J. Adams, R. Kelso, and L. Cooley, The kelch repeat superfamily of proteins: propellers of cell function, Trends in Cell Biology, vol.10, pp.17-24, 2000.

F. Ariey, B. Witkowski, C. Amaratunga, J. Beghain, A. Langlois et al., A molecular marker of artemisinin-resistant plasmodium falciparum malaria, Nature, vol.505, pp.50-55, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-00921203

E. A. Ashley, M. Dhorda, R. M. Fairhurst, C. Amaratunga, P. Lim et al., Tracking Resistance to Artemisinin Collaboration (TRAC)Tracking Resistance to Artemisinin Collaboration (TRAC)Tracking Resistance to Artemisinin Collaboration (TRAC), Spread of artemisinin resistance in plasmodium falciparum malaria, vol.371, pp.411-423, 2014.

S. Auburn, S. Campino, T. G. Clark, A. A. Djimde, I. Zongo et al., An effective method to purify plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing, PLoS ONE, vol.6, 2011.

D. R. Bentley, S. Balasubramanian, H. P. Swerdlow, G. P. Smith, J. Milton et al., Accurate whole human genome sequencing using reversible terminator chemistry, vol.456, pp.53-59, 2008.

K. Brick and E. Pizzi, A novel series of compositionally biased substitution matrices for comparing plasmodium proteins, BMC Bioinformatics, vol.9, p.236, 2008.

A. Claessens, W. L. Hamilton, M. Kekre, T. D. Otto, A. Faizullabhoy et al., Generation of antigenic diversity in plasmodium falciparum by structured rearrangement of var genes during mitosis, PLoS Genetics, vol.10, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01989273

C. Dogovski, S. C. Xie, G. Burgio, J. Bridgford, S. Mok et al., Targeting the cell stress response of plasmodium falciparum to overcome artemisinin resistance, PLOS Biology, vol.13, 2015.

A. M. Dondorp, F. Nosten, P. Yi, D. Das, A. P. Phyo et al., Artemisinin resistance in plasmodium falciparum malaria, New England Journal of Medicine, vol.361, pp.455-467, 2009.

A. M. Dondorp and P. Ringwald, Artemisinin resistance is a clear and present danger, Trends in Parasitology, vol.29, pp.359-360, 2013.

A. A. Escalante and F. J. Ayala, Evolutionary origin of plasmodium and other apicomplexa based on rRNA genes, Proceedings of the National Academy of Sciences of the United States of America, vol.92, pp.5793-5797, 1995.

J. A. Flegg, P. J. Guerin, N. J. White, and K. Stepniewska, Standardizing the measurement of parasite clearance in falciparum malaria: the parasite clearance estimator, Malaria Journal, vol.10, p.339, 2011.

K. B. Gardner, I. Sinha, L. Y. Bustamante, N. Day, N. J. White et al., Protein-based signatures of functional evolution in plasmodium falciparum, BMC Evolutionary Biology, vol.11, p.257, 2011.

N. R. Garud, P. W. Messer, E. O. Buzbas, D. A. Petrov, and G. P. Copenhaver, Recent selective sweeps in north american drosophila melanogaster show signatures of soft sweeps, PLOS Genetics, vol.11, 2015.

M. Ghorbal, M. Gorman, C. R. Macpherson, R. M. Martins, A. Scherf et al., Genome editing in the human malaria parasite plasmodium falciparum using the CRISPR-Cas9 system, Nature Biotechnology, vol.32, pp.819-821, 2014.

J. C. Gower, Some distance properties of latent root and vector methods used in multivariate analysis, Biometrika, vol.53, pp.325-338, 1966.

I. M. Hastings, Malaria control and the evolution of drug resistance: an intriguing link, Trends in Parasitology, vol.19, pp.70-73, 2003.

S. Henikoff and J. G. Henikoff, Amino acid substitution matrices from protein blocks, Proceedings of the National Academy of Sciences of the United States of America, vol.89, pp.10915-10919, 1992.

J. Hermisson and P. S. Pennings, Soft sweeps: molecular population genetics of adaptation from standing genetic variation, Genetics, vol.169, pp.2335-2352, 2005.

T. Hien, N. Thuy-nhien, N. Phu, M. F. Boni, N. Thanh et al., In vivo susceptibility of plasmodium falciparum to artesunate in binh phuoc province, vietnam, Malaria Journal, vol.11, p.355, 2012.

H. Sibley and C. , Artemisinin resistance: the more we know, the more complicated it appears, Journal of Infectious Diseases, vol.211, pp.667-669, 2015.

J. D. Jensen, On the unfounded enthusiasm for soft selective sweeps, Nature Communications, vol.5, p.5281, 2014.

D. A. Joy, X. Feng, J. Mu, T. Furuya, K. Chotivanich et al., Early origin and recent expansion of plasmodium falciparum, Science, vol.300, pp.318-321, 2003.

E. Kamau, S. Campino, L. Amenga-etego, E. Drury, D. Ishengoma et al., K13-propeller polymorphisms in plasmodium falciparum parasites from sub-saharan africa, The Journal of Infectious Diseases, vol.211, pp.1352-1355, 2015.

M. P. Kyaw, M. H. Nyunt, K. Chit, M. M. Aye, K. H. Aye et al., Reduced susceptibility of plasmodium falciparum to artesunate in southern myanmar, PLoS ONE, vol.8, p.57689, 2013.

J. Kyte and R. F. Doolittle, A simple method for displaying the hydropathic character of a protein, Journal of Molecular Biology, vol.157, pp.105-132, 1982.

M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. Mcgettigan et al., Clustal w and clustal x version 2.0, Bioinformatics, vol.23, pp.2947-2948, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00206210

D. J. Lawson, G. Hellenthal, S. Myers, D. Falush, and G. P. Copenhaver, Inference of population structure using dense haplotype data, PLoS Genetics, vol.8, p.1002453, 2012.

H. Li and R. Durbin, Fast and accurate short read alignment with burrows-wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009.

H. M. Manske and D. P. Kwiatkowski, SNP-o-matic, Bioinformatics, vol.25, pp.2434-2435, 2009.

M. Manske, O. Miotto, S. Campino, S. Auburn, J. Almagro-garcia et al., Analysis of plasmodium falciparum diversity in natural infections by deep sequencing, Nature, vol.487, pp.375-379, 2012.

A. Mbengue, S. Bhattacharjee, T. Pandharkar, H. Liu, G. Estiu et al., A molecular mechanism of artemisinin resistance in plasmodium falciparum malaria, Nature, vol.520, pp.683-687, 2015.

P. W. Messer and D. A. Petrov, Population genomics of rapid adaptation by soft selective sweeps, Trends in Ecology & Evolution, vol.28, pp.659-669, 2013.

O. Miotto, J. Almagro-garcia, M. Manske, B. Macinnis, S. Campino et al., Multiple populations of artemisinin-resistant plasmodium falciparum in cambodia, Nature Genetics, vol.45, pp.648-655, 2013.

O. Miotto, R. Amato, E. A. Ashley, B. Macinnis, J. Almagro-garcia et al., Genetic architecture of artemisininresistant plasmodium falciparum, Nature Genetics, vol.47, pp.226-234, 2015.

T. Mita, K. Tanabe, and K. Kita, Spread and evolution of plasmodium falciparum drug resistance, Parasitology International, vol.58, pp.201-209, 2009.

S. Mok, E. A. Ashley, P. E. Ferreira, L. Zhu, Z. Lin et al., Population transcriptomics of human malaria parasites reveals the mechanism of artemisinin resistance, Science, vol.347, pp.431-435, 2015.

J. Mu, P. Awadalla, J. Duan, K. M. Mcgee, D. A. Joy et al., Recombination hotspots and population structure in plasmodium falciparum, PLoS Biology, vol.3, p.335, 2005.

S. Nair, D. Nash, D. Sudimack, A. Jaidee, M. Barends et al., Recurrent gene amplification and soft selective sweeps during evolution of multidrug resistance in malaria parasites, Molecular Biology and Evolution, vol.24, pp.562-573, 2007.

R. Nielsen, M. J. Hubisz, I. Hellmann, D. Torgerson, A. M. Andres et al., Darwinian and demographic forces affecting human protein coding genes, Genome Research, vol.19, pp.838-849, 2009.

P. S. Pennings and J. Hermisson, Soft sweeps II-molecular population genetics of adaptation from recurrent mutation or migration, Molecular Biology and Evolution, vol.23, pp.1076-1084, 2006.

A. P. Phyo, S. Nkhoma, K. Stepniewska, E. A. Ashley, S. Nair et al., Emergence of artemisinin-resistant malaria on the western border of thailand: a longitudinal study, The Lancet, vol.379, issue.12, p.60484, 2012.

F. Prugnolle, P. Durand, R. F. Rousset, and F. , Effective size of the hierarchically structured populations of the agent of malaria: a coalescent-based model, Heredity, vol.104, pp.371-377, 2010.

P. Salgueiro, J. L. Vicente, C. Ferreira, V. Teó-filo, . Galvã-o-a,-do-rosá-rio et al., Tracing the origins and signatures of selection of antifolate resistance in island populations of plasmodium falciparum, BMC Infectious Diseases, vol.10, p.163, 2010.

D. L. Saunders, P. Vanachayangkul, C. Lon, and U. S. , Army Military Malaria Research Program, National Center for Parasitology, Entomology, and Malaria Control (CNM), Royal Cambodian Armed Forces, 2014.

, Dihydroartemisinin-piperaquine failure in cambodia, New England Journal of Medicine, vol.371, pp.484-485

J. Straimer, N. F. Gnadig, B. Witkowski, C. Amaratunga, V. Duru et al., K13-propeller mutations confer artemisinin resistance in plasmodium falciparum clinical isolates, Science, vol.347, pp.428-431, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01925134

S. Takala-harrison, C. G. Jacob, C. Arze, M. P. Cummings, J. C. Silva et al., Independent emergence of artemisinin resistance mutations among plasmodium falciparum in southeast asia, Journal of Infectious Diseases, vol.211, pp.670-679, 2015.

K. Tanabe, T. Mita, T. Jombart, A. Eriksson, S. Horibe et al., Plasmodium falciparum accompanied the human expansion out of africa, Current Biology, vol.20, pp.1283-1289, 2010.

S. M. Taylor, C. M. Parobek, D. K. Deconti, K. Kayentao, S. O. Coulibaly et al., Absence of putative artemisinin resistance mutations among plasmodium falciparum in sub-saharan africa: a molecular epidemiologic study, Journal of Infectious Diseases, vol.211, pp.680-688, 2015.

M. Venkatesan, C. Amaratunga, S. Campino, S. Auburn, O. Koch et al., Using CF11 cellulose columns to inexpensively and effectively remove human DNA from plasmodium falciparum-infected whole blood samples, Malaria Journal, vol.11, p.41, 2012.

B. Witkowski, C. Amaratunga, N. Khim, S. Sreng, P. Chim et al., Novel phenotypic assays for the detection of artemisinin-resistant plasmodium falciparum malaria in cambodia: invitro and ex-vivo drug-response studies, The Lancet Infectious Diseases, vol.13, issue.13, pp.70252-70256, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-00863935

, Update on Artemisinin Resistance, 2014.

, World Health Organization, 2014.