Related papers: Towards a quantitative theory of tolerance
Despite the extreme diversity of T cell repertoires, many identical T-cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely-shared sequences, often referred to as `public', have been suggested…
Pathogens drive changes in host immune systems that in turn exert pressure for pathogens to evolve. Quantifying and understanding this constant coevolutionary process has clear practical global health implications. Yet its relatively easier…
Adaptive control in biological systems, such as intestinal immunity, remains poorly understood despite detailed knowledge of underlying regulatory networks. We propose an alternative framework based on stochastic martingale turnover, in…
A joint characterisation of the controllability and observability of a particular kind of discrete system has been developed. The key idea of the procedure can be reduced to a correct choice of the sampling sequence. This freedom, owing to…
Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in…
Within the germinal center in follicles, B-cells proliferate, mutate and differentiate, while being submitted to a powerful selection~: a micro-evolutionary mechanism at the heart of adaptive immunity. A new foreign pathogen is confronted…
Risk-driven behavior provides a feedback mechanism through which individuals both shape and are collectively affected by an epidemic. We introduce a general and flexible compartmental model to study the effect of heterogeneity in the…
Biological systems, from cells to organisms, must respond to the ever changing environment in order to survive and function. This is not a simple task given the often random nature of the signals they receive, as well as the intrinsically…
Understanding and modelling the complexity of the immune system is a challenge that is shared by the ImmunoComplexiT$^1$ thematic network from the RNSC. The immune system is a complex biological, adaptive, highly diversified, self-organized…
Researching the specificity of TCR contributes to the development of immunotherapy and provides new opportunities and strategies for personalized cancer immunotherapy. Therefore, we established a TCR generative specificity detection…
Populations of heterogeneous cells play an important role in many biological systems. In this paper we consider systems where each cell can be modelled by an ordinary differential equation. To account for heterogeneity, parameter values are…
T-cell receptors (TCRs) play a crucial role in the immune system by recognizing and binding to specific antigens presented by infected or cancerous cells. Understanding the sequence patterns of TCRs is essential for developing targeted…
This paper argues that one of the most important decisions in designing and deploying censorship resistance systems is whether one set of system options should be selected (the best), or whether there should be several sets of good ones. We…
Resiliency has garnered attention in the management of critical infrastructure as a metric of system performance, but there are significant roadblocks to its implementation in a realistic decision-making framework. Contrasted to risk and…
A key challenge in molecular biology is to decipher the mapping of protein sequence to function. To perform this mapping requires the identification of sequence features most informative about function. Here, we quantify the amount of…
Quantum state tomography on a d-dimensional system demands resources that grow rapidly with d. They may be reduced by using model selection to tailor the number of parameters in the model (i.e., the size of the density matrix). Most model…
Previous work on controllable text generation has explored the idea of control from the latent space, such as optimizing a representation with attribute-related classifiers or sampling a representation from relevant discrete samples.…
This paper investigates the dynamics of immune response and autoimmunity with particular emphasis on the role of regulatory T cells (Tregs), T cells with different activation thresholds, and cytokines in mediating T cell activity. Analysis…
Multivalency is prevalent in various biological systems and applications due to the superselectivity that arises from the cooperativity of multivalent binding. Traditionally, it was thought that weaker individual binding would improve the…
Standard inference about a scalar parameter estimated via GMM amounts to applying a t-test to a particular set of observations. If the number of observations is not very large, then moderately heavy tails can lead to poor behavior of the…