Related papers: Inferring the immune response from repertoire sequ…
We use mean field theory to study the response properties of a simple randomly-connected model cortical network of leaky integrate-and-fire neurons with balanced excitation and inhibition. The formulation permits arbitrary temporal…
Gene regulatory circuits must contend with intrinsic noise that arises due to finite numbers of proteins. While some circuits act to reduce this noise, others appear to exploit it. A striking example is the competence circuit in Bacillus…
Spectroscopy infers the internal structure of physical systems by measuring their response to perturbations. We apply this principle to neural networks: perturbing the data distribution by upweighting a token $y$ in context $x$, we measure…
Viral infections trigger complex immune responses with heterogeneous outcomes shaped by nonlinear feedbacks. An ordinary differential equation model is developed to investigate immune response dynamics during viral infection, incorporating…
We introduce and analyse an individual-based evolutionary model, in which a population of genetically diverse organisms compete with each other for limited resources. Through theoretical analysis and stochastic simulations, we show that the…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only…
The set of T cells that express the same T cell receptor (TCR) sequence represents a T cell clone. The number of different naive T cell clones in an organism reflects the number of different T cell receptors (TCRs) arising from…
Scenarios requiring humans to choose from multiple seemingly optimal actions are commonplace, however standard imitation learning often fails to capture this behavior. Instead, an over-reliance on replicating expert actions induces…
Oscillations of the transcription factor NF-kappa B have been observed experimentally both for cell populations by Hoffmann et al. (2002) and for single cells by Nelson et al. (2004). The latter experiments show significant cell-to-cell…
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…
Somatic hypermutations of immunoglobulin (Ig) genes occuring during affinity maturation drive B-cell receptors' ability to evolve strong binding to their antigenic targets. The landscape of these mutations is highly heterogeneous, with…
Bacterial populations that colonize a host play important roles in host health, including serving as a reservoir that transmits to other hosts and from which invasive strains emerge, thus emphasizing the importance of understanding rates of…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
Information capacity of a symbol sequence is a measure of the unexpectedness of a continuation of given string of symbols. Continuation of a string is determined through the maximum entropy of the reconstructed frequency dictionary; the…
Response variability, as measured by fluctuating responses upon repeated performance of trials, is a major component of neural responses, and its characterization is key to interpret high dimensional population recordings. Response…
Understanding how vaccines perform against different pathogen genotypes is crucial for developing effective prevention strategies, particularly for highly genetically diverse pathogens like HIV. Sieve analysis is a statistical framework…
Understanding the structure of the human T-cell receptor repertoire is a crucial precondition to understand the ability of the immune system to recognize and respond to antigens. T-cells are often compared via the complementarity…
Feedback in cellular processes is typically inferred through cellular responses to experimental perturbations. Modular response analysis provides a theoretical framework for translating specific perturbations into feedback sensitivities…
Phoneme frequency distributions exhibit robust statistical regularities across languages, including exponential-tailed rank-frequency patterns and a negative relationship between phonemic inventory size and the relative entropy of the…