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Hematopoietic stem cells in mammals are known to reside mostly in the bone marrow, but also transitively passage in small numbers in the blood. Experimental findings have suggested that they exist in a dynamic equilibrium, continuously…
Causal inference across multiple data sources offers a promising avenue to enhance the generalizability and replicability of scientific findings. However, data integration methods for time-to-event outcomes, common in biomedical research,…
The adaptive immune system responds to pathogens by selecting clones of cells with specific receptors. While clonal selection in response to particular antigens has been studied in detail, it is unknown how a lifetime of exposures to many…
Heterogeneity in the size distribution of cancer cell populations has been recently linked to drug resistance and invasiveness. However, despite many progresses have been made in understanding how such heterogeneous size distributions arise…
T1 transitions, which are localised cell rearrangements, play an important role in the fluidization of epithelial monolayers. Using a multi-phase field model and an active elastic solid model, we show that although each cell undergoes T1…
Since its emergence in 1968, influenza A (H3N2) has evolved extensively in genotype and antigenic phenotype. Antigenic evolution occurs in the context of a two-dimensional 'antigenic map', while genetic evolution shows a characteristic…
Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature…
We investigate the potential of patent data for improving the antibody humanness prediction using a multi-stage, multi-loss training process. Humanness serves as a proxy for the immunogenic response to antibody therapeutics, one of the…
Signal transducers and activators of transcription (STATs) are key molecular determinants of T cell fate and effector function. A number of inflammatory diseases are characterized by an altered balance of T cell phenotypes and cytokine…
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes,…
Cells are known to exert forces to sense their physical surroundings for guidance of motion and fate decisions. Here, we propose that cells might do mechanical work to drive their own evolution, taking inspiration from the adaptive immune…
Modelling, analysing and inferring triggering mechanisms in population reproduction is fundamental in many biological applications. It is also an active and growing research domain in mathematical biology. In this chapter, we review the…
Among various possible causes of autoimmune disease, an important role is played by infections that can result in a breakdown of immune tolerance, primarily through the mechanism of "molecular mimicry". In this paper we propose and analyse…
In this paper we extend the Celada-Seiden (CS) model of the humoral immune response to include infectious virus and cytotoxic T lymphocytes (cellular response). The response of the system to virus involves a competition between the ability…
This paper explores a number of questions regarding optimal strategies evolved by viruses upon entry into a vertebrate host. The infected cell life cycle consists of a non-productively infected stage in which it is producing virions but not…
Immunological systems have been an abundant inspiration to contemporary computer scientists. Problem solving strategies, stemming from known immune system phenomena, have been successfully applied to challenging problems of modern computing…
The Beyond-Linear-Use-of-Equation-Superposition (BLUES) function method is extended to coupled nonlinear ordinary differential equations and applied to the epidemiological SIRS model with vaccination. Accurate analytic approximations are…
Immune cells have evolved to recognize and eliminate pathogens, and the efficiency of this process can be measured in a Petri dish. Yet, even if the cells are time-lapse recorded and tracked with high resolution, it is difficult to judge…
We propose a model of the immunity to a cyclical epidemic disease taking account not only of seasonal boosts during the infectious season, but also of residual immunity remaining from one season to the next. The focus is on the exponential…
Infectious disease forecasts can reduce mortality and morbidity by supporting evidence-based public health decision making. Most epidemic models train on surveillance and structured data (e.g. weather, mobility, media), missing contextual…