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This article reviews quantitative methods to estimate the basic reproduction number of pandemic influenza, a key threshold quantity to help determine the intensity of interventions required to control the disease. Although it is difficult…
We analyze infection spreading processes in a system where only a fraction $p$ of individuals can be affected by disease, while remaining $1-p$ individuals are immune. Such a picture can emerge as a natural consequence of previously…
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We…
Artificial intelligence (AI) is accelerating progress in modeling T and B cell receptors by enabling predictive and generative frameworks grounded in sequence data and immune context. This chapter surveys recent advances in the use of…
Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens…
Competition within the immune system may degrade immune control of viral infections. We formalize the evolution that occurs in both HIV-1 and the immune system quasispecies. Inclusion of competition in the immune system leads to a novel…
We describe methods that extend (generalize or transport) causal inferences from cluster randomized trials to a target population of clusters, under a general nonparametric model that allows for arbitrary within-cluster dependence. We…
In [Math. Comput. Sci. 12 (2018), no. 2, 111--127], a delayed model describing the dynamics of the Human Immunodeficiency Virus (HIV) with Cytotoxic T Lymphocytes (CTL) immune response is investigated by Allali, Harroudi and Torres. Here,…
The success of a vaccination program is crucially dependent on its adoption by a critical fraction of the population, as the resulting herd immunity prevents future outbreaks of an epidemic. However, the effectiveness of a campaign can…
The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
One of the key phenomena in the adaptive immune response to infection and immunization is affinity maturation, during which antibody genes are mutated and selected, typically resulting in a substantial increase in binding affinity to the…
Immune repertoires rely on diversity of T-cell and B-cell receptors to protect us against foreign threats. The ability to recognize a wide variety of pathogens is linked to the number of different clonotypes expressed by an individual. Out…
Cells of the immune system are confronted with opposing pro- and anti-inflammatory signals. Dendritic cells (DC) integrate these cues to make informed decisions whether to initiate an immune response. Confronted with exogenous microbial…
Although Vitamin D is believed to be involved in a large number of immune responses our understanding of these processes at cellular level remained at infancy. We develop and solve a coarse grained kinetic network model to quantify the…
Centrifugation is a commonly performed laboratory procedure that helps to separate blood cells such as $RBCs$, $WBCs$, and platelets from plasma or serum. Although centrifugation is a routine procedure in most medical laboratories, the…
Dendritic cells are antigen presenting cells that provide a vital link between the innate and adaptive immune system. Research into this family of cells has revealed that they perform the role of coordinating T-cell based immune responses,…
When analysing in vitro data, growth kinetics of influenza strains are often compared by computing their growth rates, which are sometimes used as proxies for fitness. However, analogous to mechanistic epidemic models, the growth rate can…
Antibodies, crucial for immune defense, primarily rely on complementarity-determining regions (CDRs) to bind and neutralize antigens, such as viruses. The design of these CDRs determines the antibody's affinity and specificity towards its…
Existing approaches to modelling antibody concentration data are mostly based on finite mixture models that rely on the assumption that individuals can be divided into two distinct groups: seronegative and seropositive. Here, we challenge…