IMMUNE MODELING

We use basic immunology principles to develop mechanistic models of immunity, simulate the progression of an immune response following vaccination or infection, and determine potential mechanisms of protection that underlie empirical observations (e.g., correlates of protection) identified in vaccine clinical studies. Specifically, we use a chemical kinetics-based approach to model 1) cellular and innate immunity, 2) B cell affinity maturation, and 3) antibody-based binding and neutralization.

Publications

Pannala, V. R., H. D. Nguyen, and A. Wallqvist. A stochastic B cell affinity maturation model to characterize mechanisms of protection for tetravalent dengue vaccine constructs. Frontiers in Molecular Biosciences. 2023 July 14; 10:1100434. [PDF, Pubmed]

Nguyen, H. D., S. Chaudhury, A. T. Waickman, H. Friberg, J. R. Currier, and A. Wallqvist. Stochastic model of the adaptive immune response predicts disease severity and captures enhanced cross-reactivity in natural dengue infections. Frontiers in Immunology. 2021 August 17; 12:696755. [PDF, PubMed]

Anderson, C. S., M. Y. Sangster, H. Yang, T. J. Mariani, S. Chaudhury, and D. J. Topham. Implementing sequence-based antigenic distance calculation into immunological shape space model. BMC Bioinformatics. 2020 June 19; 21(1):256. [PDF, PubMed]

Ripoll, D. R., A. Wallqvist, and S. Chaudhury. Molecular simulations reveal the role of antibody fine specificity and viral maturation state on antibody-dependent enhancement of infection in dengue virus. Frontiers in Cellular and Infection Microbiology. 2019 June 6; 9:200. [PDF, PubMed]

Chaudhury, S., E. H. Duncan, T. Atre, C. K. Storme, K. Beck, S. A. Kaba, D. E. Lanar, and E. S. Bergmann-Leitner. Identification of immune signatures of novel adjuvant formulations using machine learning. Scientific Reports. 2018 November 30; 8(1):17508. [PDF, PubMed]

Chaudhury, S., J. A. Regules, C. A. Darko, S. Dutta, A. Wallqvist, N. C. Waters, E. Jongert, F. Lemiale, and E. S. Bergmann-Leitner. Delayed fractional dose regimen of the RTS,S/AS01 malaria vaccine candidate enhances an IgG4 response that inhibits serum opsonophagocytosis. Scientific Reports. 2017 August 11; 7:7998. [PDF, PubMed]

Ripoll, D. R., I. Khavrutskii, A. Wallqvist, and S. Chaudhury. Modeling the role of epitope arrangement on antibody binding stoichiometry in flaviviruses. Biophysical Journal. 2016 October 18; 111(8):1641-1654. [PDF, PubMed]

Chaudhury, S., J. Reifman, and A. Wallqvist. Simulation of B cell affinity maturation explains enhanced antibody cross-reactivity induced by the polyvalent malaria vaccine AMA1. Journal of Immunology. 2014 September 1; 193(5):2073-2086. [PDF, PubMed]