanguppama J, Cerqueira D, Malleret B, Rénia L, Nosten S, von Seidlein L, Ling C, Proux S, Corbel V, Simpson JA, Dondorp AM, White NJ, Nosten FH.
Wellcome Open Research 2017 2 81 DOI: https://doi.org/10.12688/wellcomeopenres.12240.1
22 Aug 2017

Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data

Zhu SJ, Almagro-Garcia J, McVean G.
Bioinformatics 2017 DOI: 10.1093/bioinformatics/btx530
23 Jun 2017

Panoptes: web-based exploration of large scale genome variation data

Vauterin P, Jeffery B, Miles A, Amato R, Hart L, Wright I, Kwiatkowski D
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 DS, Taylor TE, Postels DG, Beare NA, Cheng J, MacCormick IJ, Seydel KB
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 N, Manjurano A, Campino SG, Lemnge M, Lusingu J, Olomi R, Rockett KA, Hubbart C, Jeffreys A, Rowlands K; MalariaGen consortium, Clark TG, Riley EM, Drakeley CJ
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 EM, Band G, Busby GBJ, Kivinen K, Le SQ, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Hugh Reyburn H, Eleanor Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius VJ, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP, Malaria Genomic Epidemiology Network
Science 2017 DOI: 10.1126/science.aam6393
19 May 2017

Resistance to malaria through structural variation of red blood cell invasion receptors

Leffler EM, Band G, Busby GBJ, Kivinen K, Le SQ, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Hugh Reyburn H, Eleanor Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius VJ, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP, Malaria Genomic Epidemiology Network
Science 2017 DOI: 10.1126/science.aam6393
11 May 2017

Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure

Diez Benavente E, Ward Z, Chan W, Mohareb FR, Sutherland CJ, Roper C, Campino S, Clark TG.
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 CW, Ba H, Assefa S, Ahouidi AD, Deh YB, Tandia A, Kirsebom FC, Kwiatkowski DP, Conway DJ
Molecular Ecology 2017 DOI: 10.1111/mec.14066
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 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, Greenhouse B
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 GG, Böhme U, Sanders M, Reid AJ, Cotton JA, Maiga-Ascofare O, Djimdé AA, Apinjoh TO, Amenga-Etego L, Manske M, Barnwell JW, Renaud F, Ollomo B, Prugnolle F, Anstey NM, Auburn S, Price RN, McCarthy JS, Kwiatkowski DP, Newbold C, Berriman M, Otto TD
Nature 2017 DOI: 10.1038/nature21038
24 Jan 2017

Culture adaptation of malaria parasites selects for convergent loss-of-function mutants

Claessens A, Affara M, Assefa SA, Kwiatkowski DP, Conway DJ
Scientific Reports 2017 7 41303 DOI: 10.1038/srep41303
9 Jan 2017

Characterisation of the opposing effects of G6PD deficiency on cerebral malaria and severe malarial anaemia

Clarke GM, Rockett K, Kivinen K, Hubbart C, Jeffreys AE, Rowlands K, Jallow M, Conway DJ, Bojang KA, Pinder M, Usen S, Sisay-Joof F, Sirugo G, Toure O, Thera MA, Konate S, Sissoko S, Niangaly A, Poudiougou B, Mangano VD, Bougouma EC, Sirima SB, Modiano D, Amenga-Etego LN, Ghansah A, Koram KA, Wilson MD, Enimil A, Evans J, Amodu OK, Olaniyan S, Apinjoh T, Mugri R, Ndi A, Ndila CM, Uyoga S, Macharia A, Peshu N, Williams TN, Manjurano A, Sepúlveda N, Clark TG, Riley E, Drakeley C, Reyburn H, Nyirongo V, Kachala D, Molyneux M, Dunstan SJ, Hoan Phu N, Ngoc Quyen N, Quang Thai C, Tinh Hien T, Manning L, Laman M, Siba P, Karunajeewa H, Allen S, Allen A, Davis TME, Michon P, Mueller I Molloy SF, Campino S, Kerasidou A, Cornelius VJ, Hart L, Shah SS, Band G, Spencer CCA, Agbenyega T, Achidi E, Doumbo OK, Farrar J, Marsh K, Taylor T, Kwiatkowski DP, MalariaGEN Consortium
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 SO, Ariani CV, Hamilton W, Kekre M, Amenga-Etego L, Ghansah A, Rutledge GR, Redmond S, Manske M, Jyothi D, Jacob CG, Otto T, Rockett K, Newbold CI, Berriman M, Kwiatkowski P
Malaria Journal 2016 15 597 DOI: 10.1186/s12936-016-1641-7
20 Dec 2016

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

Oyola SO, Ariani CV, Hamilton W, Kekre M, Amenga-Etego L, Ghansah A, Rutledge GR, Redmond S, Manske M, Jyothi D, Jacob CG, Otto T, Rockett K, Newbold CI, Berriman M, Kwiatkowski P
Malaria Journal 2016 15 597 DOI: 10.1186/s12936-016-1641-7
19 Dec 2016

Extreme mutation bias and high AT content in Plasmodium falciparum

Hamilton WL, Claessens A, Otto TD, Kekre M, Fairhurst RM, Rayner JC, Kwiatkowski D
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 S, Böhme U, Steinbiss S, Trimarsanto H, Hostetler J, Sanders M, Gao Q, Nosten F, Newbold CI, Berriman M, Price RN, Otto TD.
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 R, Lim P, Miotto O, Amaratunga C, Dek D, Pearson RD, Almagro-Garcia J, Neal AT, Sreng S, Suon S, Drury E, Jyothi D, Stalker J, Kwiatkowski DP, Fairhurst RM
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 S, Serre D, Pearson RD, Amato R, Sriprawat K, To S, Handayuni I, Suwanarusk R, Russell B, Drury E, Stalker J, Miotto O, Kwiatkowski DP, Nosten F, Price RN.
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 JB, Lo E, Kanjee U, Amaratunga C, Suon S, Sreng S, Mao S, Yewhalaw D, Mascarenhas A, Kwiatkowski DP, Ferreira MU, Rathod PK, Yan G, Fairhurst RM, Duraisingh MT, Rayner JC
PLoS Neglected Tropical Diseases 2016 10(10) e0005091 DOI: 10.1371/journal.pntd.0005091
16 Aug 2016

Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum

Miles A, Iqbal Z, Vauterin P, Pearson R, Campino S, Theron M, Gould K, Mead D, Drury E, O'Brien J, Ruano Rubio V, MacInnis B, Mwangi J, Samarakoon U, Ranford-Cartwright L, Ferdig M, Hayton K, Su XZ, Wellems T, Rayner J, McVean G, Kwiatkowski D
Genome Research 2016 26 1288-1299 DOI: 10.1101/gr.203711.115.
21 Jun 2016

Admixture into and within sub-Saharan Africa

Busby G, Band G, Le SQ, Jallow M, Bougama E, Mangano V, Amenga-Etego L, Emil A, Apinjoh T, Ndila C, Manjurano A, Nyirongo V, Doumbo O, Rockett K, Kwiatkowski D, Spencer C, The Malaria Genomic Epidemiology Network
eLife 2016 5:e15266 DOI: 10.7554/eLife.15266
24 Mar 2016

Persistent Plasmodium falciparum and Plasmodium vivax infections in a western Cambodian population: implications for prevention, treatment and elimination strategies

Tripura R, Peto TJ, Chalk J, Lee SJ, Sirithiranont P, Nguon C, Dhorda M, von Seidlein L, Maude RJ, Day NP, Imwong M, White NJ, Dondorp AM.
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