@article{bib1,
	author = {Amato, R and Pearson, RD and Almagro-Garcia, J and Amaratunga, C and Lim, P and Suon, S and Sreng, S and Drury, E and Stalker, J and Miotto, O and Fairhurst, RM and Kwiatkowski, DP},
	journal = {The Lancet Infectious Diseases},
	year = {2018},
	pages = {337--345},
	title = {Origins of the current outbreak of multidrug-resistant malaria in southeast {Asia}: a retrospective genetic study},
	volume = {18},
}

@article{bib2,
	author = {Antao, T and Hastings, IM},
	journal = {Proceedings. Biological Sciences},
	year = {2011},
	pages = {1705--1712},
	title = {Environmental, pharmacological and genetic influences on the spread of drug-resistant malaria},
	volume = {278},
}

@article{bib3,
	author = {Ashley, EA and Dhorda, M and Fairhurst, RM and Amaratunga, C and Lim, P and Suon, S and Sreng, S and Anderson, JM and Mao, S and Sam, B and Sopha, C and Chuor, CM and Nguon, C and Sovannaroth, S and Pukrittayakamee, S and Jittamala, P and Chotivanich, K and Chutasmit, K and Suchatsoonthorn, C and Runcharoen, R and Hien, TT and Thuy-Nhien, NT and Thanh, NV and Phu, NH and Htut, Y and Han, KT and Aye, KH and Mokuolu, OA and Olaosebikan, RR and Folaranmi, OO and Mayxay, M and Khanthavong, M and Hongvanthong, B and Newton, PN and Onyamboko, MA and Fanello, CI and Tshefu, AK and Mishra, N and Valecha, N and Phyo, AP and Nosten, F and Yi, P and Tripura, R and Borrmann, S and Bashraheil, M and Peshu, J and Faiz, MA and Ghose, A and Hossain, MA and Samad, R and Rahman, MR and Hasan, MM and Islam, A and Miotto, O and Amato, R and MacInnis, B and Stalker, J and Kwiatkowski, DP and Bozdech, Z and Jeeyapant, A and Cheah, PY and Sakulthaew, T and Chalk, J and Intharabut, B and Silamut, K and Lee, SJ and Vihokhern, B and Kunasol, C and Imwong, M and Tarning, J and Taylor, WJ and Yeung, S and Woodrow, CJ and Flegg, JA and Das, D and Smith, J and Venkatesan, M and Plowe, CV and Stepniewska, K and Guerin, PJ and Dondorp, AM and Day, NP and White, NJ},
	journal = {The New England Journal of Medicine},
	year = {2014},
	pages = {411--423},
	title = {Spread of artemisinin resistance in {Plasmodium} falciparum malaria},
	volume = {371},
}

@article{bib4,
	author = {Balikagala, B and Fukuda, N and Ikeda, M and Katuro, OT and Tachibana, S-I and Yamauchi, M and Opio, W and Emoto, S and Anywar, DA and Kimura, E and Palacpac, NMQ and Odongo-Aginya, EI and Ogwang, M and Horii, T and Mita, T},
	journal = {The New England Journal of Medicine},
	year = {2021},
	pages = {1163--1171},
	title = {Evidence of {Artemisinin}-{Resistant} {Malaria} in {Africa}},
	volume = {385},
}

@article{bib5,
	author = {Bertrand, J and Mentr{\' e}, F},
	year = {2008},
	publisher = {Paris Diderot University},
	title = {Mathematical {Expressions} of the {Pharmacokinetic} and {Pharmacodynamic} {Models} {Implemented} in the {Monolix} {Software}},
}

@article{bib6,
	author = {Binois, M and Gramacy, R},
	journal = {Journal of Statistical Software},
	year = {2021},
	pages = {1--44},
	title = {hetGP: Heteroskedastic {Gaussian} process modeling and sequential design in {R}},
	volume = {98},
}

@article{bib7,
	author = {Brock, AR and Ross, JV and Parikh, S and Esterman, A},
	journal = {Medical Hypotheses},
	year = {2018},
	pages = {49--54},
	title = {The role of antimalarial quality in the emergence and transmission of resistance},
	volume = {111},
}

@article{bib8,
	author = {Bruxvoort, K and Goodman, C and Kachur, SP and Schellenberg, D and Ribera, JM},
	journal = {PLOS ONE},
	year = {2014},
	title = {How {Patients} {Take} {Malaria} {Treatment}: A {Systematic} {Review} of the {Literature} on {Adherence} to {Antimalarial} {Drugs}},
	volume = {9},
}

@article{bib9,
	author = {Bushman, M and Antia, R and Udhayakumar, V and de Roode, JC},
	journal = {PLOS Biology},
	year = {2018},
	title = {Within-host competition can delay evolution of drug resistance in malaria},
	volume = {16},
}

@article{bib10,
	author = {Chaorattanakawee, S and Saunders, DL and Sea, D and Chanarat, N and Yingyuen, K and Sundrakes, S and Saingam, P and Buathong, N and Sriwichai, S and Chann, S and Se, Y and Yom, Y and Heng, TK and Kong, N and Kuntawunginn, W and Tangthongchaiwiriya, K and Jacob, C and Takala-Harrison, S and Plowe, C and Lin, JT and Chuor, CM and Prom, S and Tyner, SD and Gosi, P and Teja-Isavadharm, P and Lon, C and Lanteri, CA},
	journal = {Antimicrobial Agents and Chemotherapy},
	year = {2015},
	pages = {4631--4643},
	title = {Ex {Vivo} {Drug} {Susceptibility} {Testing} and {Molecular} {Profiling} of {Clinical} {Plasmodium} falciparum {Isolates} from {Cambodia} from 2008 to 2013 {Suggest} {Emerging} {Piperaquine} {Resistance}},
	volume = {59},
}

@article{bib11,
	author = {Chaorattanakawee, S and Lon, C and Jongsakul, K and Gawee, J and Sok, S and Sundrakes, S and Kong, N and Thamnurak, C and Chann, S and Chattrakarn, S and Praditpol, C and Buathong, N and Uthaimongkol, N and Smith, P and Sirisopana, N and Huy, R and Prom, S and Fukuda, MM and Bethell, D and Walsh, DS and Lanteri, C and Saunders, D},
	journal = {Malaria Journal},
	year = {2016},
	pages = {1--12},
	title = {Ex vivo piperaquine resistance developed rapidly in {Plasmodium} falciparum isolates in northern {Cambodia} compared to {Thailand}},
	volume = {15},
}

@article{bib12,
	author = {Charles, BG and Blomgren, A and Nasveld, PE and Kitchener, SJ and Jensen, A and Gregory, RM and Robertson, B and Harris, IE and Reid, MP and Edstein, MD},
	journal = {European Journal of Clinical Pharmacology},
	year = {2007},
	pages = {271--278},
	title = {Population pharmacokinetics of mefloquine in military personnel for prophylaxis against malaria infection during field deployment},
	volume = {63},
}

@article{bib13,
	author = {Chaumeau, V and Fustec, B and Nay Hsel, S and Montazeau, C and Naw Nyo, S and Metaane, S and Sawasdichai, S and Kittiphanakun, P and Phatharakokordbun, P and Kwansomboon, N and Andolina, C and Cerqueira, D and Chareonviriyaphap, T and Nosten, FH and Corbel, V},
	journal = {Wellcome Open Research},
	year = {2018},
	title = {Entomological determinants of malaria transmission in {Kayin} state, {Eastern} {Myanmar}: A 24-month longitudinal study in four villages},
	volume = {3},
}

@article{bib14,
	author = {Chenet, SM and Akinyi Okoth, S and Huber, CS and Chandrabose, J and Lucchi, NW and Talundzic, E and Krishnalall, K and Ceron, N and Musset, L and Macedo de Oliveira, A and Venkatesan, M and Rahman, R and Barnwell, JW and Udhayakumar, V},
	journal = {Journal of Infectious Diseases},
	year = {2016},
	pages = {1472--1475},
	title = {Independent {Emergence} of the {Plasmodium} falciparum {Kelch} {Propeller} {Domain} {Mutant} {Allele} {C580Y} in {Guyana}},
	volume = {213},
}

@article{bib15,
	author = {Cheng, S and Argaud, JP and Iooss, B and Pon{\c c}ot, A and Lucor, D},
	journal = {Mathematical Geosciences},
	year = {2021},
	pages = {1751--1780},
	title = {A {Graph} {Clustering} {Approach} to {Localization} for {Adaptive} {Covariance} {Tuning} in {Data} {Assimilation} {Based} on {State}-{Observation} {Mapping}},
	volume = {53},
}

@article{bib16,
	author = {Chitnis, N and Hardy, D and Smith, T},
	journal = {Bulletin of Mathematical Biology},
	year = {2012},
	pages = {1098--1124},
	title = {A periodically-forced mathematical model for the seasonal dynamics of malaria in mosquitoes},
	volume = {74},
}

@article{bib17,
	author = {Chiyaka, C and Garira, W and Dube, S},
	journal = {Theoretical Population Biology},
	year = {2009},
	pages = {14--29},
	title = {Effects of treatment and drug resistance on the transmission dynamics of malaria in endemic areas},
	volume = {75},
}

@article{bib18,
	author = {Crow, JF and Motoo, K},
	year = {2017},
	publisher = {Scientific Publishers},
	title = {An {Introduction} to {Population} {Genetics} {Theory}},
}

@article{bib19,
	author = {Dekking, FM and Kraaikamp, C and Lopuha{\" a}, HP and Meester, LE},
	year = {2005},
	publisher = {Springer Science & Business Media},
	title = {A {Modern} {Introduction} to {Probability} and {Statistics}: Understanding {Why} and {How}},
}

@article{bib20,
	author = {Dogovski, C and Xie, SC and Burgio, G and Bridgford, J and Mok, S and McCaw, JM and Chotivanich, K and Kenny, S and Gn{\" a}dig, N and Straimer, J and Bozdech, Z and Fidock, DA and Simpson, JA and Dondorp, AM and Foote, S and Klonis, N and Tilley, L},
	journal = {PLOS Biology},
	year = {2015},
	title = {Targeting the cell stress response of {Plasmodium} falciparum to overcome artemisinin resistance},
	volume = {13},
}

@article{bib21,
	author = {Dye, C and Williams, BG},
	journal = {Proceedings. Biological Sciences},
	year = {1997},
	pages = {61--67},
	title = {Multigenic drug resistance among inbred malaria parasites},
	volume = {264},
}

@article{bib22,
	author = {Edwards, HM and Chinh, VD and Le Duy, B and Thanh, PV and Thang, ND and Trang, DM and Chavez, I and Hii, J},
	journal = {Parasites & Vectors},
	year = {2019},
	title = {Characterising residual malaria transmission in forested areas with low coverage of core vector control in central {Viet} {Nam}},
	volume = {12},
}

@article{bib23,
	author = {Edwards, HM and Sriwichai, P and Kirabittir, K and Prachumsri, J and Chavez, IF and Hii, J},
	journal = {Malaria Journal},
	year = {2019},
	pages = {1--20},
	title = {Transmission risk beyond the village: entomological and human factors contributing to residual malaria transmission in an area approaching malaria elimination on the {Thailand}-{Myanmar} border},
	volume = {18},
}

@article{bib24,
	author = {Ehrlich, HY and Bei, AK and Weinberger, DM and Warren, JL and Parikh, S},
	journal = {PNAS},
	year = {2021},
	title = {Mapping partner drug resistance to guide antimalarial combination therapy policies in sub-{Saharan} {Africa}},
	volume = {118},
}

@article{bib25,
	author = {Ekstr{\" o}m, AM and Clark, J and Byass, P and Lopez, A and De Savigny, D and Moyer, CA and Campbell, H and Gage, AJ and Bocquier, P and AbouZahr, C and Sankoh, O},
	journal = {The Lancet. Diabetes & Endocrinology},
	year = {2016},
	title = {INDEPTH {Network}: contributing to the data revolution},
	volume = {4},
}

@article{bib26,
	author = {Esteva, L and Gumel, AB and de Le{\' o}n, CV},
	journal = {Mathematical and Computer Modelling},
	year = {2009},
	pages = {611--630},
	title = {Qualitative study of transmission dynamics of drug-resistant malaria},
	volume = {50},
}

@article{bib27,
	author = {Farooq, U and Mahajan, RC},
	journal = {Journal of Vector Borne Diseases},
	year = {2004},
	pages = {45--53},
	title = {Drug resistance in malaria},
	volume = {41},
}

@article{bib28,
	author = {Golumbeanu, M and Yang, GJ and Camponovo, F and Stuckey, EM and Hamon, N and Mondy, M and Rees, S and Chitnis, N and Cameron, E and Penny, MA},
	journal = {Infectious Diseases of Poverty},
	year = {2022},
	pages = {61},
	title = {Leveraging mathematical models of disease dynamics and machine learning to improve development of novel malaria interventions},
	volume = {11},
}

@article{bib29,
	author = {Gramacy, RB},
	journal = {Journal of Statistical Software},
	year = {2007},
	title = {tgp: An {R} {Package} for {Bayesian} {Nonstationary}, {Semiparametric} {Nonlinear} {Regression} and {Design} by {Treed} {Gaussian} {Process} {Models}},
	volume = {19},
}

@article{bib30,
	author = {Grow, A and Hilton, J},
	journal = {Wiley Online Library},
	year = {2018},
	title = {Statistical emulation},
	volume = {1},
}

@article{bib31,
	author = {Hamilton, WL and Amato, R and van der Pluijm, RW and Jacob, CG and Quang, HH and Thuy-Nhien, NT and Hien, TT and Hongvanthong, B and Chindavongsa, K and Mayxay, M and Huy, R and Leang, R and Huch, C and Dysoley, L and Amaratunga, C and Suon, S and Fairhurst, RM and Tripura, R and Peto, TJ and Sovann, Y and Jittamala, P and Hanboonkunupakarn, B and Pukrittayakamee, S and Chau, NH and Imwong, M and Dhorda, M and Vongpromek, R and Chan, XHS and Maude, RJ and Pearson, RD and Nguyen, T and Rockett, K and Drury, E and Gon{\c c}alves, S and White, NJ and Day, NP and Kwiatkowski, DP and Dondorp, AM and Miotto, O},
	journal = {The Lancet Infectious Diseases},
	year = {2019},
	pages = {943--951},
	title = {Evolution and expansion of multidrug-resistant malaria in southeast {Asia}: a genomic epidemiology study},
	volume = {19},
}

@article{bib32,
	author = {Hastings, IM},
	journal = {Parasitology},
	year = {1997},
	pages = {133--141},
	title = {A model for the origins and spread of drug-resistant malaria},
	volume = {115},
}

@article{bib33,
	author = {Hastings, IM and Mackinnon, MJ},
	journal = {Parasitology},
	year = {1998},
	pages = {411--417},
	title = {The emergence of drug-resistant malaria},
	volume = {117},
}

@article{bib34,
	author = {Hastings, IM and Watkins, WM and White, NJ},
	journal = {Philosophical Transactions of the Royal Society of London. Series B},
	year = {2002},
	pages = {505--519},
	title = {The evolution of drug--resistant malaria: the role of drug elimination half--life},
	volume = {357},
}

@article{bib35,
	author = {Hastings, IM},
	journal = {Trends in Parasitology},
	year = {2004},
	pages = {512--518},
	title = {The origins of antimalarial drug resistance},
	volume = {20},
}

@article{bib36,
	author = {Hastings, IM and Hodel, EM},
	journal = {Malaria Journal},
	year = {2014},
	pages = {1--15},
	title = {Pharmacological considerations in the design of anti-malarial drug combination therapies -- is matching half-lives enough?},
	volume = {13},
}

@article{bib37,
	author = {Hastings, IM and Hodel, EM and Kay, K},
	journal = {Scientific Reports},
	year = {2016},
	title = {Quantifying the pharmacology of antimalarial drug combination therapy},
	volume = {6},
}

@article{bib38,
	author = {Hastings, IM and Hardy, D and Kay, K and Sharma, R},
	journal = {Evolutionary Applications},
	year = {2020},
	pages = {2723--2739},
	title = {Incorporating genetic selection into individual-based models of malaria and other infectious diseases},
	volume = {13},
}

@article{bib39,
	author = {Hay, SI and Rogers, DJ and Toomer, JF and Snow, RW},
	journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
	year = {2000},
	pages = {113--127},
	title = {Annual {Plasmodium} falciparum entomological inoculation rates ({EIR}) across {Africa}: literature survey, {Internet} access and review},
	volume = {94},
}

@article{bib40,
	author = {Hodel, EM and Kay, K and Hastings, IM},
	journal = {Antimicrobial Agents and Chemotherapy},
	year = {2016},
	pages = {2747--2756},
	title = {Incorporating {Stage}-{Specific} {Drug} {Action} into {Pharmacological} {Modeling} of {Antimalarial} {Drug} {Treatment}},
	volume = {60},
}

@article{bib41,
	author = {Hughes, D and Andersson, DI},
	journal = {Nature Reviews. Genetics},
	year = {2015},
	pages = {459--471},
	title = {Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms},
	volume = {16},
}

@article{bib42,
	author = {Huijben, S and Bell, AS and Sim, DG and Tomasello, D and Mideo, N and Day, T and Read, AF},
	journal = {PLOS Pathogens},
	year = {2013},
	title = {Aggressive chemotherapy and the selection of drug resistant pathogens},
	volume = {9},
}

@article{bib43,
	author = {Johnston, GL and Gething, PW and Hay, SI and Smith, DL and Fidock, DA and Ferguson, NM},
	journal = {PLOS Computational Biology},
	year = {2014},
	title = {Modeling {Within}-{Host} {Effects} of {Drugs} on {Plasmodium} falciparum {Transmission} and {Prospects} for {Malaria} {Elimination}},
	volume = {10},
}

@article{bib44,
	author = {Jullien, V and Valecha, N and Srivastava, B and Sharma, B and Kiechel, JR},
	journal = {Malaria Journal},
	year = {2014},
	title = {Population pharmacokinetics of mefloquine, administered as a fixed-dose combination of artesunate-mefloquine in {Indian} patients for the treatment of acute uncomplicated {Plasmodium} falciparum malaria},
	volume = {13},
}

@article{bib45,
	author = {Karunajeewa, HA and Ilett, KF and Mueller, I and Siba, P and Law, I and Page-Sharp, M and Lin, E and Lammey, J and Batty, KT and Davis, TME},
	journal = {Antimicrobial Agents and Chemotherapy},
	year = {2008},
	pages = {237--243},
	title = {Pharmacokinetics and efficacy of piperaquine and chloroquine in {Melanesian} children with uncomplicated malaria},
	volume = {52},
}

@article{bib46,
	author = {Kay, K and Hastings, IM and Ferguson, N},
	journal = {PLOS Computational Biology},
	year = {2013},
	title = {Improving {Pharmacokinetic}-{Pharmacodynamic} {Modeling} to {Investigate} {Anti}-{Infective} {Chemotherapy} with {Application} to the {Current} {Generation} of {Antimalarial} {Drugs}},
	volume = {9},
}

@article{bib47,
	author = {Kay, K and Hastings, IM},
	journal = {Malaria Journal},
	year = {2015},
	pages = {1--10},
	title = {Measuring windows of selection for anti-malarial drug treatments},
	volume = {14},
}

@article{bib48,
	author = {Kay, K and Hodel, EM and Hastings, IM},
	journal = {Antimicrobial Agents and Chemotherapy},
	year = {2015},
	pages = {6419--6427},
	title = {Altering {Antimalarial} {Drug} {Regimens} {May} {Dramatically} {Enhance} and {Restore} {Drug} {Effectiveness}},
	volume = {59},
}

@article{bib49,
	author = {Khoury, DS and Cao, P and Zaloumis, SG and Davenport, MP and IAtM, C},
	journal = {Trends in Parasitology},
	year = {2020},
	pages = {884--887},
	title = {Artemisinin {Resistance} and the {Unique} {Selection} {Pressure} of a {Short}-acting {Antimalarial}},
	volume = {36},
}

@article{bib50,
	author = {Kilian, AH and Metzger, WG and Mutschelknauss, EJ and Kabagambe, G and Langi, P and Korte, R and von Sonnenburg, F},
	journal = {Tropical Medicine & International Health},
	year = {2000},
	pages = {3--8},
	title = {Reliability of malaria microscopy in epidemiological studies: results of quality control},
	volume = {5},
}

@article{bib51,
	author = {Klein, EY},
	journal = {Journal of Theoretical Biology},
	year = {2014},
	pages = {177--185},
	title = {The impact of heterogeneous transmission on the establishment and spread of antimalarial drug resistance},
	volume = {340},
}

@article{bib52,
	author = {Klonis, N and Xie, SC and McCaw, JM and Crespo-Ortiz, MP and Zaloumis, SG and Simpson, JA and Tilley, L},
	journal = {PNAS},
	year = {2013},
	pages = {5157--5162},
	title = {Altered temporal response of malaria parasites determines differential sensitivity to artemisinin},
	volume = {110},
}

@article{bib53,
	author = {Koella, JC and Antia, R},
	journal = {Malaria Journal},
	year = {2003},
	title = {Epidemiological models for the spread of anti-malarial resistance},
	volume = {2},
}

@article{bib54,
	author = {Krishna, S},
	journal = {Malaria Journal},
	year = {2019},
	title = {Triple artemisinin-containing combination anti-malarial treatments should be implemented now to delay the emergence of resistance: the case against},
	volume = {18},
}

@article{bib55,
	author = {Kublin, JG and Cortese, JF and Njunju, EM and Mukadam, RAG and Wirima, JJ and Kazembe, PN and Djimd{\' e}, AA and Kouriba, B and Taylor, TE and Plowe, CV},
	journal = {The Journal of Infectious Diseases},
	year = {2003},
	pages = {1870--1875},
	title = {Reemergence of chloroquine-sensitive {Plasmodium} falciparum malaria after cessation of chloroquine use in {Malawi}},
	volume = {187},
}

@article{bib56,
	author = {Lee, TE and Penny, MA},
	journal = {Journal of Theoretical Biology},
	year = {2019},
	pages = {210--220},
	title = {Identifying key factors of the transmission dynamics of drug-resistant malaria},
	volume = {462},
}

@article{bib57,
	author = {Lee, TE and Bonhoeffer, S and Penny, MA},
	journal = {Results in Physics},
	year = {2022},
	pages = {105181},
	title = {The competition dynamics of resistant and sensitive infections},
	volume = {34},
}

@article{bib58,
	author = {Legros, M and Bonhoeffer, S},
	journal = {Journal of the Royal Society, Interface},
	year = {2016},
	title = {A combined within-host and between-hosts modelling framework for the evolution of resistance to antimalarial drugs},
	volume = {13},
}

@article{bib59,
	author = {Lohy Das, J and Dondorp, AM and Nosten, F and Phyo, AP and Hanpithakpong, W and Ringwald, P and Lim, P and White, NJ and Karlsson, MO and Bergstrand, M and Tarning, J},
	journal = {The AAPS Journal},
	year = {2017},
	pages = {1842--1854},
	title = {Population {Pharmacokinetic} and {Pharmacodynamic} {Modeling} of {Artemisinin} {Resistance} in {Southeast} {Asia}},
	volume = {19},
}

@article{bib60,
	author = {Lohy Das, JP and Kyaw, MP and Nyunt, MH and Chit, K and Aye, KH and Aye, MM and Karlsson, MO and Bergstrand, M and Tarning, J},
	journal = {Malaria Journal},
	year = {2018},
	title = {Population pharmacokinetic and pharmacodynamic properties of artesunate in patients with artemisinin sensitive and resistant infections in {Southern} {Myanmar}},
	volume = {17},
}

@article{bib61,
	address = {London},
	author = {Macdonald, G},
	year = {1957},
	publisher = {Oxford University Press},
	title = {The {Epidemiology} and {Control} of {Malaria}},
}

@article{bib62,
	author = {Mackinnon, MJ},
	journal = {Acta Tropica},
	year = {2005},
	pages = {207--217},
	title = {Drug resistance models for malaria},
	volume = {94},
}

@article{bib63,
	author = {Mackinnon, MJ and Marsh, K},
	journal = {Science (New York, N.Y.)},
	year = {2010},
	pages = {866--871},
	title = {The selection landscape of malaria parasites},
	volume = {328},
}

@article{bib64,
	author = {Maganda, BA and Ngaimisi, E and Kamuhabwa, AAR and Aklillu, E and Minzi, OMS},
	journal = {Malaria Journal},
	year = {2015},
	title = {The influence of nevirapine and efavirenz-based anti-retroviral therapy on the pharmacokinetics of lumefantrine and anti-malarial dose recommendation in {HIV}-malaria co-treatment},
	volume = {14},
}

@article{bib65,
	author = {Maire, N and Smith, T and Ross, A and Owusu-Agyei, S and Dietz, K and Molineaux, L},
	journal = {The American Journal of Tropical Medicine and Hygiene},
	year = {2006},
	pages = {19--31},
	title = {A model for natural immunity to asexual blood stages of {Plasmodium} falciparum malaria in endemic areas},
	volume = {75},
}

@article{bib66,
	author = {Maire, N and Tediosi, F and Ross, A and Smith, T},
	journal = {The American Journal of Tropical Medicine and Hygiene},
	year = {2006},
	pages = {111--118},
	title = {Predictions of the epidemiologic impact of introducing a pre-erythrocytic vaccine into the expanded program on immunization in sub-{Saharan} {Africa}},
	volume = {75},
}

@article{bib67,
	author = {Miotto, O and Amato, R and Ashley, EA and MacInnis, B and Almagro-Garcia, J and Amaratunga, C and Lim, P and Mead, D and Oyola, SO and Dhorda, M and Imwong, M and Woodrow, C and Manske, M and Stalker, J and Drury, E and Campino, S and Amenga-Etego, L and Thanh, T-NN and Tran, HT and Ringwald, P and Bethell, D and Nosten, F and Phyo, AP and Pukrittayakamee, S and Chotivanich, K and Chuor, CM and Nguon, C and Suon, S and Sreng, S and Newton, PN and Mayxay, M and Khanthavong, M and Hongvanthong, B and Htut, Y and Han, KT and Kyaw, MP and Faiz, MA and Fanello, CI and Onyamboko, M and Mokuolu, OA and Jacob, CG and Takala-Harrison, S and Plowe, CV and Day, NP and Dondorp, AM and Spencer, CCA and McVean, G and Fairhurst, RM and White, NJ and Kwiatkowski, DP},
	journal = {Nature Genetics},
	year = {2015},
	pages = {226--234},
	title = {Genetic architecture of artemisinin-resistant {Plasmodium} falciparum},
	volume = {47},
}

@article{bib68,
	author = {Miotto, O and Sekihara, M and Tachibana, S-I and Yamauchi, M and Pearson, RD and Amato, R and Gon{\c c}alves, S and Mehra, S and Noviyanti, R and Marfurt, J and Auburn, S and Price, RN and Mueller, I and Ikeda, M and Mori, T and Hirai, M and Tavul, L and Hetzel, MW and Laman, M and Barry, AE and Ringwald, P and Ohashi, J and Hombhanje, F and Kwiatkowski, DP and Mita, T and Billker, O},
	journal = {PLOS Pathogens},
	year = {2020},
	title = {Emergence of artemisinin-resistant {Plasmodium} falciparum with kelch13 {C580Y} mutations on the island of {New} {Guinea}},
	volume = {16},
}

@article{bib69,
	author = {Mita, T and Kaneko, A and Lum, JK and Bwijo, B and Takechi, M and Zungu, IL and Tsukahara, T and Tanabe, K and Kobayakawa, T and Bj{\" o}rkman, A},
	journal = {The American Journal of Tropical Medicine and Hygiene},
	year = {2003},
	pages = {413--415},
	title = {Recovery of chloroquine sensitivity and low prevalence of the {Plasmodium} falciparum chloroquine resistance transporter gene mutation {K76T} following the discontinuance of chloroquine use in {Malawi}},
	volume = {68},
}

@article{bib70,
	author = {Molineaux, L and Diebner, HH and Eichner, M and Collins, WE and Jeffery, GM and Dietz, K},
	journal = {Parasitology},
	year = {2002},
	pages = {379--391},
	title = {Plasmodium falciparum parasitaemia described by a new mathematical model},
	volume = {122},
}

@article{bib71,
	author = {Murray, CK and Gasser, RA and Magill, AJ and Miller, RS},
	journal = {Clinical Microbiology Reviews},
	year = {2008},
	pages = {97--110},
	title = {Update on rapid diagnostic testing for malaria},
	volume = {21},
}

@article{bib72,
	author = {Pongtavornpinyo, W and Yeung, S and Hastings, IM and Dondorp, AM and Day, NPJ and White, NJ},
	journal = {Malaria Journal},
	year = {2008},
	title = {Spread of anti-malarial drug resistance: mathematical model with implications for {ACT} drug policies},
	volume = {7},
}

@article{bib73,
	author = {Reiker, T and Golumbeanu, M and Shattock, A and Burgert, L and Smith, TA and Filippi, S and Cameron, E and Penny, MA},
	journal = {Nature Communications},
	year = {2021},
	pages = {1--11},
	title = {Emulator-based {Bayesian} optimization for efficient multi-objective calibration of an individual-based model of malaria},
	volume = {12},
}

@article{bib74,
	author = {Ross, R},
	journal = {BMJ},
	year = {1915},
	pages = {546--547},
	title = {SOME {A} {PRIORI} {PATHOMETRIC} {EQUATIONS}},
	volume = {1},
}

@article{bib75,
	author = {Ross, A and Killeen, G and Smith, T},
	journal = {The American Journal of Tropical Medicine and Hygiene},
	year = {2006},
	pages = {32--37},
	title = {Relationships between host infectivity to mosquitoes and asexual parasite density in {Plasmodium} falciparum},
	volume = {75},
}

@article{bib76,
	author = {Ross, A and Maire, N and Molineaux, L and Smith, T},
	journal = {The American Journal of Tropical Medicine and Hygiene},
	year = {2006},
	pages = {63--73},
	title = {An epidemiologic model of severe morbidity and mortality caused by {Plasmodium} falciparum},
	volume = {75},
}

@article{bib77,
	author = {Ross, A and Smith, T},
	journal = {The American Journal of Tropical Medicine and Hygiene},
	year = {2006},
	pages = {74--81},
	title = {The effect of malaria transmission intensity on neonatal mortality in endemic areas},
	volume = {75},
}

@article{bib78,
	author = {S{\' a}, JM},
	journal = {PNAS},
	year = {2018},
	pages = {12513--12518},
	title = {Artemisinin resistance phenotypes and {K13} inheritance in a {Plasmodium} falciparum cross and {Aotus} model},
	volume = {115},
}

@article{bib79,
	author = {Siddiqui, MR and Willis, A and Bil, K and Singh, J and Mukomena Sompwe, E and Ariti, C},
	journal = {F1000Research},
	year = {2015},
	title = {Adherence to {Artemisinin} {Combination} {Therapy} for the treatment of uncomplicated malaria in the {Democratic} {Republic} of the {Congo}},
	volume = {4},
}

@article{bib80,
	author = {Slater, HC and Okell, LC and Ghani, AC},
	journal = {Trends in Parasitology},
	year = {2017},
	pages = {175--184},
	title = {Mathematical {Modelling} to {Guide} {Drug} {Development} for {Malaria} {Elimination}},
	volume = {33},
}

@article{bib81,
	author = {Smith, T and Killeen, GF and Maire, N and Ross, A and Molineaux, L and Tediosi, F and Hutton, G and Utzinger, J and Dietz, K and Tanner, M},
	journal = {The American Journal of Tropical Medicine and Hygiene},
	year = {2006},
	pages = {1--10},
	title = {Mathematical modeling of the impact of malaria vaccines on the clinical epidemiology and natural history of {Plasmodium} falciparum malaria: Overview},
	volume = {75},
}

@article{bib82,
	author = {Smith, T and Ross, A and Maire, N and Rogier, C and Trape, JF and Molineaux, L},
	journal = {The American Journal of Tropical Medicine and Hygiene},
	year = {2006},
	pages = {56--62},
	title = {An epidemiologic model of the incidence of acute illness in {Plasmodium} falciparum malaria},
	volume = {75},
}

@article{bib83,
	author = {Smith, T and Maire, N and Ross, A and Penny, M and Chitnis, N and Schapira, A and Studer, A and Genton, B and Lengeler, C and Tediosi, F and de Savigny, D and Tanner, M},
	journal = {Parasitology},
	year = {2008},
	pages = {1507--1516},
	title = {Towards a comprehensive simulation model of malaria epidemiology and control},
	volume = {135},
}

@article{bib84,
	author = {Sobol, IM},
	journal = {Mathematics and Computers in Simulation},
	year = {2001},
	pages = {271--280},
	title = {Global sensitivity indices for nonlinear mathematical models and their {Monte} {Carlo} estimates},
	volume = {55},
}

@article{bib85,
	author = {Staehli Hodel, EM and Guidi, M and Zanolari, B and Mercier, T and Duong, S and Kabanywanyi, AM and Ariey, F and Buclin, T and Beck, H-P and Decosterd, LA and Olliaro, P and Genton, B and Csajka, C},
	journal = {Malaria Journal},
	year = {2013},
	title = {Population pharmacokinetics of mefloquine, piperaquine and artemether-lumefantrine in {Cambodian} and {Tanzanian} malaria patients},
	volume = {12},
}

@article{bib86,
	author = {Stokes, BH and Dhingra, SK and Rubiano, K and Mok, S and Straimer, J and Gn{\" a}dig, NF},
	journal = {eLife},
	year = {2021},
	title = {Plasmodium falciparum {K13} mutations in {Africa} and {Asia} impact artemisinin resistance and parasite fitness},
	volume = {10},
}

@article{bib87,
	author = {Tahita, MC and Tinto, H and Yarga, S and Kazienga, A and Traore Coulibaly, M and Valea, I and Van Overmeir, C and Rosanas-Urgell, A and Ouedraogo, J-B and Guiguemde, RT and van Geertruyden, J-P and Erhart, A and D\textquoteright{}Alessandro, U},
	journal = {Malaria Journal},
	year = {2015},
	pages = {1--6},
	title = {Ex vivo anti-malarial drug susceptibility of {Plasmodium} falciparum isolates from pregnant women in an area of highly seasonal transmission in {Burkina} {Faso}},
	volume = {14},
}

@article{bib88,
	author = {Tchuenche, JM and Chiyaka, C and Chan, D and Matthews, A and Mayer, G},
	journal = {Mathematical Medicine and Biology},
	year = {2011},
	pages = {335--355},
	title = {A mathematical model for antimalarial drug resistance},
	volume = {28},
}

@article{bib89,
	author = {Tediosi, F and Maire, N and Smith, T and Hutton, G and Utzinger, J and Ross, A and Tanner, M},
	journal = {The American Journal of Tropical Medicine and Hygiene},
	year = {2006},
	pages = {90--103},
	title = {An approach to model the costs and effects of case management of {Plasmodium} falciparum malaria in sub-saharan {Africa}},
	volume = {75},
}

@article{bib90,
	author = {Th{\" u}ring, T and Hardy, D and Reed, N and {pemberto} and {Making GitHub Delicious}},
	year = {2022},
	title = {Open {Malaria}},
	howpublished = {https://github.com/SwissTPH/openmalaria},
}

@article{bib91,
	author = {Tumwiine, J and Mugisha, JYT and Luboobi, LS},
	journal = {Applied Mathematics and Computation},
	year = {2007},
	pages = {1953--1965},
	title = {A mathematical model for the dynamics of malaria in {A} human host and mosquito vector with temporary immunity},
	volume = {189},
}

@article{bib92,
	author = {Uwimana, A and Legrand, E and Stokes, BH and Ndikumana, J-LM and Warsame, M and Umulisa, N and Ngamije, D and Munyaneza, T and Mazarati, J-B and Munguti, K and Campagne, P and Criscuolo, A and Ariey, F and Murindahabi, M and Ringwald, P and Fidock, DA and Mbituyumuremyi, A and Menard, D},
	journal = {Nature Medicine},
	year = {2020},
	pages = {1602--1608},
	title = {Emergence and clonal expansion of in vitro artemisinin-resistant {Plasmodium} falciparum kelch13 {R561H} mutant parasites in {Rwanda}},
	volume = {26},
}

@article{bib93,
	author = {Uwimana, A and Umulisa, N and Venkatesan, M and Svigel, SS and Zhou, Z and Munyaneza, T and Habimana, RM and Rucogoza, A and Moriarty, LF and Sandford, R and Piercefield, E and Goldman, I and Ezema, B and Talundzic, E and Pacheco, MA and Escalante, AA and Ngamije, D and Mangala, J-LN and Kabera, M and Munguti, K and Murindahabi, M and Brieger, W and Musanabaganwa, C and Mutesa, L and Udhayakumar, V and Mbituyumuremyi, A and Halsey, ES and Lucchi, NW},
	journal = {The Lancet Infectious Diseases},
	year = {2021},
	pages = {1120--1128},
	title = {Association of {Plasmodium} falciparum kelch13 {R561H} genotypes with delayed parasite clearance in {Rwanda}: an open-label, single-arm, multicentre, therapeutic efficacy study},
	volume = {21},
}

@article{bib94,
	author = {van der Pluijm, RW and Tripura, R and Hoglund, RM and Pyae Phyo, A and Lek, D and Ul Islam, A and Anvikar, AR and Satpathi, P and Satpathi, S and Behera, PK and Tripura, A and Baidya, S and Onyamboko, M and Chau, NH and Sovann, Y and Suon, S and Sreng, S and Mao, S and Oun, S and Yen, S and Amaratunga, C and Chutasmit, K and Saelow, C and Runcharern, R and Kaewmok, W and Hoa, NT and Thanh, NV and Hanboonkunupakarn, B and Callery, JJ and Mohanty, AK and Heaton, J and Thant, M and Gantait, K and Ghosh, T and Amato, R and Pearson, RD and Jacob, CG and Gon{\c c}alves, S and Mukaka, M and Waithira, N and Woodrow, CJ and Grobusch, MP and van Vugt, M and Fairhurst, RM and Cheah, PY and Peto, TJ and von Seidlein, L and Dhorda, M and Maude, RJ and Winterberg, M and Thuy-Nhien, NT and Kwiatkowski, DP and Imwong, M and Jittamala, P and Lin, K and Hlaing, TM and Chotivanich, K and Huy, R and Fanello, C and Ashley, E and Mayxay, M and Newton, PN and Hien, TT and Valecha, N and Smithuis, F and Pukrittayakamee, S and Faiz, A and Miotto, O and Tarning, J and Day, NPJ and White, NJ and Dondorp, AM and {Tracking Resistance to Artemisinin Collaboration}},
	journal = {Lancet (London, England)},
	year = {2020},
	pages = {1345--1360},
	title = {Triple artemisinin-based combination therapies versus artemisinin-based combination therapies for uncomplicated {Plasmodium} falciparum malaria: a multicentre, open-label, randomised clinical trial},
	volume = {395},
}

@article{bib95,
	author = {Wang, J and Xu, C and Lun, ZR and Meshnick, SR},
	journal = {Trends in Pharmacological Sciences},
	year = {2017},
	pages = {506--511},
	title = {Unpacking \textquoteleft{}{Artemisinin} {Resistance}.\textquoteright{}},
	volume = {38},
}

@article{bib96,
	author = {Watkins, WM and Mosobo, M},
	journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
	year = {1993},
	pages = {75--78},
	title = {Treatment of {Plasmodium} falciparum malaria with pyrimethamine-sulfadoxine: selective pressure for resistance is a function of long elimination half-life},
	volume = {87},
}

@article{bib97,
	author = {Watson, OJ and Gao, B and Nguyen, TD and Tran, TNA and Penny, MA and Smith, DL and Okell, L and Aguas, R and Boni, MF},
	journal = {bioRxiv},
	year = {2021},
	title = {Pre-{Existing} {Partner}-{Drug} {Resistance} {Facilitates} the {Emergence} and {Spread} of {Artemisinin} {Resistance}: A {Consensus} {Modelling} {Study}},
}

@article{bib98,
	author = {Waxman, D},
	journal = {Genetics},
	year = {2011},
	pages = {907--913},
	title = {A unified treatment of the probability of fixation when population size and the strength of selection change over time},
	volume = {188},
}

@article{bib99,
	author = {White, N},
	journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
	year = {1999},
	pages = {739--749},
	title = {Antimalarial drug resistance and combination chemotherapy},
	volume = {354},
}

@article{bib100,
	author = {White, NJ},
	journal = {The Journal of Clinical Investigation},
	year = {2004},
	pages = {1084--1092},
	title = {Antimalarial drug resistance},
	volume = {113},
}

@article{bib101,
	author = {White, NJ and Pongtavornpinyo, W and Maude, RJ and Saralamba, S and Aguas, R and Stepniewska, K and Lee, SJ and Dondorp, AM and White, LJ and Day, NPJ},
	journal = {Malaria Journal},
	year = {2009},
	title = {Hyperparasitaemia and low dosing are an important source of anti-malarial drug resistance},
	volume = {8},
}

@article{bib102,
	author = {Whitlock, AOB and Juliano, JJ and Mideo, N and Antia, R},
	journal = {PLOS Computational Biology},
	year = {2021},
	title = {Immune selection suppresses the emergence of drug resistance in malaria parasites but facilitates its spread},
	volume = {17},
}

@article{bib103,
	author = {{WHO}},
	year = {2020},
	publisher = {WHO},
	title = {World malaria report 2020},
}

@article{bib104,
	author = {{WHO}},
	year = {2020},
	publisher = {WHO},
	title = {Report on antimalarial drug efficacy, resistance and response: 10 years of surveillance (2010-2019},
}

@article{bib105,
	author = {{WHO}},
	year = {2021},
	publisher = {WHO},
	title = {WHO {Guidelines} for malaria},
}

@article{bib106,
	author = {Winter, K and Hastings, IM},
	journal = {Antimicrobial Agents and Chemotherapy},
	year = {2011},
	pages = {3380--3392},
	title = {Development, {Evaluation}, and {Application} of an {In} {Silico} {Model} for {Antimalarial} {Drug} {Treatment} and {Failure}},
	volume = {55},
}

@article{bib107,
	author = {Witkowski, B and Khim, N and Chim, P and Kim, S and Ke, S and Kloeung, N and Chy, S and Duong, S and Leang, R and Ringwald, P and Dondorp, AM and Tripura, R and Benoit-Vical, F and Berry, A and Gorgette, O and Ariey, F and Barale, J-C and Mercereau-Puijalon, O and Menard, D},
	journal = {Antimicrobial Agents and Chemotherapy},
	year = {2013},
	pages = {914--923},
	title = {Reduced artemisinin susceptibility of {Plasmodium} falciparum ring stages in western {Cambodia}},
	volume = {57},
}

@article{bib108,
	author = {Witmer, K and Dahalan, FA and Delves, MJ and Yahiya, S and Watson, OJ and Straschil, U and Chiwcharoen, D and Sornboon, B and Pukrittayakamee, S and Pearson, RD and Howick, VM and Lawniczak, MKN and White, NJ and Dondorp, AM and Okell, LC and Chotivanich, K and Ruecker, A and Baum, J},
	journal = {Antimicrobial Agents and Chemotherapy},
	year = {2020},
	title = {Transmission of {Artemisinin}-{Resistant} {Malaria} {Parasites} to {Mosquitoes} under {Antimalarial} {Drug} {Pressure}},
	volume = {65},
}

@article{bib109,
	author = {Wongsrichanalai, C and Pickard, AL and Wernsdorfer, WH and Meshnick, SR},
	journal = {The Lancet Infectious Diseases},
	year = {2002},
	pages = {209--218},
	title = {Epidemiology of drug-resistant malaria},
	volume = {2},
}

@article{bib110,
	author = {Wongsrichanalai, C and Meshnick, SR},
	journal = {Emerging Infectious Diseases},
	year = {2008},
	pages = {716--719},
	title = {Declining {Artesunate}-{Mefloquine} {Efficacy} against {Falciparum} {Malaria} on the {Cambodia}--{Thailand} {Border}},
	volume = {14},
}

@article{bib111,
	author = {Yamba, EI and Tompkins, AM and Fink, AH and Ermert, V and Amelie, MD and Amekudzi, LK and Bri{\" e}t, OJT},
	journal = {Data},
	year = {2020},
	title = {Monthly {Entomological} {Inoculation} {Rate} {Data} for {Studying} the {Seasonality} of {Malaria} {Transmission} in {Africa}},
	volume = {5},
}

@article{bib112,
	author = {Ye, R and Hu, D and Zhang, Y and Huang, Y and Sun, X and Wang, J and Chen, X and Zhou, H and Zhang, D and Mungthin, M and Pan, W},
	journal = {Scientific Reports},
	year = {2016},
	title = {Distinctive origin of artemisinin-resistant {Plasmodium} falciparum on the {China}-{Myanmar} border},
	volume = {6},
}

@article{bib113,
	author = {zur Wiesch, PA and Kouyos, R and Engelst{\" a}dter, J and Regoes, RR and Bonhoeffer, S},
	journal = {The Lancet. Infectious Diseases},
	year = {2011},
	pages = {236--247},
	title = {Population biological principles of drug-resistance evolution in infectious diseases},
	volume = {11},
}