Spatially resolved modelling of immune responses following a multiscale approach: from computational implementation to quantitative predictions

References

[1] J. Argilaguet, M. Pedragosa, A. Esteve-Codina, G. Riera, E. Vidal, C. Peligero-Cruz, V. Casella, D. Andreu, T. Kaisho, G. Bocharov, B. Ludewig, S. Heath, S. and A. Meyerhans, Systems analysis reveals complex biological processes during virus infection fate decisions. Genome Research29 (2019), No. 6, 907–919.10.1101/gr.241372.118Search in Google Scholar PubMed PubMed Central

[2] G. Bocharov, V. Chereshnev, I. Gainova, S. Bazhan, B. Bachmetyev, J. Argilaguet, J. Martinez, and A. Meyerhans, Human immunodeficiency virus infection : from biological observations to mechanistic mathematical modelling. Math. Model. Natur. Phenomena7 (2012), No. 5, 78–104.10.1051/mmnp/20127507Search in Google Scholar

[3] A. Bouchnita, G. Bocharov, A. Meyerhans, and V. Volpert, Hybrid approach to model the spatial regulation of T cell responses. BMC Immunology18 (2017), No. 1, 29.10.1186/s12865-017-0205-0Search in Google Scholar PubMed PubMed Central

[4] A. Bouchnita, G. Bocharov, A. Meyerhans, and V. Volpert, Towards a multiscale model of acute HIV infection. Computation5 (2017), No. 1, 6.10.3390/computation5010006Search in Google Scholar

[5] A. Cappuccio, P. Tieri, and F. Castiglione, Multiscale modelling in immunology: a review. Briefings in Bioinformatics17 (2016), No. 3, 408–418.10.1093/bib/bbv012Search in Google Scholar PubMed

[6] N. A. Cilfone, D. E. Kirschner, and J. J. Linderman, Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems. Cellular and Molecular Bioengineering8 (2015), No. 1, 119–136.10.1007/s12195-014-0363-6Search in Google Scholar PubMed PubMed Central

[7] N. M. Dixit and A. S. Perelson, Multiplicity of human immunodeficiency virus infections in lymphoid tissue. J. Virology78 (2004), No. 16, 8942–8945.10.1128/JVI.78.16.8942-8945.2004Search in Google Scholar PubMed PubMed Central

[8] R. N. Germain, M. Meier-Schellersheim, A. Nita-Lazar, and I. D. Fraser, Systems biology in immunology: A computational modelling perspective. Annual Review of Immunology29 (2011), No. 1, 527–585.10.1146/annurev-immunol-030409-101317Search in Google Scholar PubMed PubMed Central

[9] S. Girel, C. Arpin, J. Marvel, O. Gandrillon, and F.Crauste, Model-based assessment of the role of uneven partitioning of molecular content on heterogeneity and regulation of differentiation in CD8 T-cell immune responses. Frontiers in Immunology10 (2019), 230.10.3389/fimmu.2019.00230Search in Google Scholar PubMed PubMed Central

[10] D. Grebennikov, A. Bouchnita, V. Volpert, N. Bessonov, A. Meyerhans, and G. Bocharov, Spatial lymphocyte dynamics in lymph nodes predicts the cytotoxic T cell frequency needed for HIV infection control. Frontiers in Immunology10 (2019), 1213.10.3389/fimmu.2019.01213Search in Google Scholar PubMed PubMed Central

[11] H. Kim and J. Yin, Robust growth of human immunodeficiency virus type 1 (HIV-1). Biophysical J. 89 (2005), No. 4, 2210–2221.10.1529/biophysj.104.058438Search in Google Scholar PubMed PubMed Central

[12] D. Kirschner, E. Pienaar, S. Marino, and J. J. Linderman, A review of computational and mathematical modelling contributions to our understanding of Mycobacterium tuberculosis within-host infection and treatment. Current Opinion in Systems Biology3 (2017), 170–185.10.1016/j.coisb.2017.05.014Search in Google Scholar PubMed PubMed Central

[13] W. Li, R. N. Germain, and M. Y. Gerner, High-dimensional cell-level analysis of tissues with Ce3D multiplex volume imaging. Nature Protocols14 (2019), No. 6, 1708–1733.10.1038/s41596-019-0156-4Search in Google Scholar PubMed PubMed Central

[14] V. M. Liarski, A. Sibley, N. van Panhuys, J. Ai, A. Chang, D. Kennedy, M. Merolle, R. N. Germain, M. L. Giger, and M. R. Clark, Quantifying in situ adaptive immune cell cognate interactions in humans. Nature Immunology20 (2019), No. 4, 503–513.10.1038/s41590-019-0315-3Search in Google Scholar PubMed PubMed Central

[15] B. Reddy and J. Yin, Quantitative intracellular kinetics of HIV type 1. AIDS Research and Human Retroviruses15 (1999), No. 3, 273–283.10.1089/088922299311457Search in Google Scholar PubMed

[16] M. Rinas, Data-driven modelling of the dynamic competition between virus infection and the antiviral interferon response. PhD Thesis, University of Heidelberg, Heidelberg, 2015.Search in Google Scholar

[17] I. Sazonov, D. Grebennikov, M. Kelbert, and G. Bocharov, Modelling stochastic and deterministic behaviours in virus infection dynamics. Math. Model. Natur. Phenomena12 (2017), No. 5, 63–77.10.1051/mmnp/201712505Search in Google Scholar

[18] C. L. Sershen, S. J. Plimpton, and E. E. May, Oxygen modulates the effectiveness of granuloma mediated host response to mycobacterium tuberculosis: A multiscale computational biology approach. Frontiers in Cellular and Infection Microbiology6 (2016), 6.10.3389/fcimb.2016.00006Search in Google Scholar PubMed PubMed Central

[19] A. Sigal, J. T. Kim, A. B. Balazs, E. Dekel, A. Mayo, R. Milo, and D. Baltimore, Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy. Nature477 (2011), No. 7362, 95–98.10.1038/nature10347Search in Google Scholar PubMed

[20] M. Solis, P. Nakhaei, M. Jalalirad, J. Lacoste, R. Douville, M. Arguello, T. Zhao, M. Laughrea, M. A. Wainberg, and J. Hiscott, RIG-I-mediated antiviral signaling is inhibited in HIV-1 infection by a protease-mediated sequestration of RIG-I. J. Virology85 (2011), No. 3, 1224–1236.10.1128/JVI.01635-10Search in Google Scholar PubMed PubMed Central

[21] C. L. Vestergaard and M. Génois, Temporal Gillespie algorithm: Fast simulation of contagion processes on time-varying networks. PLOS Comput. Biology11 (2015), No. 10, e1004579.10.1371/journal.pcbi.1004579Search in Google Scholar PubMed PubMed Central

[22] C. Zhang, S. Zhou, E. Groppelli, P. Pellegrino, I. Williams, P. Borrow, B. M. Chain, and C. Jolly, Hybrid spreading mechanisms and T cell activation shape the dynamics of HIV-1 infection. PLOS Comput. Biology11 (2015), No. 4, e1004179.10.1371/journal.pcbi.1004179Search in Google Scholar PubMed PubMed Central