Catherine A.A. Beauchemin
Associate Professor, Physics

Catherine Beauchemin is an Associate Professor in the Department of Physics at Ryerson University in Toronto, Canada, and a Visiting Senior Scientist in the Interdisciplinary Theoretical and Mathematical Sciences (iTHES, iTHEMS) research programme at RIKEN in Wako, Japan. Her research interest is in self-organizing systems, particularly in mathematical and computer modelling of infectious disease dynamics. Originally from Montreal, she received her undergraduate degree in Computational Physics from the University of Ottawa in 2001, completing her 4th year capstone project in NeuroPhysics under the supervision of Dr. André Longtin. She obtained her Ph.D. under the supervision of Dr. Jack Tuszynski in the Physics Department of the University of Alberta in 2005, working on spatiotemporal modelling of viral infections. Before starting at Ryerson, she was a postdoctoral fellow jointly at the Los Alamos National Laboratory with Dr. Alan S. Perelson, and at the Adaptive Computation Laboratory in the Computer Science Department of the University of New Mexico with Dr. Stephanie Forrest.

Mailing Address:
Department of Physics
Ryerson University
350 Victoria Street
Toronto, ON, M5B 2K3
Office: Kerr Hall South (KHS) 331   [Map]
Phone: (416) 979-5000 ext. 2508
Fax: (416) 979-5343


I am always looking for students and postdocs. For more info, please visit the Jobs page.

Research Interests

The dynamics and mechanisms of self-organizing systems, computational/mathematical modelling of self-organizing systems, with a particular interest in modelling the dynamics of diseases and the immune system. To learn more about the type of research conducted in my group, visit the Research and Publications page.

Études - Studies

  • Ph.D. Biophysics, University of Alberta (2005)
       Advisor:   Jack Tuszynski
       Dissertation:   Spatiotemporal Modelling of Viral Infection Dynamics [PDF]

  • B.Sc. Physique numérique, Université d'Ottawa (2001)
       Advisor:   André Longtin (undergraduate project)
       Project:   L'influence du bruit sur la dynamique d'un neurone [PDF (French)]



  1. Liao, LE, S Kowal, DA Cardenas, and CAA Beauchemin. Exploring virus release as a bottleneck for the spread of influenza A virus infection in vitro and the implications for antiviral therapy with neuraminidase inhibitors. PLoS ONE, TBA, 2017. doi:10.1371/journal.pone.TBA

  2. Dobrovolny, HM and CAA Beauchemin. Modelling the emergence of influenza drug resistance: The roles of surface proteins, the immune response, and antiviral mechanisms. PLoS ONE, 12(7):e0180582, 2017. doi:10.1371/journal.pone.0180582

  3. CAA Beauchemin, T. Miura, and S. Iwami. Duration of SHIV production by infected cells is not exponentially distributed: Implications for estimates of infection parameters and antiviral efficacy. Sci. Rep., 7:42765, 2017. doi:10.1038/srep42765

  4. Palmer, J, HM Dobrovolny, and CAA Beauchemin. The in vivo efficacy of neuraminidase inhibitors cannot be determined from the decay rates of influenza viral titers observed in treated patients. Sci. Rep., 7:40210, 2017. doi:10.1038/srep40210

  5. Liao, LE, S Iwami, and CAA Beauchemin. (In)validating experimentally derived knowledge about influenza A defective interfering particles. J. R. Soc. Interface, 13(124):20160412, 2016. doi:10.1098/rsif.2016.0412

  6. Lipsitch, M, W Barclay, R Raman, CJ Russell, JA Belser, S Cobey, PM Kasson, JO Lloyd-Smith, S Maurer-Stroh, S Riley, CAA Beauchemin, T Bedford, TC Friedrich, A Handel, S Herfst, PR Murcia, B Roche, CO Wilke, and CA Russell. Viral factors in influenza pandemic risk assessment. eLife, 5:e18491, 2016. doi:10.7554/eLife.18491

  7. Simon, PF, MA de La Vega, E Paradis, E Mendoza, KM Coombs, D Kobasa, and CAA Beauchemin. Avian influenza viruses that cause highly virulent infections in humans exhibit distinct replicative properties in contrast to human H1N1 viruses. Sci. Rep., 6:24154, 2016. doi:10.1038/srep24154

  8. Kamal, MA, R Gieschke, A Lemenuel-Diot, CAA Beauchemin, PF Smith, and CR Rayner. A drug-disease model decribing the effect of oseltamivir neuraminidase inhibition on influenza virus progression. Antimicrob. Agents Chemother., 59(9):5388-5395, 2015. doi:10.1128/AAC.00069-15

  9. Kakizoe, Y, S Morita, S Nakaoka, Y Takeuchi, K Sato, T Miura, CAA Beauchemin, and S Iwami. A conservation law for virus infection in vitro. J. Theor. Biol., 376:39-47, 2015. doi:10.1016/j.jtbi.2015.03.034

  10. Kakizoe, Y, S Nakaoka, CAA Beauchemin, S Morita, H Mori, T Igarashi, K Aihara, T Miura, and S Iwami. A method to determine the duration of the eclipse phase for in vitro infection with a highly pathogenic simian human immunodeficiency virus strain. Sci. Rep., 5:10371, 2015. doi:10.1038/srep10371

  11. Paradis, EG, LT Pinilla, BP Holder, Y Abed, G Boivin, and CAA Beauchemin. Impact of the H275Y and I223V mutations in the neuraminidase of the 2009 pandemic influenza virus in vitro and evaluating experimental reproducibility.. PLoS ONE, 10(5):e0126115, 2015. doi:10.1371/journal.pone.0126115

  12. Beauchemin, CAA. Agent-Based Models in Infectious Disease and Immunology. Entry in Björn Engquist, editor, Encyclopedia of Applied and Computational Mathematics, Springer-Verlag, Germany, 2013. [Online: Book's website or Online access to entry]

  13. Dobrovolny, HM, MB Reddy, MA Kamal, CR Rayner, and CAA Beauchemin. Assessing mathematical models of influenza infections using features of the immune response. PLoS ONE, 8(2):e57088, 2013. doi:10.1371/journal.pone.0057088

  14. Pinilla, LT, BP Holder, Y Abed, G Boivin, and CAA Beauchemin. The H275Y neuraminidase mutation of the pandemic A/H1N1 virus lengthens the eclipse phase and reduces viral output of infected cells, potentially compromising fitness in ferrets. J. Virol., 86(19):10651-10660, 2012. doi:10.1128/JVI.07244-11

  15. Iwami, S, BP Holder, CAA Beauchemin, S Morita, T Tada, K Sato, T Igarashi, and T Miura. Quantification system for the viral dynamics of a highly pathogenic simian/human immunodeficiency virus based on an in vitro experiment and a mathematical model. Retrovirology, 9(1):18, 2012. doi:10.1186/1742-4690-9-18

  16. Holder, BP, LE Liao, P Simon, G Boivin, and CAA Beauchemin. Design considerations in building in silico equivalents of common experimental influenza virus assays and the benefits of such an approach. Autoimmunity, 44(4), 2011. doi:10.3109/08916934.2011.523267

  17. Holder, BP, P Simon, LE Liao, Y Abed, X Bouhy, CAA Beauchemin, and G Boivin. Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. PLoS ONE, 6(3):e14767, 2011. doi:10.1371/journal.pone.0014767

  18. Simon, P, BP Holder, X Bouhy, Y Abed, CAA Beauchemin, and G Boivin. The I222V neuraminidase mutation has a compensatory role in the replication of an oseltamivir-resistant A/H3N2 E119V mutant. J. Clin. Microbiol., 49(2):715-717, 2011. doi:10.1128/JCM.01732-10

  19. Holder, BP, and CAA Beauchemin. Exploring the effect of biological delays in kinetic models of influenza within a host or cell culture. BMC Public Health, 11(Suppl 1):S10, 2011. doi:10.1186/1471-2458-11-S1-S10

  20. Beauchemin, CAA, and A Handel. A review of mathematical models of influenza A infections within a host or cell culture: Lessons learned and challenges ahead. BMC Public Health, 11(Suppl 1):S7, 2011. doi:10.1186/1471-2458-11-S1-S7

  21. Dobrovolny, HM, R Gieschke, BE Davies, NL Jumbe, and CAA Beauchemin. Neuraminidase inhibitors for treatment of human and avian strain influenza: A comparative modeling study. J. Theor. Biol., 269(1):234-244, 2011. doi:10.1016/j.jtbi.2010.10.017

  22. Mitchell, H, D Levin, S Forrest, CAA Beauchemin, J Tipper, J Knight, N Donart, RC Layton, J Pyles, P Gao, KS Harrod, AS Perelson, and F Koster. Higher replication efficiency of 2009 (H1N1) pandemic influenza than seasonal and avian strains: Kinetics from epithelial cell culture and computational modeling. J. Virol., 85(2):1125-1135, 2011. doi:10.1128/JVI.01722-10

  23. Dobrovolny, HM, MJ Baron, R Gieschke, BE Davies, NL Jumbe, and CAA Beauchemin. Exploring cell tropism as a possible contributor to influenza infection severity. PLoS ONE, 5(11):e13811, 2010. doi:10.1371/journal.pone.0013811

  24. Craddock, TJA, C Beauchemin, and JA Tuszynski. Information processing mechanisms in microtubules at physiological temperature: Model predictions for experimental tests. BioSystems, 97(1):28-34, 2009. doi:10.1016/j.biosystems.2009.04.001

  25. Bauer, AL, CAA Beauchemin, and AS Perelson. Agent-based modeling of host-pathogen systems: The successes and challenges. Inform. Sciences, 179(10):1379-1389, 2009. doi:10.1016/j.ins.2008.11.012 [Draft: arXiv:0807.0247 q-bio.CB]

  26. Beauchemin, CAA, JJ McSharry, GL Drusano, JT Nguyen, GT Went, RM Ribeiro, and AS Perelson. Modeling amantadine treatment of influenza A virus in vitro. J. Theor. Biol., 254(2):439-451, 2008. doi:10.1016/j.jtbi.2008.05.031

  27. Beauchemin, C, NM Dixit, and AS Perelson. Characterizing T cell movement within lymph nodes in the absence of antigen. J. Immunol., 178(9):5505-5512, 2007. doi:10.4049/jimmunol.178.9.5505

  28. Forrest, S, and C Beauchemin. Computer immunology. Immunol. Rev., 216(1):176-197, 2007. doi:10.1111/j.1600-065X.2007.00499.x

  29. Beauchemin, C, S Forrest, and FT Koster. Modeling influenza viral dynamics in tissue. In H Bersini and J Carneiro, editor, Proceedings of the Fifth International Conference on Artificial Immune Systems, ICARIS 2006, pages 23-36, 4-6 September, Oeiras, Portugal, 2006. Springer Verlag Berlin Heidelberg. doi:10.1007/11823940_3

  30. Beauchemin, C. Probing the effects of the well-mixed assumption on viral infection dynamics. J. Theor. Biol., 242(2):464-477, 2006. doi:10.1016/j.jtbi.2006.03.014 [Draft: arXiv:q-bio.CB/0505043]

  31. Baccam, P, C Beauchemin, CA Macken, FG Hayden, and AS Perelson. Kinetics of influenza A virus infection in humans. J. Virol., 80(15):7590-7599, 2006. doi:10.1128/JVI.01623-05 [Supplemental Material: here]

  32. Beauchemin, C, J Samuel, and J Tuszynski. A simple cellular automaton model for influenza A viral infections. J. Theor. Biol., 232(2):223-234, 2005. doi:10.1016/j.jtbi.2004.08.001 [Draft: arXiv:q-bio.CB/0402012]

  33. Voorhees, B, and C Beauchemin. Point mutations and transitions between cellular automata attractor basins. Complex Systems, 15(1), 2004.
    [Draft: arXiv:nlin.CG/0306033] [Published: Complex Systems]

Recherche et Projets - Research and Projects

My old class projects

  • Reading course on the Immune System (2002-2003)
    [Fall 2002][Winter 2003]

  • Cellular Automata: Statistical Models With Various Applications (2002)

Liens utiles / Useful Links

Ultimate Linux Apps

My favorite applications for doing what I do:

Last modified: June 16, 2017, 01:11.