Refereed journal papers

44. A. Alahmadi, S. Belet, A. Black, D. Cromer, J.A. Flegg, T. House, P. Jayasundara, J.M. Keith, J.M. McCaw, R. Moss, J.V. Ross, F.M. Shearer, S. Thein Than Tun, L.Walker, J. White, J.M. Whyte, A.W.C. Yan, and A.E. Zarebski (2020). Influencing public health policy with data-informed mathematical models of infectious diseases: Recent developments and new challenges. Epidemics, 100393. doi: 10.1016/j.epidem.2020.100393

43. M.B. Flegg, M.A. Munoz, K. Smith-Miles, J.A. Flegg, and J.G. Carroll (2020). Parameter estimation of a point-source diffusion-decay morphogen model. Journal of Mathematical Biology, 80:2227-2255. doi: 10.1007/s00285-020-01494-x

42. J. Hall, T. Robinson, J.A. Flegg, and J. Wilkinson (2020). First-year and final-year undergraduate students perceptions of university mathematics departments. Mathematics Education Research Journal, pages 1 – 26. doi:

41.  D.S. Khoury, S.G. Zaloumis, M.J. Grigg, A. Haque, M.P. Davenport, D. Cromer, M. Rebelo, P. Cao, J.M. McCaw, J.A. Simpson, J.A. Flegg, D.W. Wilson, N.M. Anstey, and J.S. McCarthy (2020). Malaria Parasite Clearance: What Are We Really Measuring? Trends in Parasitology, 36: 414-426. doi: 10.1016/

40. A.A. Alahmadi, J.A. Flegg, D.G. Cochrane, C.C. Drovandi, J.M. Keith (2020). A comparison of approximate versus exact techniques for Bayesian parameter inference in nonlinear ordinary differential equation models, Royal Society Open Science, 7: 191315.  doi: 10.1098/rsos.191315

39. S. Mehra, J.M. McCaw, M.B. Flegg, P.G. Taylor, J.A. Flegg (2020). An activation-clearance model for Plasmodium vivax malaria, Bulletin of Mathematical Biology, 82: 32. doi: 10.1007/s11538-020-00706-1

38. J.A. Flegg, S.N. Menon, H.M. Byrne, D.L.S. McElwain (2020). A current perspective on wound healing and tumour-induced angiogenesis, Bulletin of Mathematical Biology, 82: 23. doi: 10.1007/s11538-020-00696-0

37. C. Weller, A. Bouguettaya, V. Team, J.A. Flegg, J. Kasza, C. Jayathilake (2020). Associations among patient, treatment, or wound-level factors and venous leg ulcer healing: wound characteristics are the key factors in determining healing outcomes, Wound Repair and Regeneration, 28: 211-218. doi: 10.1111/wrr.12773.

36. C. Jayathilake, P.K. Maini, H.W. Hopf, D.L.S. McElwain, H.M. Byrne, M.B. Flegg, J.A. Flegg (2019). A mathematical model of the use of supplemental oxygen to combat surgical site infection, Journal of Theoretical Biology, 466: 11-23. doi:  0.1016/j.jtbi.2019.01.021.

35. S. Sharifi‑Malvajerdi, F. Zhu, C.B. Fogarty, M.P. Fay, R.M. Fairhurst, J.A. Flegg, K. Stepniewska and D.S. Small (2019). Malaria parasite clearance rate regression: an R software package for a Bayesian hierarchical regression model, Malaria Journal, 18: 4. doi: 10.1186/s12936-018-2631-8.

34. N.R. Smith, J.M. Trauer, M. Gambhir, J.S. Richards, R.J. Maude, J.M. Keith and J.A. Flegg (2018). Agent-based models of malaria transmission: a systematic review, Malaria Journal, 17: 299. doi: 10.1186/s12936-018-2442-y.

33. D.L. Maderazo, J.A. Flegg, M.R. Neeland, M.J. de Veer and M.B. Flegg (2018). Physiological factors leading to successful vaccination: a computational approach, Journal of Theoretical Biology, 454: 215-230. doi: 10.1016/j.jtbi.2018.06.008.

32. Q. Zhang, W.S. Yuen, D. Adhikari, J.A., Flegg, G. Fitzharris, M. Conti, P. Sicinski, I. Nabti, P. Marangos, J. Carroll (2017). Cyclin A2 modulates kinetochore-microtubule attachment in meiosis II. Journal Cell Biology, 216(10): 3133-3143. doi: 10.1083/jcb.201607111

31. A.R. Taylor, J.A. Flegg, C.C. Holmes, P.J. Guérin, C.H. Sibley, M.D. Conrad, G. Dorsey, P.J. Rosenthal (2017). Artemether-lumefantrine and dihydroartemisinin-piperaquine exert inverse selective pressure on Plasmodium falciparum drug sensitivity associated haplotypes in Uganda. Open Forum Infectious Diseases, 4(1): 1-6. doi: 10.1093/ofid/ofw229

30. E.P.M. Grist, J.A. Flegg, G. Humphreys, I.S. Mas, T.J.C. Anderson, E.A. Ashley, N.P.J. Day, M. Dhorda, A.M. Dondorp, M.A. Faiz, P.W. Gething, T.T. Hien, T.M. Hlaing, M. Imwong, J. Kindermans, R.J. Maude, M. Mayxay, M. McDew-White, D. Menard, S. Nair, F. Nosten, P.N. Newton, R.N. Price, A. Pukrittayakamee, S. Takala-Harrison, F. Smithuis, N.T. Nguyen, K.M. Tun, N.J. White, B. Witkowski, C.J. Woodrow, R.M. Fairhurst, C. Sibley, P.J. Guerin (2016). Optimal health and disease management using spatial uncertainty: a geographic characterization of emergent artemisinin resistant Plasmodium falciparum distributions in Southeast Asia. International Journal of Health Geographics, 15:37. doi: 10.1186/s12942-016-0064-6

29. WorldWide Antimalarial Resistance Network (WWARN) WWARN Artemisinin based Combination Therapy (ACT) Africa Baseline Study Group (2015). Clinical determinants of early parasitological response to ACTs in African patients with uncomplicated falciparum malaria: a literature review and meta-analysis of individual patient data. BMC Medicine, 13:212. doi: 10.1186/s12916-015-0445-x

28. J.A Flegg, S. N. Menon, P.K. Maini, D. L. S. McElwain (2015). On the mathematical modeling of wound healing angiogenesis in skin as a reaction-transport process. Frontiers in Physiology, 6:262. doi: 10.3389/fphys.2015.00262

27. WorldWide Antimalarial Resistance Network (WWARN) Parasite Clearance Study Group (2015). Baseline data of parasite clearance in patients with falciparum malaria treated with an artemisinin derivative: an individual patient data meta-analysis. Malaria Journal. 14:359. doi: 10.1186/s12936-015-0874-1

26. J.A Flegg, J. Kasza, I. Darby, C. Weller (2015). Healing of venous ulcers using compression therapy: predictions of a mathematical model. Journal Theoretical Biology, 379: 1-9. doi: 10.1016/j.jtbi.2015.04.028

25. L.J. White, J.A. Flegg, A.P. Phyo, J. Wiladpai-ngern, D. Bethell, C. Plowe, T. Anderson, S. Nkhoma, S. Nair, R. Tripura, K. Stepniewska, W. Pan-Ngum, K. Silamut, B.S. Cooper, Y. Lubell, E.A. Ashley, C. Nguon, C. M. Chuor, F. Nosten, N.J. White, A.M. Dondorp (2015). Defining the in-vivo phenotype of artemisinin resistant falciparum malaria: A modelling approach. PLoS Medicine, 12(4): e1001823. doi: 10.1371/journal.pmed.1001823

24. WorldWide Antimalarial Resistance Network (WWARN) AS-AQ Study Group (2015). The Effect of Dosing Strategies on the Therapeutic Efficacy of Artesunate Amodiaquine for Uncomplicated Malaria: A Meta-Analysis of Individual Patient Data. BMC Medicine, 13:66. doi: 10.1186/s12916-015-0301-z
This is a WWARN publication (, published under a Study Group. Full author list available at

23. WorldWide Antimalarial Resistance Network (WWARN) AL Study Group (2015). The effect of dose on the antimalarial efficacy of artemether-lumefantrine: a pooled analysis of individual patient data. Lancet Infectious Diseases, 15(6): 692-702. doi: 10.1016/S1473-3099(15)70024-1
This is a WWARN publication (, published under a Study Group. Full author list available at

22. C.B. Fogarty, M.P. Fay, J.A. Flegg, K. Stepniewska, R.M. Fairhurst, and D.S. Small (2015). Bayesian Hierarchical Regression on Clearance Rates in the Presence of “Lag” and “Tail” Phases with an Application to Malaria Parasites. Biometrics, 71(3): 751–759. doi: 10.1111/biom.12307.

21. K.M. Tun, M. Imwong, K.M. Lwin, A.A. Win, T.M. Hlaing, T. Hlaing, K. Lin, M.P. Kyaw, K. Plewes, M.A. Faiz, M. Dhorda, P. Cheah, S. Pukrittayakamee, E.A. Ashley, T.J.C. Anderson, S. Nair, M. McDew-White, J.A Flegg, E.P.M. Grist, P. Guerin, R. Maude, F. Smithuis, A.M. Dondorp, N.P.J. Day, F. Nosten, N.J. White, C.J. Woodrow (2015). Spread of artemisinin resistant Plasmodium falciparum across Myanmar: a cross-sectional survey of the K13 molecular marker. Lancet Infectious Diseases, 15(4): 415–421. doi: 10.1016/S1473-3099(15)70032-0

20. Tracking Resistance to Artemisinin Collaboration (2014). The spread of artemisinin resistance in Plasmodium falciparum malaria. New England Journal of Medicine, 371: 411-423. doi: 10.1056/NEJMoa1314981
Full author list available at

19. A.R. Taylor, J.A. Flegg, S.L. Nsobya, A. Yeka, M.R. Kamya, P.J. Rosenthal, G. Dorsey, C.H. Sibley, P.J. Guerin and C. Holmes (2014). Estimation of malaria haplotype and genotype frequencies: a statistical approach to overcome the challenge associated with multiclonal infections. Malaria Journal, 13:102. doi: 10.1186/1475-2875-13-102

18. J.A. Flegg, P.J. Guérin, F. Nosten, E.A. Ashley, A. Pyae Phyo, A.M. Dondorp, R.M. Fairhurst, D. Socheat, S. Borrmann, A. Björkman, A. Mårtensson, M. Mayxay, P.N. Newton, D. Bethell, Y. Se, H. Noedl, M. Diakite, A.A Djimde, T.T. Hien, N.J. White, K. Stepniewska (2013). Optimal sampling designs for estimation of Plasmodium falciparum clearance rates in patients treated with artemisinin derivatives. Malaria Journal, 12:411. doi: 10.1186/1475-2875-12-411

17. M. Gharbi, J.A. Flegg, B. Pradines, A. Berenger, M. Ndiaye, A.A. Djimdé, C. Roper, V. Hubert, E. Kendjo, M. Venkatesan, P. Brasseur, O. Gaye, A.T. Offianan, L. Penali, J. Le Bras, P. J. Guérin (2013). Surveillance of travellers: an additional tool for tracking antimalarial drug resistance in endemic countries. PLoS One, 8(10): e77775. doi: 10.1371/journal.pone.0077775

16. WorldWide Antimalarial Resistance Network (WWARN) DP Study Group (2013). The Effect of Dosing Regimens on the Antimalarial Efficacy of Dihydroartemisinin-Piperaquine: A Pooled Analysis of Individual Patient Data. PLoS Medicine, 10(12): e1001564. doi: 10.1371/journal.pmed.1001564
This is a WWARN publication (, published under a Study Group.
Full author list available at

15. J.A. Flegg, C.J.E. Metcalf, M. Gharbi, M. Venkatesan, T. Shewchuk, C.H. Sibley, P.J. Guerin (2013). Trends in antimalarial drug use in Africa. American Journal of Tropical Medicine and Hygiene, 89(5): 857-865. doi: 10.4269/ajtmh.13-0129

14. J.A. Flegg, A.P. Patil, M. Venkatesan, C. Roper, I. Naidoo, S.I. Hay, C.H.Sibley, P. J. Guerin (2013). Spatio-temporal mathematical modelling of mutations of the dhps gene in African Plasmodium falciparum. Malaria Journal, 12:249. doi: 10.1186/1475-2875-12-249

13. C.J. Woodrow, S. Dahlström, R. Cooksey, J.A. Flegg, H. Le Nagard, F. Mentré, C. Murillo, D. Ménard, F. Nosten, K. Sriprawat, L. Musset, N. B. Quashie, P. Lim, R. M. Fairhurst, S. L. Nsobya, V. Sinou, H. Noedl, B. Pradines, J.D. Johnson, P.J. Guerin, C. H. Sibley, J. Le Bras (2013). High-throughput analysis of antimalarial susceptibility data by the WWARN In Vitro Analysis and Reporting Tool (IVART). Antimicrobial Agents and Chemotherapy, 57(7): 3121-30. doi: 10.1128/AAC.02350-12.

12. M. Gharbi, J.A. Flegg, V. Hubert, E. Kendjo, J. E. Metcalf, L. Bertaux, P.J. Guérin, J. Le Bras (2013). Longitudinal study assessing the return of chloroquine susceptibility of Plasmodium falciparum in isolates from travellers returning from West and Central Africa, 2000-2011. Malaria Journal, 12:35. doi: 10.1186/1475-2875-12-35

11. D. Loessner, J.A. Flegg, H.M. Byrne, J.A. Clements, D.W. Hutmacher (2013). Growth of confined cancer spheroids: a combined experimental and mathematical modelling approach. Integrative Biology, 5(3): 597-605. doi: 10.1039/c3ib20252f

10. S. Takala-Harrison, T.G. Clark, C.G. Jacob, M.P. Cummings, O. Miotto, A.M. Dondorp, M.M. Fukuda, F. Nosten, H. Noedl, M. Imwong, D. Bethell, Y. Se, C. Lon, S. D. Tyner, D. L. Saunders, D. Socheat, F. Ariey, A. Pyae Phyo, P. Starzengruber, H. Fuehrer, P. Swoboda, K. Stepniewska, J.A.Flegg, C. Arze, G. C. Cerqueira, J.C. Silva, S.M. Ricklefs, S.F. Porcella, R.M. Stephens, M. Adams, L.J. Kenefic, S. Campino, S. Auburn, B. MacInnis, D. P. Kwiatkowski, X. Sur, N.J. White, P. Ringwald, C. V. Plowe (2013). Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. PNAS, 110(1): 240-245. doi: 10.1073/pnas.1211205110

9. J.A. Flegg, D.G. Mallet and M. Upton (2013). Students’ approaches to learning a new mathematical model. Teaching Mathematics and Its Applications, 32(1): 28-37. doi: 10.1093/teamat/hrs014

8. S. N. Menon, J.A. Flegg, S. W. McCue, R. C. Schugart, R. A. Dawson and D. L. S. McElwain (2012). Modelling the interaction of keratinocytes and fibroblasts during normal and abnormal wound healing processes. Proceedings Royal Society B, 279(1741): 3329-3338. doi: 10.1098/rspb.2012.0319

7. J.A. Flegg, H. M. Byrne, M. B. Flegg, D. L. S. McElwain (2012). Wound healing angiogenesis: the clinical implications of a simple mathematical model. Journal Theoretical Biology, 300: 309–316. doi: 10.1016/j.jtbi.2012.01.043

6. J.A. Flegg, P. J. Guerin, N.J. White, K. Stepniewska (2011). Standardizing the measurement of parasite clearance in falciparum malaria: the parasite clearance estimator. Malaria Journal, 10:339. doi: 10.1186/1475-2875-10-339

5. J.A. Flegg, D.G. Mallet, M. Lupton (2011). Students’ perceptions of the relevance of mathematics in engineering. International Journal of Mathematical Education in Science and Technology, 43(6): 717-732. doi: 10.1080/0020739X.2011.644333

4. J.A. Flegg, H.M. Byrne, D.L.S. McElwain (2010). Mathematical model of hyperbaric oxygen therapy applied to chronic diabetic wounds. Bulletin Mathematical Biology, 72(7): 1867-1891. doi: 10.1007/s11538-010-9514-7

3. J.A. Flegg, D.L.S. McElwain, H.M. Byrne, I.W. Turner (2009). A three species model to simulate application of hyperbaric oxygen therapy to chronic wounds. PLoS Computational Biology, 5(7): e1000451. doi: 10.1371/journal.pcbi.1000451

2. J.A. Thackham, D.L.S. McElwain, I.W. Turner (2009). Computational approaches to solving equations arising from wound healing. Bulletin Mathematical Biology, 71(1): 211-246. doi: 10.1007/s11538-008-9360-z

1. J.A. Thackham, D.L.S. McElwain, R.J. Long (2008). The use of hyperbaric oxygen therapy to treat chronic wounds: A review. Wound Repair Regeneration, 16(3): 321–330. doi: 10.1111/j.1524-475X.2008.00372.x

Refereed conference papers

5. J. Hall, J.A. Flegg, T. Robinson, and H. Wilkinson (2019). First and nal year undergraduate students’ perceptions of university mathematics departments. In A. Weinberg, D. Moore-Russo, H. Soto, and M. Wawro (Eds), Proceedings of the 22nd Annual Conference on Research in Undergraduate Mathematics Education. Oklahoma City, OK, pages 910-917.

4. J. Hall,  T. Robinson, J.A. Flegg, J. Wilkinson (2019). Visual representations of undergraduate students’ experiences of university mathematics departments. In S. Otten, A. G. Candela, Z. de Araujo, C. Haines, & C. Munter (Eds.), Proceedings of the 41st Annual Meeting of the North American Chapter of the International Group for the Psychology of Mathematics Education, St. Louis, USA, pp. 1,494-1,498.

3. J. Hall,  T. Robinson, J.A. Flegg, J. Wilkinson (2019). Students’ gendered experiences in undergraduate programs in university mathematics departments. In M. Graven, H. Venkat, A. Essien, & P. Vale (Eds.), Proceedings of the 43rd Conference of the International Group for the Psychology of Mathematics Education, Pretoria, South Africa, pp. 320-327.

2. D.G. Mallet, J.A. Flegg (2011). Towards a classification of criterion referenced assessment models in mathematics courses: student and academic perspectives. In Barton, S. (Ed.), Proceedings of Global Learn Asia Pacific 2011, AACE, Melbourne, Australia, pp. 479-482.

1. M. Burchill, M.B. Flegg, D. Gramotnev, G. Gramotnev, D. Katoshevski, and J.A. Thackham (2008). Ultrasonic manipulation and trapping of airborne nano-particles. In Clay, R. (Ed.), Proceedings of the Australian Institute of Physics 18th National Congress incorporating the 27th AINSE Plasma Science Conference, Adelaide, Australia, pp 9-12.