1. Organization, T.W.H. Malaria Report 2019. (2019).
2. van der Pluijm, R.W. et al. Triple artemisinin-based combination therapies versus artemisinin-based combination therapies for uncomplicated Plasmodium falciparum malaria: a multicentre, open-label, randomised clinical trial. Lancet (2020).
3. Phyo, A.P. et al. Declining Efficacy of Artemisinin Combination Therapy Against P. Falciparum Malaria on the Thai-Myanmar Border (2003-2013): The Role of Parasite Genetic Factors. Clin Infect Dis 63, 784-791 (2016).
4. Uwimana, A. et al. Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda. Nat Med 26, 1602-1608 (2020).
5. Chotivanich, K. et al. Laboratory detection of artemisinin-resistant Plasmodium falciparum. Antimicrob Agents Chemother 58, 3157-61 (2014).
6. Witkowski, B. et al. Reduced artemisinin susceptibility of Plasmodium falciparum ring stages in western Cambodia. Antimicrob Agents Chemother 57, 914-23 (2013).
7. Ariey, F. et al. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria. Nature 505, 50-5 (2014).
8. Ashley, E.A. et al. Spread of artemisinin resistance in Plasmodium falciparum malaria. The New England journal of medicine 371, 411-23 (2014).
9. Group, W.K.G.-P.S. Association of mutations in the Plasmodium falciparum Kelch13 gene (Pf3D7_1343700) with parasite clearance rates after artemisinin-based treatments-a WWARN individual patient data meta-analysis. BMC Med 17, 1 (2019).
10. Takala-Harrison, S. et al. Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia. J Infect Dis (2014).
11. Imwong, M. et al. The spread of artemisinin-resistant Plasmodium falciparum in the Greater Mekong subregion: a molecular epidemiology observational study. Lancet Infect Dis 17, 491-497 (2017).
12. Dondorp, A.M. et al. Artemisinin resistance in Plasmodium falciparum malaria. N Engl J Med 361, 455-467 (2009).
13. van der Pluijm, R.W. et al. Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study. Lancet Infect Dis 19, 952-961 (2019).
14. Boulle, M. et al. Artemisinin-Resistant Plasmodium falciparum K13 Mutant Alleles, Thailand-Myanmar Border. Emerg Infect Dis 22, 1503-5 (2016).
15. Mishra, N. et al. Emerging polymorphisms in falciparum Kelch 13 gene in Northeastern region of India. Malar J 15, 583 (2016).
16. Miotto, O. et al. Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of New Guinea. PLoS Pathog 16, e1009133 (2020).
17. Bayih, A.G. et al. A Unique Plasmodium falciparum K13 Gene Mutation in Northwest Ethiopia. Am J Trop Med Hyg 94, 132-5 (2016).
18. Kamau, E. et al. K13-propeller polymorphisms in Plasmodium falciparum parasites from sub-Saharan Africa. J Infect Dis 211, 1352-5 (2015).
19. Ng, C.L. & Fidock, D.A. Plasmodium falciparum In Vitro Drug Resistance Selections and Gene Editing. Methods Mol Biol 2013, 123-140 (2019).
20. Rosenthal, M.R. & Ng, C.L. Plasmodium falciparum Artemisinin Resistance: The Effect of Heme, Protein Damage, and Parasite Cell Stress Response. ACS Infect Dis 6, 1599-1614 (2020).
21. Talman, A.M., Clain, J., Duval, R., Menard, R. & Ariey, F. Artemisinin Bioactivity and Resistance in Malaria Parasites. Trends Parasitol 35, 953-963 (2019).
22. Tilley, L., Straimer, J., Gnadig, N.F., Ralph, S.A. & Fidock, D.A. Artemisinin Action and Resistance in Plasmodium falciparum. Trends Parasitol 32, 682-696 (2016).
23. Wang, J., Xu, C., Lun, Z.R. & Meshnick, S.R. Unpacking 'Artemisinin Resistance'. Trends Pharmacol Sci 38, 506-511 (2017).
24. Zhang, M. et al. Inhibiting the Plasmodium eIF2alpha Kinase PK4 Prevents Artemisinin-Induced Latency. Cell Host Microbe 22, 766-776 e4 (2017).
25. Demas, A.R. et al. Mutations in Plasmodium falciparum actin-binding protein coronin confer reduced artemisinin susceptibility. Proc Natl Acad Sci U S A 115, 12799-12804 (2018).
26. Klonis, N. et al. Artemisinin activity against Plasmodium falciparum requires hemoglobin uptake and digestion. Proc Natl Acad Sci U S A 108, 11405-10 (2011).
27. Henrici, R.C., van Schalkwyk, D.A. & Sutherland, C.J. Modification of pfap2mu and pfubp1 Markedly Reduces Ring-Stage Susceptibility of Plasmodium falciparum to Artemisinin In Vitro. Antimicrob Agents Chemother 64(2019).
28. Paloque, L., Ramadani, A.P., Mercereau-Puijalon, O., Augereau, J.M. & Benoit-Vical, F. Plasmodium falciparum: multifaceted resistance to artemisinins. Malar J 15, 149 (2016).
29. LeRoux, M., Lakshmanan, V. & Daily, J.P. Plasmodium falciparum biology: analysis of in vitro versus in vivo growth conditions. Trends Parasitol 25, 474-81 (2009).
30. Cheeseman, I.H. et al. A major genome region underlying artemisinin resistance in malaria. Science 336, 79-82 (2012).
31. Takala-Harrison, S. et al. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. Proc Natl Acad Sci U S A 110, 240-5 (2013).
32. Miotto, O. et al. Genetic architecture of artemisinin-resistant Plasmodium falciparum. Nat Genet (2015).
33. Cerqueira, G.C. et al. Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance. Genome Biol 18, 78 (2017).
34. Ma, Y. et al. Combined transcriptome GWAS and TWAS reveal genetic elements leading to male sterility during high temperature stress in cotton. New Phytol (2021).
35. Wainberg, M. et al. Opportunities and challenges for transcriptome-wide association studies. Nat Genet 51, 592-599 (2019).
36. Visscher, P.M. et al. 10 Years of GWAS Discovery: Biology, Function, and Translation. Am J Hum Genet 101, 5-22 (2017).
37. Cano-Gamez, E. & Trynka, G. From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases. Front Genet 11, 424 (2020).
38. Zhu, L. et al. The origins of malaria artemisinin resistance defined by a genetic and transcriptomic background. Nat Commun 9, 5158 (2018).
39. Mok, S. et al. Drug resistance. Population transcriptomics of human malaria parasites reveals the mechanism of artemisinin resistance. Science 347, 431-5 (2015).
40. Kucharski, M. et al. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 19, 363 (2020).
41. Hamilton, W.L. et al. Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study. Lancet Infect Dis 19, 943-951 (2019).
42. Pourhoseingholi, M.A., Baghestani, A.R. & Vahedi, M. How to control confounding effects by statistical analysis. Gastroenterol Hepatol Bed Bench 5, 79-83 (2012).
43. Westra, H.J. et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat Genet 45, 1238-1243 (2013).
44. Shaw, P.J. et al. Plasmodium parasites mount an arrest response to dihydroartemisinin, as revealed by whole transcriptome shotgun sequencing (RNA-seq) and microarray study. BMC Genomics 16, 830 (2015).
45. Natalang, O. et al. Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate. BMC Genomics 9, 388 (2008).
46. Mok, S. et al. Artemisinin-resistant K13 mutations rewire Plasmodium falciparum's intra-erythrocytic metabolic program to enhance survival. Nat Commun 12, 530 (2021).
47. Rocamora, F. et al. Oxidative stress and protein damage responses mediate artemisinin resistance in malaria parasites. PLoS Pathog 14, e1006930 (2018).
48. Wang, J. et al. Haem-activated promiscuous targeting of artemisinin in Plasmodium falciparum. Nat Commun 6, 10111 (2015).
49. Ismail, H.M. et al. Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7. Proc Natl Acad Sci U S A 113, 2080-5 (2016).
50. Kasaragod, V.B. et al. Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission. Proc Natl Acad Sci U S A 117, 33235-33245 (2020).
51. Birnbaum, J. et al. A Kelch13-defined endocytosis pathway mediates artemisinin resistance in malaria parasites. Science 367, 51-59 (2020).
52. Dogovski, C. et al. Targeting the cell stress response of Plasmodium falciparum to overcome artemisinin resistance. PLoS Biol 13, e1002132 (2015).
53. Yang, T. et al. Decreased K13 Abundance Reduces Hemoglobin Catabolism and Proteotoxic Stress, Underpinning Artemisinin Resistance. Cell Rep 29, 2917-2928 e5 (2019).
54. Bridgford, J.L. et al. Artemisinin kills malaria parasites by damaging proteins and inhibiting the proteasome. Nat Commun 9, 3801 (2018).
55. Simwela, N.V. et al. Plasmodium berghei K13 Mutations Mediate In Vivo Artemisinin Resistance That Is Reversed by Proteasome Inhibition. mBio 11(2020).
56. Mbengue, A. et al. A molecular mechanism of artemisinin resistance in Plasmodium falciparum malaria. Nature 520, 683-7 (2015).
57. Bhattacharjee, S. et al. Remodeling of the malaria parasite and host human red cell by vesicle amplification that induces artemisinin resistance. Blood 131, 1234-1247 (2018).
58. Cui, L. et al. Mechanisms of in vitro resistance to dihydroartemisinin in Plasmodium falciparum. Mol Microbiol 86, 111-28 (2012).
59. Painter, H.J., Morrisey, J.M., Mather, M.W. & Vaidya, A.B. Specific role of mitochondrial electron transport in blood-stage Plasmodium falciparum. Nature 446, 88-91 (2007).
60. Moreira, C.K. et al. The Plasmodium PHIST and RESA-Like Protein Families of Human and Rodent Malaria Parasites. PLoS One 11, e0152510 (2016).
61. Oberli, A. et al. Plasmodium falciparum Plasmodium helical interspersed subtelomeric proteins contribute to cytoadherence and anchor P. falciparum erythrocyte membrane protein 1 to the host cell cytoskeleton. Cell Microbiol 18, 1415-28 (2016).
62. Schneider, A.G. & Mercereau-Puijalon, O. A new Apicomplexa-specific protein kinase family: multiple members in Plasmodium falciparum, all with an export signature. BMC Genomics 6, 30 (2005).
63. Ward, P., Equinet, L., Packer, J. & Doerig, C. Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote. BMC Genomics 5, 79 (2004).
64. Min Zhanga, C.W., Jenna Oberstallera, Phaedra Thomasa, Thomas D., Ottob,c, Debora Casandra, Sandhya Boyapalle, Swamy R. Adapa, Shulin Xua, Katrina Button-Simonsd, Matthew Mayhob, Julian C. Rayner,, Michael T. Ferdig, Rays H. Y. Jiang, John H. Adams. The endosymbiotic origins of the apicoplast link fever-survival and artemisinin-resistance in the malaria parasite. bioRxiv https://doi.org/10.1101/2020.12.10.419788doi(2021).
65. Miotto, O. et al. Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nature genetics 45, 648-55 (2013).
66. Miles, A. et al. Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum. Genome Res 26, 1288-99 (2016).