E. Ashley, M. Dhorda, R. Fairhurst, C. Amaratunga, P. Lim et al., Malaria, New England Journal of Medicine, vol.371, issue.5, pp.411-434, 2014.
DOI : 10.1056/NEJMoa1314981

URL : https://hal.archives-ouvertes.fr/inserm-00903747

F. Huang, S. Takala-harrison, C. Jacob, H. Liu, X. Sun et al., Following Artemisinin Treatment, Journal of Infectious Diseases, vol.212, issue.10, pp.1629-1664, 2015.
DOI : 10.1093/infdis/jiv249

C. Amaratunga, B. Witkowski, N. Khim, D. Menard, and R. Fairhurst, Artemisinin resistance in Plasmodium falciparum, The Lancet Infectious Diseases, vol.14, issue.6, pp.449-50, 2014.
DOI : 10.1016/S1473-3099(14)70777-7

S. Takala-harrison, C. Jacob, C. Arze, M. Cummings, J. Silva et al., Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia, The Journal of Infectious Diseases, vol.211, issue.5, pp.670-679, 2015.
DOI : 10.1093/infdis/jiu491

M. Nyunt, T. Hlaing, H. Oo, L. Tin-oo, H. Phway et al., Molecular Assessment of Artemisinin Resistance Markers, Polymorphisms in the K13 Propeller, and a Multidrug-Resistance Gene in the Eastern and Western Border Areas of Myanmar, Clinical Infectious Diseases, vol.60, issue.8, pp.1208-1223, 2015.
DOI : 10.1093/cid/ciu1160

D. Ménard, N. Khim, J. Beghain, A. Adegnika, M. Shafiul-alam et al., K13-Propeller Polymorphisms, New England Journal of Medicine, vol.374, issue.25, pp.2453-64, 2016.
DOI : 10.1056/NEJMoa1513137

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, issue.7407, pp.375-384, 2012.
DOI : 10.1186/1471-2164-13-1

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.89, issue.6, pp.648-55, 2013.
DOI : 10.1101/gr.094052.109

A. Dwivedi, N. Khim, C. Reynes, P. Ravel, L. Ma et al., Plasmodium falciparum parasite population structure and gene flow associated to anti-malarial drugs resistance in Cambodia, Malaria Journal, vol.59, issue.1, p.319, 2016.
DOI : 10.1128/AAC.00366-15

F. Ariey, B. Witkowski, C. Amaratunga, J. Beghain, A. Langlois et al., A molecular marker of artemisinin-resistant Plasmodium falciparum malaria, Nature, vol.10, issue.7481, pp.50-55, 2014.
DOI : 10.1038/nsb899

URL : https://hal.archives-ouvertes.fr/pasteur-00921203

M. Imwong, K. Suwannasin, C. Kunasol, K. Sutawong, M. Mayxay et al., The spread of artemisinin-resistant Plasmodium falciparum in the Greater Mekong subregion: a molecular epidemiology observational study, The Lancet Infectious Diseases, vol.17, issue.5, pp.491-498, 2017.
DOI : 10.1016/S1473-3099(17)30048-8

A. Phyo, E. Ashley, T. Anderson, Z. Bozdech, V. Carrara et al., Malaria on the Thai???Myanmar Border (2003???2013): The Role of Parasite Genetic Factors, Clinical Infectious Diseases, vol.63, issue.6, pp.784-91, 2003.
DOI : 10.1093/cid/ciw388

T. Mita and K. Tanabe, Evolution of Plasmodium falciparum drug resistance: implications for the development and containment of artemisinin resistance, Japanese Journal of Infectious Diseases, vol.65, issue.6, pp.465-75, 2012.
DOI : 10.7883/yoken.65.465

T. Mita, K. Tanabe, and K. Kita, Spread and evolution of Plasmodium falciparum drug resistance, Parasitology International, vol.58, issue.3, pp.201-210, 2009.
DOI : 10.1016/j.parint.2009.04.004

T. Anderson, B. Haubold, J. Williams, J. Estrada-franco, L. Richardson et al., Microsatellite Markers Reveal a Spectrum of Population Structures in the Malaria Parasite Plasmodium falciparum, Molecular Biology and Evolution, vol.17, issue.10, pp.1467-82, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026247

D. Payne, Did medicated salt hasten the spread of chloroquine resistance in Plasmodium falciparum? Parasitol Today, pp.112-117, 1988.

I. Hastings, The origins of antimalarial drug resistance, Trends in Parasitology, vol.20, issue.11, pp.512-520, 2004.
DOI : 10.1016/j.pt.2004.08.006

A. Mbengue, S. Bhattacharjee, T. Pandharkar, H. Liu, G. Estiu et al., A molecular mechanism of artemisinin resistance in Plasmodium falciparum malaria, Nature, vol.103, issue.7549, pp.683-690, 2015.
DOI : 10.1063/1.470043

C. Dogovski, S. 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, issue.4, p.1002132, 2015.
DOI : 10.1371/journal.pbio.1002132.s014

S. Mok, E. Ashley, P. Ferreira, L. Zhu, Z. Lin et al., Population transcriptomics of human malaria parasites reveals the mechanism of artemisinin resistance, Science, vol.13, issue.11, pp.431-436, 2015.
DOI : 10.1101/gr.1239303

F. Ariey, J. Duchemin, and V. Robert, Metapopulation concepts applied to falciparum malaria and their impacts on the emergence and spread of chloroquine resistance, Infection, Genetics and Evolution, vol.2, issue.3, pp.185-92, 2003.
DOI : 10.1016/S1567-1348(02)00099-0

H. Chang, E. Moss, D. Park, D. Ndiaye, S. Mboup et al., Malaria life cycle intensifies both natural selection and random genetic drift, Proceedings of the National Academy of Sciences, vol.8, issue.3, pp.20129-20163, 2013.
DOI : 10.1371/journal.pone.0060780

M. Hofree, J. Shen, H. Carter, A. Gross, and T. Ideker, Network-based stratification of tumor mutations, Nature Methods, vol.39, issue.11, pp.1108-1123, 2013.
DOI : 10.1101/gr.229102. Article published online before print in May 2002

P. Danecek, A. Auton, G. Abecasis, C. Albers, E. Banks et al., The variant call format and VCFtools, Bioinformatics, vol.27, issue.15, pp.2156-2164, 2011.
DOI : 10.1093/bioinformatics/btr330

URL : https://academic.oup.com/bioinformatics/article-pdf/27/15/2156/1125001/btr330.pdf

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009.
DOI : 10.1093/bioinformatics/btp352

URL : https://academic.oup.com/bioinformatics/article-pdf/25/16/2078/531810/btp352.pdf

C. Aurrecoechea, J. Brestelli, B. Brunk, J. Dommer, S. Fischer et al., PlasmoDB: a functional genomic database for malaria parasites, Nucleic Acids Research, vol.37, issue.Database, pp.539-582, 2009.
DOI : 10.1093/nar/gkn814

D. Szklarczyk, A. Franceschini, S. Wyder, K. Forslund, D. Heller et al., STRING v10: protein???protein interaction networks, integrated over the tree of life, Nucleic Acids Research, vol.43, issue.D1, pp.447-52, 2015.
DOI : 10.1093/nar/gku1003

P. Shannon, A. Markiel, O. Ozier, N. Baliga, J. Wang et al., Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks, Genome Research, vol.13, issue.11, pp.2498-504, 2003.
DOI : 10.1101/gr.1239303

L. Roch, K. Zhou, Y. Blair, P. Grainger, M. Moch et al., Discovery of Gene Function by Expression Profiling of the Malaria Parasite Life Cycle, Science, vol.301, issue.5639, pp.1503-1511, 2003.
DOI : 10.1126/science.1087025

G. Bindea, B. Mlecnik, H. Hackl, P. Charoentong, M. Tosolini et al., ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks, Bioinformatics, vol.25, issue.8, pp.1091-1094, 2009.
DOI : 10.1093/bioinformatics/btp101

G. Bindea, J. Galon, and B. Mlecnik, CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data, Bioinformatics, vol.29, issue.5, pp.661-664, 2013.
DOI : 10.1093/bioinformatics/btt019

URL : https://academic.oup.com/bioinformatics/article-pdf/29/5/661/16918665/btt019.pdf

D. Lee and H. Seung, Learning the parts of objects by non-negative matrix factorization, Nature, vol.401, pp.788-91, 1999.

L. Mcguffin, J. Atkins, B. Salehe, A. Shuid, and D. Roche, IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences: Figure 1., Nucleic Acids Research, vol.43, issue.W1, pp.169-73, 2015.
DOI : 10.1093/nar/gkv236

L. Kelley, S. Mezulis, C. Yates, M. Wass, and M. Sternberg, The Phyre2 web portal for protein modeling, prediction and analysis, Nature Protocols, vol.1, issue.6, pp.845-58, 2015.
DOI : 10.1093/bioinformatics/btl677

M. Källberg, H. Wang, S. Wang, J. Peng, Z. Wang et al., Template-based protein structure modeling using the RaptorX web server, Nature Protocols, vol.374, issue.8, pp.1511-1533, 2012.
DOI : 10.1093/nar/gkh468

S. Wu and Y. Zhang, LOMETS: A local meta-threading-server for protein structure prediction, Nucleic Acids Research, vol.35, issue.10, pp.3375-82, 2007.
DOI : 10.1093/nar/gkm251

URL : https://academic.oup.com/nar/article-pdf/35/10/3375/16763318/gkm251.pdf

L. Mcguffin and D. Roche, Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments, Bioinformatics, vol.26, issue.2, pp.182-190, 2010.
DOI : 10.1093/bioinformatics/btp629

Y. Zhang and J. Skolnick, TM-align: a protein structure alignment algorithm based on the TM-score, Nucleic Acids Research, vol.33, issue.7, pp.2302-2311, 2005.
DOI : 10.1093/nar/gki524

M. Hu, S. Nandi, C. Davies, and R. Nicholas, High-Level Chromosomally Mediated Tetracycline Resistance in Neisseria gonorrhoeae Results from a Point Mutation in the rpsJ Gene Encoding Ribosomal Protein S10 in Combination with the mtrR and penB Resistance Determinants, Antimicrobial Agents and Chemotherapy, vol.49, issue.10, pp.4327-4361, 2005.
DOI : 10.1128/AAC.49.10.4327-4334.2005

A. Spitzmüller and J. Mestres, Prediction of the P. falciparum Target Space Relevant to Malaria Drug Discovery, PLoS Computational Biology, vol.37, issue.10, p.1003257, 2013.
DOI : 10.1371/journal.pcbi.1003257.s003

L. Wentzinger, S. Bopp, H. Tenor, J. Klar, R. Brun et al., Cyclic nucleotide-specific phosphodiesterases of Plasmodium falciparum: PfPDE??, a non-essential cGMP-specific PDE that is an integral membrane protein, International Journal for Parasitology, vol.38, issue.14, pp.1625-1662, 2008.
DOI : 10.1016/j.ijpara.2008.05.016

C. Hopp, P. Bowyer, and D. Baker, The role of cGMP signalling in regulating life cycle progression of??Plasmodium, Microbes and Infection, vol.14, issue.10, pp.831-838, 2012.
DOI : 10.1016/j.micinf.2012.04.011

J. Wang, L. Huang, J. Li, Q. Fan, Y. Long et al., Artemisinin Directly Targets Malarial Mitochondria through Its Specific Mitochondrial Activation, PLoS ONE, vol.5, issue.3, p.9582, 2010.
DOI : 10.1371/journal.pone.0009582.g007

W. Feng, W. Zhang, H. Wang, L. Ma, D. Miao et al., Analysis of phosphorylation sites on autophagy proteins, Protein & Cell, vol.7, issue.9, pp.698-701, 2015.
DOI : 10.4161/auto.7.7.15155

N. Mizushima, T. Yoshimori, and Y. Ohsumi, The Role of Atg Proteins in Autophagosome Formation, Annual Review of Cell and Developmental Biology, vol.27, issue.1, pp.107-139, 2011.
DOI : 10.1146/annurev-cellbio-092910-154005

G. Kroemer, G. Mariño, and B. Levine, Autophagy and the Integrated Stress Response, Molecular Cell, vol.40, issue.2, pp.280-93, 2010.
DOI : 10.1016/j.molcel.2010.09.023

URL : https://doi.org/10.1016/j.molcel.2010.09.023

A. Matsui, Y. Kamada, and A. Matsuura, The Role of Autophagy in Genome Stability through Suppression of Abnormal Mitosis under Starvation, PLoS Genetics, vol.279, issue.2, p.1003245, 2013.
DOI : 10.1371/journal.pgen.1003245.s006

J. Kaplon, L. Dam, and D. Peeper, Two-way communication between the metabolic and cell cycle machineries: the molecular basis, Cell Cycle, vol.2005, issue.13, pp.2022-2054, 2015.
DOI : 10.1016/S0092-8674(02)00961-3

B. Altman and J. Rathmell, Metabolic Stress in Autophagy and Cell Death Pathways, Cold Spring Harbor Perspectives in Biology, vol.4, issue.9, p.8763, 2012.
DOI : 10.1101/cshperspect.a008763

S. Zhang, J. Feng, Y. Cao, L. Meng, and S. Wang, Autophagy prevents autophagic cell death in Tetrahymena in response to oxidative stress, Zool Res, vol.36, pp.167-73, 2015.

L. Solyakov, J. Halbert, M. Alam, J. Semblat, D. Dorin-semblat et al., Global kinomic and phospho-proteomic analyses of the human malaria parasite Plasmodium falciparum, Nature Communications, vol.137, p.565, 2011.
DOI : 10.1016/j.molbiopara.2004.05.009

L. Paloque, A. Ramadani, O. Mercereau-puijalon, J. Augereau, and F. Benoit-vical, Plasmodium falciparum: multifaceted resistance to artemisinins, Malaria Journal, vol.32, issue.1, p.149, 2016.
DOI : 10.1016/S0020-7519(02)00186-8

URL : https://hal.archives-ouvertes.fr/inserm-01322524

S. Wright, The theoretical variance within and among subdivisions of a population that is in a steady state, Genetics, vol.37, pp.312-333, 1952.

P. Bray, R. Martin, L. Tilley, S. Ward, K. Kirk et al., Defining the role of PfCRT in Plasmodium falciparum chloroquine resistance, Molecular Microbiology, vol.43, issue.2, pp.323-356, 2005.
DOI : 10.1016/S0764-4469(98)80009-7

N. Juge, S. Moriyama, T. Miyaji, M. Kawakami, H. Iwai et al., -coupled polyspecific nutrient and drug exporter, Proceedings of the National Academy of Sciences, vol.77, issue.6, pp.3356-61, 2015.
DOI : 10.1021/cb4008953

URL : http://www.pnas.org/content/112/11/3356.full.pdf

S. Briolant, H. Bogreau, M. Gil, H. Bouchiba, E. Baret et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.56, issue.5, pp.2750-2752, 2012.
DOI : 10.1128/AAC.05618-11

T. Triglia, J. Menting, C. Wilson, and A. Cowman, Mutations in dihydropteroate synthase are responsible for sulfone and sulfonamide resistance in Plasmodium falciparum, Proceedings of the National Academy of Sciences, vol.14, issue.1, pp.13944-13953, 1997.
DOI : 10.1016/0166-6851(85)90105-7

T. Gaillard, M. Madamet, and B. Pradines, Tetracyclines in malaria, Malaria Journal, vol.57, issue.24, p.445, 2015.
DOI : 10.1128/AAC.44.9.2395-2398.2000

URL : https://hal.archives-ouvertes.fr/hal-01453317

K. Phimda, S. Hoontrakul, C. Suttinont, S. Chareonwat, K. Losuwanaluk et al., Doxycycline versus Azithromycin for Treatment of Leptospirosis and Scrub Typhus, Antimicrobial Agents and Chemotherapy, vol.51, issue.9, pp.3259-63, 2007.
DOI : 10.1128/AAC.00508-07