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T-cells are a crucial subset of white blood cells that play a central role in the immune system. When T-cells bind antigens, it leads to cell activation and the induction of an immune response. If T-cells are activated by antigens in vivo…

The mammalian adaptive immune system has evolved over millions of years to become an incredibly effective defense against foreign antigens. The adaptive immune system's humoral response creates plasma B cells and memory B cells, each with…

Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…

The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of…

The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea ('ceRNA hypothesis') that…

The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a…

The similarity between neural and immune networks has been known for decades, but so far we did not understand the mechanism that allows the immune system, unlike associative neural networks, to recall and execute a large number of…

Our main purpose is to compare classical nonself-centered, two-signal theoretical models of the adaptive immune system with a novel, self-centered, one-signal model developed by our research group. Our model hypothesizes that the immune…

With the rapid evolution of wireless mobile devices, there emerges an increased need to design effective collaboration mechanisms between intelligent agents, so as to gradually approach the final collective objective through continuously…

The immune system recognizes a myriad of invading pathogens and their toxic products. It does so with a finite repertoire of antibodies and T cell receptors. We here describe theories that quantify the immune system dynamics. We describe…

In previous work, we studied host response to a pathogen which uses a cycle of immunologically distinct stages to establish and maintain infection. We showed that for generic parameter values, the system has a unique biologically meaningful…

Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…

The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…

The recent development of diffusion models has led to significant progress in solving inverse problems by leveraging these models as powerful generative priors. However, challenges persist due to the ill-posed nature of such problems, often…

Tensor renormalization group (TRG) constitutes an important methodology for accurate simulations of strongly correlated lattice models. Facilitated by the automatic differentiation technique widely used in deep learning, we propose a…

The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…

We study a dynamical system model of an idiotypic immune network with a small number of degrees of freedom, mainly focusing on the effect of a threshold above which antibodies can recognise antibodies. The response of the system to…

Humans have been able to tackle biosphere complexities by acting as ecosystem engineers, profoundly changing the flows of matter, energy and information. This includes major innovations that allowed to reduce and control the impact of…

Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…

Tumor-immune interactions are central to cancer progression and treatment outcomes. In this study, we present a stochastic agent-based model that integrates cellular heterogeneity, spatial cell-cell interactions, and drug resistance…