virophysics



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Publications by the Virophysics group

the names of virophysics group members (past and present) are underlined



  1. Srivastava, A, Q Wang, CD Orrù, M Fernandez, Y Compta, B Ghetti, G Zanusso, WQ Zou, B Caughey, and CAA Beauchemin. Enhanced quantitation of pathological ɑ-synuclein in patient biospecimens by RT-QuIC seed amplification assays. PLOS Pathog., 20(9):e1012554, 20 September 2024. doi:10.1371/journal.ppat.1012554.

  2. Porthiyas, J, D Nussey, CAA Beauchemin, DC Warren, C Quirouette, and KP Wilkie. Practical parameter identifiability and handling of censored data with Bayesian inference in mathematical tumour models. NPJ Syst. Biol. Appl., 10:89, 14 August 2024. doi:10.1038/s41540-024-00409-6. [arXiv:2309.13319]

  3. Fung, KYY, TWW Ho, Z Xu, D Neculai, CAA Beauchemin, WL Lee, GD Fairn. Apolipoprotein A1 and high-density lipoprotein limit low-density lipoprotein transcytosis by binding SR-B1. J. Lipid Res., 65(4):100530, April 2024. doi:10.1016/j.jlr.2024.100530.

  4. Kieran, TJ, X Sun, TR Maines, CAA Beauchemin, JA Belser. Exploring associations between viral titer measurements and disease outcomes in ferrets inoculated with 125 contemporary influenza A viruses. J. Virol., 98(2):e0166123, 20 February 2024. doi:10.1128/jvi.01661-23.

  5. Quirouette, C, D Cresta, J Li, KP Wilkie, H Liang, CAA Beauchemin. The effect of random virus failure following cell entry on infection outcome and the success of antiviral therapy. Sci Rep., 13:17243, October 2023. doi:10.1038/s41598-023-44180-w.
    [arXiv:2208.00637]

  6. Creager, H, TJ Kieran, H Zeng, X Sun, JA Pulit-Penaloza, KE Holmes, AF Johnson, TM Tumpey, TR Maines, CAA Beauchemin, JA Belser. Utility of human in vitro data in risk assessments of influenza A virus using the ferret model. J. Virol., 97(1):e0153622, January 2023. doi:10.1128/jvi.01536-22.

  7. Cresta, D, DC Warren, C Quirouette, AP Smith, LC Lane, AM Smith, CAA Beauchemin. Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample's infection concentration. PLOS Comput. Biol., 17(10):e1009480, October, 2021. doi:10.1371/journal.pcbi.1009480.
    [arXiv:2101.11526] [code on GitHub] [web application]

  8. Warren, DC, CAA Beauchemin, MV Barkov, S Nagataki. The maximum energy of shock-accelerated electrons in a microturbulent magnetic field. ApJ, 906(1):33, January 1, 2021. doi:10.3847/1538-4357/abc694 [arXiv:2010.06234]

  9. Liao, LE, J Carruthers, SJ Smither, CL4 Virology Team, SA Weller, D Williamson, TR Laws, I García-Dorival, J Hiscox, BP Holder, CAA Beauchemin, AS Perelson, M López-García, G Lythe, J Barr, C Molina-París. Quantification of Ebola virus replication kinetics in vitro. PLOS Comput. Biol., 16(11):e1008375, November, 2020. doi:10.1371/journal.pcbi.1008375 [arXiv:2010.09898]

  10. Yan, AWC, J Zhou, CAA Beauchemin, CA Russell, WS Barclay, S Riley. Quantifying mechanistic traits of influenza viral dynamics using in vitro data. Epidemics, 33:100406, December, 2020. doi:10.1016/j.epidem.2020.100406 [arXiv:1903.08054]

  11. Quirouette, C, NP Younis, MB Reddy, CAA Beauchemin. A mathematical model describing the localization and spread of influenza A virus infection within the human respiratory tract. PLOS Comput. Biol., 16(4):e1007705, April 13, 2020. doi:10.1371/journal.pcbi.1007705. [arXiv:1908.08482]

  12. Beauchemin, CAA, YI Kim, Q Yu, G Ciaramella, JP DeVincenzo. Uncovering critical properties of the human respiratory syncytial virus by combining in vitro assays and in silico analyses. PLOS ONE, 14(4):e0214708, 2019. doi:10.1371/journal.pone.0214708

  13. Beauchemin, CAA, LE Liao, and K Blahut. Tutorial on agent-based models in NetLogo applied to immunology and virology. arXiv:1808.09499, August 2018. [arXiv:1808.09499]

  14. Handel, A, LE Liao, and CAA Beauchemin. Progress and trends in mathematical modelling of influenza A virus infections. Curr. Opin. Syst. Biol., 12:30-36, 2018. doi:10.1016/j.coisb.2018.08.009 [PDF]

  15. Rose, LM, CAA Beauchemin, and WP Neumann. Modelling endurance and resumption times for repetitive one-hand pushing. Ergonomics, 61(7):891-901, 2018. doi:10.1080/00140139.2018.1427282

  16. 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, 12(8):e0183621, 2017. doi:10.1371/journal.pone.0183621

  17. 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

  18. Beauchemin, CAA, 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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]

  28. 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

  29. 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 [PDF]

  30. 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

  31. 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 [PDF]

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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 [PDF]

  37. 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

  38. 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

  39. 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

  40. 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 [arXiv:0807.0247] [PDF]

  41. 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 [PDF]

  42. 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 [PDF]

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

  44. 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 [PDF]

  45. 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 [arXiv:q-bio.CB/0505043] [PDF]

  46. 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] [PDF]

  47. 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 [arXiv:q-bio.CB/0402012] [PDF]

  48. 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] [PDF]




Last modified: October 10, 2020, 22:41.
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