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