Publications

Preprints

• Villa, C., Maini, P.K., Browning, A.P., Jenner, A.L., Hamis, S., Cassidy, T., Reducing phenotype-structured PDE models of cancer evolution to systems of ODEs: a generalised moment dynamics approach, arXiv: 2406.01505, link

• Iyaniwura$^{+}$, A., Cassidy$^{+}$, T., Ribeiro, R.M., Perelson, A.S., A multiscale model of the action of a capsid assembly modulator for the treatment of chronic hepatitis B, biorXiv: 2024.07.16.603658 link

• Hamis, S., Browning, A.P., Jenner, A.L., Villa, C., Maini, P.K., Cassidy, T., Growth rate-driven modelling reveals how phenotypic adaptation drives drug resistance in BRAFV600E-mutant melanoma, biorXiv: 2024.08.14.607616, link

• Browning, A.P., Crossley, R.M., Villa, C., Maini, P.K., Jenner, A.L., Cassidy, T., Hamis, S., Identifiability of heterogeneous phenotype adaptation from low-cell-count experiments and a stochastic model, biorXiv: 2024.08.19.608540, link

• Cassidy, T., Using multi-delay discrete delay differential equations to accurately simulate models with distributed delays, arXiv:2410.09451, link

Publications

Some of these papers are unfortunately behind paywalls. Please contact me and I will be happy to send you the published PDF.

• Braniff, N., Joshi, T., Cassidy, T., Trogdon, M., Kumar, R., Poels, K., Allen, R., Musante, C.J., and Shtylla, B., An integrated quantitative systems pharmacology virtual population approach for calibration with oncology efficacy endpoints, to appear, CPT: Pharmacometrics & Systems Pharmacology}_

• Cassidy, T., Stephenson, K.E., Barouch, D.H., Perelson, A.S., Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1, PLoS Computational Biology, 20, 3 (2024). link

• Cassidy, T., A continuation technique for maximum likelihood estimators in biological models, Bulletin of Mathematical Biology, 85, 90 (2023). link

• Cassidy, T., Gillich, P.*, Humphries, A.R., and van Dorp, C.H., Numerical methods and hypoexponential approximations for Gamma distributed delay differential equations, 87, 6, 1043–1089 (2022), The IMA Journal of Applied Mathematics, link Virtual talk on this work applied to cancer modelling

• Sanche, S., Cassidy, T., Chu, P., Perelson, A.S., Ribeiro, R.M., and Ke, R., A simple model of COVID-19 explains disease severity and the effect of treatments, Scientific Reports, 12, 14210 (2022), DOI: 10.1038/s41598-022-18244-2. link

• Stephenson, K.E., Julg, B., Tan, C.S., Zash, R., Walsh, S.R., Rolle, C-P., Monczor, A.N., Lupo, S., Gelderblom, H.C., Ansel, J.L., Kanhilal, D.G., Maxfield, L.F., Nkolola, J., Borducchi, E.N., Abbink, P., Liu, J., Peter, L., Chandrashekar, A., Nityanandam, R., Lin, Z., Setaro, A., Sapiente, J., Chen, Z., Sunner, L., Cassidy, T., Bennett, C., Sato, A., Mayer, B., Perelson, A.S., deCamp, A., Priddy, F.H., Wagh, K., Giorgi, E.E., Yates, N.L., Arduino, R.C., DeJesus, E., Tomaras, G.D., Seaman, M.S., Korber, B., and Barouch, D.H., Safety, pharmacokinetics, and antiviral activity of PGT121, a broadly neutralizing monoclonal antibody against HIV-1: a randomized, placebocontrolled, phase 1 clinical trial, Nature Medicine, 27, 1718–1724 (2021), DOI: 10.1038/s41591-021-01509-0. link

• Cassidy, T., Nichol, D., Robertson-Tessi, M., Craig, M., and Anderson, A.R.A., The role of memory in non-genetic inheritance and its impact on cancer treatment resistance, PLOS Computational Biology, 17(8), 2021, e1009348, DOI: 10.1371/journal.pcbi.1009348. link

• Ismail, S.D., Riou, C., Joseph, S.B., Archin, N.M., Margolis, D.M., Perelson, A.S., Cassidy, T., Abrahams, MR., Moeser, M., Council, O.D., McKinnon, L.R., Osman, F., Karim, Q.A., Abdool Karim, S.S., Swanstrom, R., Williamson, C., Garrett, N.J., Burgers, W.A., Immunological correlates of the HIV-1 replication-competent reservoir size, Clinical Infectious Diseases, 73, 8 (2021), 1528–1531. link

• Cassidy, T., Distributed Delay Differential Equation Representations of Cyclic Differential Equations, SIAM Journal on Applied Mathematics, 81(4), 1742–1766, DOI: doi.org/10.1137/20M1351606. link

• Jenner, A.L., Cassidy, T., Belaid*, K., Bourgeois-Daigneault, M.C., and Craig, M., In silico trials predict that combination strategies for enhancing vesicular stomatisis oncolytic virus are determined by tumour aggressivity, Journal for ImmunoTherapy of Cancer (2021), 9:e001387. doi: 10.1136/jitc-2020-001387. link

• Cassidy, T., Humphries, A.R., Craig, M., and Mackey, M.C., Characterizing chemotherapy-induced neutropenia and monocytopenia through mathematical modelling, Bulletin of Mathematical Biology, 82, 104, (2020), DOI: 10.1007/s11538-020-00777-0. link

• Cassidy, T. and Craig. M, Determinants of combination GM-CSF immunotherapy and oncolytic virotherapy success identified through in silico treatment personalization, PLOS Computational Biology (2019). link

• Cassidy, T. and Humphries, A.R., A Mathematical Model Of Viral Oncology As An Immuno-Oncology Instigator, Mathematical Medicine and Biology: A Journal of the IMA, 37(1):117-151, (2020), DOI:10.1093/imammb/dqz008. link

• Cassidy, T., Craig, M. and Humphries, A.R., Equivalences Between Age Structured Models and State Dependent Distributed Delay Differential Equations, Mathematical Biosciences and Engineering, (2019), 16(5): 5419-5450. DOI: 10.3934/mbe.2019270. link

• De Souza, D.C, Craig, M., Cassidy, T., Li, J., Nekka, F., Bélair, J. and Humphries, A.R., Transit and lifespan in neutrophil production: implications for drug intervention, Journal of Pharmacokinetics and Pharmacodynamics, (2018) 45: 59. DOI: 10.1007/s10928-017-9560-y. link

• Cassidy, T., Gaudreau, P. and Safouhi, H. On the Computation of Eigenvalues of the Anharmonic Coulombic Potential. Journal of Mathematical Chemistry, (2018) 56: 477. DOI:10.1007/s10910-017-0801-5 . link

*: Student under my supervision

$^{+}$: Equal contribution