By Dr David Samuel Khoury

Journal articles

Rebelo M; Pawliw R; Gower J; Webb L; Mitchell H; Pava Z; Watts RE; Davenport MP; McCarthy JS; Khoury DS, 2021, 'Parasite Viability as a Superior Measure of Antimalarial Drug Activity in Humans', Journal of Infectious Diseases, 223, pp. 2154 - 2163, http://dx.doi.org/10.1093/infdis/jiaa678

Cromer D; Juno JA; Khoury D; Reynaldi A; Wheatley AK; Kent SJ; Davenport MP, 2021, 'Prospects for durable immune control of SARS-CoV-2 and prevention of reinfection', Nature Reviews Immunology, 21, pp. 395 - 404, http://dx.doi.org/10.1038/s41577-021-00550-x

Khoury DS; Wheatley AK; Ramuta MD; Reynaldi A; Cromer D; Subbarao K; O’Connor DH; Kent SJ; Davenport MP, 2020, 'Measuring immunity to SARS-CoV-2 infection: comparing assays and animal models', Nature Reviews Immunology, 20, pp. 727 - 738, http://dx.doi.org/10.1038/s41577-020-00471-1

Soon MSF; Lee HJ; Engel JA; Straube J; Thomas BS; Pernold CPS; Clarke LS; Laohamonthonkul P; Haldar RN; Williams CG; Lansink LIM; Moreira ML; Bramhall M; Koufariotis LT; Wood S; Chen X; James KR; Lönnberg T; Lane SW; Belz GT; Engwerda CR; Khoury DS; Davenport MP; Svensson V; Teichmann SA; Haque A, 2020, 'Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory.', Nature Immunology, 21, pp. 1597 - 1610, http://dx.doi.org/10.1038/s41590-020-0800-8

Khoury DS; Cao P; Zaloumis SG; Davenport MP, 2020, 'Artemisinin Resistance and the Unique Selection Pressure of a Short-acting Antimalarial', Trends in Parasitology, 36, pp. 884 - 887, http://dx.doi.org/10.1016/j.pt.2020.07.004

Corder RM; de Lima ACP; Khoury DS; Docken SS; Davenport MP; Ferreira MU, 2020, 'Quantifying and preventing plasmodium vivax recurrences in primaquine-untreated pregnant women: An observational and modeling study in Brazil', Plos Neglected Tropical Diseases, 14, pp. 1 - 16, http://dx.doi.org/10.1371/journal.pntd.0008526

Collins KA; Wang CYT; Adams M; Mitchell H; Robinson GJ; Rampton M; Elliott S; Odedra A; Khoury D; Ballard E; Shelper TB; Lucantoni L; Avery VM; Chalon S; Moehrle JJ; McCarthy JS, 2020, 'A Plasmodium vivax experimental human infection model for evaluating efficacy of interventions', Journal of Clinical Investigation, 130, pp. 2920 - 2927, http://dx.doi.org/10.1172/JCI134923

Khoury DS; Zaloumis SG; Grigg MJ; Haque A; Davenport MP; Cromer D; Rebelo M; Cao P; McCaw JM; Simpson JA; Flegg JA; Wilson DW; Anstey NM; McCarthy JS, 2020, 'Malaria Parasite Clearance: What Are We Really Measuring?', Trends in Parasitology, 36, pp. 413 - 426, http://dx.doi.org/10.1016/j.pt.2020.02.005

Khoury DS; Cromer D; Möhrle JJ; McCarthy JS; Davenport MP, 2019, 'Corrigendum: Defining the effectiveness of antimalarial chemotherapy: Investigation of the lag in parasite clearance following drug administration (Journal of Infectious Diseases (2016) 214 (753-761) DOI: 10.1093/infdis/jiw234)', Journal of Infectious Diseases, 219, pp. 1852 - 1853, http://dx.doi.org/10.1093/infdis/jiy729

Akter J; Khoury DS; Aogo R; Lansink LIM; SheelaNair A; Thomas BS; Laohamonthonkul P; Pernold CPS; Dixon MWA; Soon MSF; Fogg LG; Engel JA; Elliott T; Sebina I; James KR; Cromer D; Davenport MP; Haque A, 2019, 'Plasmodium-specific antibodies block in vivo parasite growth without clearing infected red blood cells', Plos Pathogens, 15, pp. e1007599, http://dx.doi.org/10.1371/journal.ppat.1007599

Davenport MP; Khoury DS; Cromer D; Lewin SR; Kelleher AD; Kent SJ, 2019, 'Functional cure of HIV: the scale of the challenge', Nature Reviews Immunology, 19, pp. 45 - 54, http://dx.doi.org/10.1038/s41577-018-0085-4

Betts M; Kuri Cervantes L; Pampena MB; Samer S; Khoury D; Frank I; Paiardini M; Davenport M; Bar K; Veazey R, 2019, 'Peripheral blood SIV/HIV originates from infected cells in tissues', Journal of Virus Eradication, 5, pp. 27 - 27, http://dx.doi.org/10.1016/s2055-6640(20)30142-4

Zaloumis SG; Cao P; Dini S; Davenport MP; Cromer D; Khoury DS; Fowkes FJI; McCaw JM; Simpson JA, 2018, 'In silico investigation of the decline in clinical efficacy of artemisinin combination therapies due to increasing artemisinin and partner drug resistance', Antimicrobial Agents and Chemotherapy, 62, pp. 10.1128/aac.01292 - 10.1128/aac.01218, http://dx.doi.org/10.1128/AAC.01292-18

Aogo RA; Khoury DS; Cromer D; Elliott T; Akter J; Fogg LG; Nair AS; Liligeto UN; Soon MSF; Thomas BS; Pernold CPS; Romanczuk AS; Laohamonthonkul P; Haque A; Davenport MP, 2018, 'Quantification of host-mediated parasite clearance during blood-stage Plasmodium infection and anti-malarial drug treatment in mice', International Journal for Parasitology, 48, pp. 903 - 913, http://dx.doi.org/10.1016/j.ijpara.2018.05.010

Khoury DS; Aogo R; Randriafanomezantsoa-Radohery G; McCaw JM; Simpson JA; McCarthy JS; Haque A; Cromer D; Davenport MP, 2018, 'Within-host modeling of blood-stage malaria', Immunological Reviews, 285, pp. 168 - 193, http://dx.doi.org/10.1111/imr.12697

Khoury DS; Cromer D; Elliott T; Soon MSF; Thomas BS; James KR; Best SE; Aogo RA; Engel JA; Gartlan KH; Akter J; Sebina I; Haque A; Davenport MP, 2017, 'Characterising the effect of antimalarial drugs on the maturation and clearance of murine blood-stage Plasmodium parasites in vivo', International Journal for Parasitology, 47, pp. 913 - 922, http://dx.doi.org/10.1016/j.ijpara.2017.05.009

Cao P; Klonis N; Zaloumis S; Khoury DS; Cromer D; Davenport MP; Tilley L; Simpson JA; McCaw JM, 2017, 'A mechanistic model quantifies artemisinin-induced parasite growth retardation in blood-stage Plasmodium falciparum infection', Journal of Theoretical Biology, 430, pp. 117 - 127, http://dx.doi.org/10.1016/j.jtbi.2017.07.017

Khoury DS; Cromer D; Akter J; Sebina I; Elliott T; Thomas BS; Soon MSF; James KR; Best SE; Haque A; Davenport MP, 2017, 'Host-mediated impairment of parasite maturation during blood-stage Plasmodium infection', Proceedings of the National Academy of Sciences of the United States of America, 114, pp. 7701 - 7706, http://dx.doi.org/10.1073/pnas.1618939114

Griffin P; Pasay C; Elliott S; Sekuloski S; Sikulu M; Hugo L; Khoury D; Cromer D; Davenport M; Sattabongkot J; Ivinson K; Ockenhouse C; McCarthy J, 2016, 'Safety and Reproducibility of a Clinical Trial System Using Induced Blood Stage Plasmodium vivax Infection and Its Potential as a Model to Evaluate Malaria Transmission', Plos Neglected Tropical Diseases, 10, pp. e0005139, http://dx.doi.org/10.1371/journal.pntd.0005139

Khoury DS; Cromer D; Möhrle JJ; McCarthy JS; Davenport MP, 2016, 'Defining the effectiveness of antimalarial chemotherapy: Investigation of the lag in parasite clearance following drug administration', Journal of Infectious Diseases, 214, pp. 753 - 761, http://dx.doi.org/10.1093/infdis/jiw234

Khoury DS; Cromer D; Best SE; James KR; Sebina I; Haque A; Davenport MP, 2015, 'Reduced erythrocyte susceptibility and increased host clearance of young parasites slows Plasmodium growth in a murine model of severe malaria', Scientific Reports, 5, pp. 9412, http://dx.doi.org/10.1038/srep09412

Khoury DS; Cromer D; Best SE; James KR; Kim PS; Engwerda CR; Haque A; Davenport MP, 2014, 'Effect of mature blood-stage Plasmodium parasite sequestration on pathogen biomass in mathematical and in vivo models of malaria.', Infect Immun, 82, pp. 212 - 220, http://dx.doi.org/10.1128/IAI.00705-13

Delaney GW; Khoury D, 2013, 'Onset of rigidity in 3D stretched string networks', European Physical Journal B, 86, http://dx.doi.org/10.1140/epjb/e2012-30445-y

Khoury DS; Barron AB; Myerscough MR, 2013, 'Modelling food and population dynamics in honey bee colonies.', PLoS One, 8, pp. e59084, http://dx.doi.org/10.1371/journal.pone.0059084

Khoury DS; Myerscough MR; Barron AB, 2011, 'A quantitative model of honey bee colony population dynamics', Plos One, 6, http://dx.doi.org/10.1371/journal.pone.0018491

Conference Papers

Myerscough MR; Khoury DS; Ronzani S; Barron AB, 2017, 'Why Do Hives Die? Using Mathematics to Solve the Problem of Honey Bee Colony Collapse', in Mathematics for Industry, Springer Nature, pp. 35 - 50, http://dx.doi.org/10.1007/978-981-10-0962-4_4

Conference Abstracts

Lansink LIM; Engel JA; Lee HJ; Soon MSF; Williams CG; Aogo RA; Cromer D; Davenport MP; Khoury DS; Haque A, 2021, 'Exposure to host inflammation in vivo induces rapid transcriptomic change and impaired maturation in malaria parasites', in JOURNAL OF IMMUNOLOGY, AMER ASSOC IMMUNOLOGISTS, Vol. 206, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000713665801305&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Working Papers

Goel RR; Painter MM; Lundgreen KA; Apostolidis SA; Baxter AE; Giles JR; Mathew D; Pattekar A; Reynaldi A; Khoury DS; Gouma S; Hicks P; Dysinger S; Hicks A; Sharma H; Herring S; Korte S; Kc W; Oldridge DA; Erickson RI; Weirick ME; McAllister CM; Awofolaju M; Tanenbaum N; Dougherty J; Long S; D'Andrea K; Hamilton JT; McLaughlin M; Williams JC; Adamski S; Kuthuru O; Drapeau EM; Davenport MP; Hensley SE; Bates P; Greenplate AR; Wherry EJ, Efficient recall of Omicron-reactive B cell memory after a third dose of SARS-CoV-2 mRNA vaccine, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/2022.02.20.481163

Cele S; Jackson L; Khoury DS; Khan K; Moyo-Gwete T; Tegally H; San JE; Cromer D; Scheepers C; Amoako D; Karim F; Bernstein M; Lustig G; Archary D; Smith M; Ganga Y; Jule Z; Reedoy K; Hwa S-H; Giandhari J; Blackburn JM; Gosnell BI; Karim SSA; Hanekom W; NGS-SA ; Team C-K; von Gottberg A; Bhiman J; Lessells RJ; Moosa M-YS; Davenport MP; de Oliveira T; Moore PL; Sigal A, SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/2021.12.08.21267417

Preprints

Stadler E; Khan SR; Elias KM; Egilmezer E; Phetsouphanh C; Hastak P; Hewavisenti RV; Joshi RV; Turner T; Cromer D; Sasson SC; Davenport MP; Khoury DS, 2026, Immunogenicity and vaccine effectiveness of COVID-19 vaccines in people on immunosuppressive therapies, http://dx.doi.org/10.64898/2026.09.16.26363194

Hogan AB; Wu SL; Toor J; Doohan P; Watson OJ; Winskill P; Charles G; Barnsley G; Riley EM; Khoury DS; Ferguson NM; Ghani AC, 2022, Long Term Vaccination Strategies to Mitigate the Global Impact of SARS-CoV-2 Transmission: A Modelling Study, http://dx.doi.org/10.2139/ssrn.4135323

Koutsakos M; Reynaldi A; Lee WS; Nguyen J; Amarasena T; Taiaroa G; Kinsella P; Liew KC; Tran T; Kent H; Tan H-X; Rowntree L; Nguyen T; Thomas P; Kedzierska K; Petersen J; Rossjohn J; Williamson D; Khoury D; Davenport M; Kent S; Wheatley A; Juno J, 2022, Rapid Recall and de novo T Cell Responses During SARS-CoV-2 Breakthrough Infection, http://dx.doi.org/10.2139/ssrn.4311124

Aggarwal A; Stella A; Walker G; Akerman A; Milogiannakis V; Brilot F; Amatayakul-Chantler S; Roth N; Coppola G; Schofield P; Jackson J; Lenthall H; Mazigi O; Langley D; Lu Y; Forster C; McAllery S; Mathivanan V; Fitcher C; Hoppe AC; Munier CML; Jack H-M; Cromer D; Darley D; Matthews G; Christ D; Khoury D; Davenport M; Rawlinson W; Kelleher A; Turville S, 2022, SARS-CoV-2 Omicron: evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern, http://dx.doi.org/10.21203/rs.3.rs-1207364/v1

Mehra S; Stadler E; Khoury D; McCaw JM; Flegg JA, 2021, Hypnozoite dynamics for Plasmodium vivax malaria: the epidemiological effects of radical cure, http://dx.doi.org/10.48550/arxiv.2107.00779

Cromer D; Steain M; Reynaldi A; Schlub TE; Wheatley AK; Juno JA; Kent SJ; Triccas JA; Khoury DS; Davenport MP, 2021, SARS-CoV-2 variants: levels of neutralisation required for protective immunity, http://dx.doi.org/10.1101/2021.08.11.21261876

Khoury DS; Cromer D; Reynaldi A; Schlub TE; Wheatley AK; Juno JA; Subbarao K; Kent SJ; Triccas JA; Davenport MP, 2021, What level of neutralising antibody protects from COVID-19?, http://dx.doi.org/10.1101/2021.03.09.21252641

Soon M; Lee HJ; Engel J; Straube J; Thomas B; Clarke L; Laohamonthonkul P; Pernold C; Haldar R; Williams C; Lansink L; Koufariotis R; Lakis V; Wood S; Chen X; James K; Lönnberg T; Lane S; Davenport M; Khoury D; Svensson V; Teichmann S; Haque A, 2019, Transcriptome Dynamics Reveals Progressive Transition from Effector to Memory in CD4 ⁺ T cells, http://dx.doi.org/10.1101/675967

Cao P; Klonis N; Zaloumis S; Khoury DS; Cromer D; Davenport MP; Tilley L; Simpson JA; McCaw JM, 2017, A mechanistic model quantifies artemisinin-induced parasite growth retardation in blood-stage Plasmodium falciparum infection, http://dx.doi.org/10.48550/arxiv.1701.05302

Khoury DS; Steain M; Triccas JA; Sigal A; Davenport MP; Cromer D, A meta-analysis of Early Results to predict Vaccine efficacy against Omicron, http://dx.doi.org/10.1101/2021.12.13.21267748

Stadler E; Cromer D; Ogunlade S; Ongoiba A; Doumbo S; Kayentao K; Traore B; Crompton PD; Portugal S; Davenport MP; Khoury DS, A role for super-spreaders in carrying malaria parasites across the months-long dry season, http://dx.doi.org/10.1101/2022.04.28.22274398

Singanayagam A; Wagstaffe HR; Slater L; Fox-Sheehan P; Wu M-S; Mawer A; Preston-Jones H; Daly O; Low JM; Ramon RL; Hughes E; Zhou J; Badhan A; Guy J; Harris SA; Smith SP; Govender M; Laidlaw SM; Tipton T; Satti I; Yaden M; Ascough S; Sukhova K; Moshe M; McKenzie J; Siddiqui H; Ateere A; Nassanga B; Stiff F; Khoury DS; Reynaldi A; Davenport MP; Carroll M; Thwaites RS; Taylor GP; Barclay W; Bracchi M; McShane H; Chiu C; team TCS, Biomarkers of protection against controlled human SARS-CoV-2 Delta variant breakthrough infection, http://dx.doi.org/10.64898/2026.07.24.26358855

Khoury DS; Schlub TE; Cromer D; Steain M; Fong Y; Gilbert PB; Subbarao K; Triccas JA; Kent SJ; Davenport MP, Correlates of protection, thresholds of protection, and immunobridging in SARS-CoV-2 infection, http://dx.doi.org/10.1101/2022.06.05.22275943

Stadler E; Chai KL; Schlub TE; Cromer D; Polizzotto MN; Kent SJ; Beecher C; White H; Turner T; Skoetz N; Estcourt L; McQuilten ZK; Wood EM; Khoury DS; Davenport MP, Determinants of passive antibody efficacy in SARS-CoV-2 infection, http://dx.doi.org/10.1101/2022.03.21.22272672

Lee WS; Tan H-X; Reynaldi A; Esterbauer R; Koutsakos M; Nguyen J; Amarasena T; Kent HE; Aggarwal A; Turville SG; Taiaroa G; Kinsella P; Liew KC; Tran T; Williamson DA; Cromer D; Davenport MP; Kent SJ; Juno JA; Khoury DS; Wheatley AK, Durable reprogramming of neutralising antibody responses following breakthrough Omicron infection, http://dx.doi.org/10.1101/2023.02.19.23286159

Koutsakos M; Lee WS; Reynaldi A; Tan H-X; Gare G; Kinsella P; Liew KC; Williamson DA; Kent HE; Stadler E; Cromer D; Khoury DS; Wheatley AK; Juno JA; Davenport MP; Kent SJ, Dynamics of immune recall following SARS-CoV-2 vaccination or breakthrough infection, http://dx.doi.org/10.1101/2021.12.23.21268285

Hogan AB; Doohan P; Wu SL; Mesa DO; Toor J; Watson OJ; Winskill P; Charles G; Barnsley G; Riley EM; Khoury DS; Ferguson NM; Ghani AC, Estimating long-term vaccine effectiveness against SARS-CoV-2 variants: a model-based approach, http://dx.doi.org/10.1101/2023.01.03.23284131

Stadler E; Csolle M; Mitchell A; Egilmezer E; Elias KM; Bailey BA; Cromer D; Turner T; Khoury DS; Davenport MP, Evidence for cross-reactivity and protection against Bundibugyo virus disease after heterologous vaccination: a systematic review and meta-analysis, http://dx.doi.org/10.64898/2026.09.14.26362805

Wheatley AK; Juno JA; Wang JJ; Selva KJ; Reynaldi A; Tan H-X; Lee WS; Wragg KM; Kelly HG; Esterbauer R; Davis SK; Kent HE; Mordant FL; Schlub TE; Gordon DL; Khoury DS; Subbarao K; Cromer D; Gordon TP; Chung AW; Davenport MP; Kent SJ, Evolution of immunity to SARS-CoV-2, http://dx.doi.org/10.1101/2020.09.09.20191205

Chung Y; Bailey BA; Bowden-Reid E; Csolle M; Docken SS; Jachno K; Khoury DS; McDonald S; Pattuwage L; White H; Zazryn T; Turner T; Davenport MP, Filovirus Evidence Maps: A community resource to identify and curate the published evidence on immunity and vaccination for BDBV, EBOV, MARV, and SUDV, http://dx.doi.org/10.64898/2026.05.22.26353826

Berry MT; Palmer MR; Khan SR; Bowden-Reid E; Egilmezer E; Smith MA; Bateson D; Canfell K; Davenport MP; Khoury DS, HPV binding antibodies as a correlate of protection, http://dx.doi.org/10.1101/2025.11.26.25341002

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