Related papers: Bayesian inference of antibody evolutionary dynami…
The mechanisms underlying the formation of post-infection sequelae are complex and remain controversial. This hypothesis integrates Bystryn's antibody feedback phenomenon and Imbiakha's immune cost theory, proposing for the first time a…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
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,…
Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to…
We develop a Bayesian approach to predict a continuous or binary outcome from data that are collected from multiple sources with a multi-way (i.e.. multidimensional tensor) structure. As a motivating example we consider molecular data from…
Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology. We introduce an approach that identifies a disease phenotype from…
It is difficult to predict how antibodies will behave when mixed together, even after each has been independently characterized. Here, we present a statistical mechanical model for the activity of antibody mixtures that accounts for whether…
Likelihood-free Bayesian inference algorithms are popular methods for calibrating the parameters of complex, stochastic models, required when the likelihood of the observed data is intractable. These algorithms characteristically rely…
Understanding the dynamics of antibody levels is crucial for characterizing the time-dependent response to immune events: either infections or vaccinations. The sequence and timing of these events significantly influence antibody level…
We present a flexible branching process model for cell population dynamics in synchrony/time-series experiments used to study important cellular processes. Its formulation is constructive, based on an accounting of the unique cohorts in the…
Motivation: The clinical efficacy of antibody therapeutics critically depends on high-affinity target engagement, yet laboratory affinity-maturation campaigns are slow and costly. In computational settings, most protein language models…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…
The vulnerability of machine learning models to adversarial attacks remains a critical security challenge. Traditional defenses, such as adversarial training, typically robustify models by minimizing a worst-case loss. However, these…
Accurate quantification of intracellular metabolic fluxes is central to systems biology and biotechnology. Flux estimation relies on biochemical network models, with $^{13}$C metabolic flux analysis (MFA) being the state-of-the-art…
Biological synaptic transmission is unreliable, and this unreliability likely degrades neural circuit performance. While there are biophysical mechanisms that can increase reliability, for instance by increasing vesicle release probability,…
Consider a branching process with a homogeneous reproduction law. Sampling a single cell uniformly from the population at a time $T > 0$ and looking along the sampled cell's ancestral lineage, we find that the reproduction law is…
In this paper we consider a model based on branching process theory for the proliferation and the dissemination network of T cells in the adaptive immune response. A multi-type Galton Watson branching process is assumed as the basic…
B cell receptor sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is a major contributor to somatic hypermutation, and therefore…
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…