相关论文: Model for Diversity Analysis of Antigen Receptor R…

To recognize pathogens, B and T lymphocytes are endowed with a wide repertoire of receptors generated stochastically by V(D)J recombination. Measuring and estimating the diversity of these receptors is of great importance for understanding…

Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens…

Studies of T cells and their clonally unique receptors have shown promise in elucidating the association between immune response and human disease. Methods to identify T-cell receptor clones which expand or contract in response to certain…

Multivariate count data are commonly encountered through high-throughput sequencing technologies in bioinformatics, text mining, or in sports analytics. Although the Poisson distribution seems a natural fit to these count data, its…

Biological organisms have evolved a wide range of immune mechanisms to defend themselves against pathogens. Beyond molecular details, these mechanisms differ in how protection is acquired, processed and passed on to subsequent generations…

We present a novel model that describes the within-host evolutionary dynamics of parasites undergoing antigenic variation. The approach uses a multi-type branching process with two types of entities defined according to their relationship…

We derive a Poisson random field model for population site polymorphisms differences within and between two species that share a relatively recent common ancestor. The model can be either equilibrium or time inhomogeneous. We first consider…

We consider the estimation of densities in multiple subpopulations, where the available sample size in each subpopulation greatly varies. This problem occurs in epidemiology, for example, where different diseases may share similar…

We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of…

T cells are central to the adaptive immune response, capable of detecting pathogenic antigens while ignoring healthy tissues with remarkable specificity and sensitivity. Quantitatively understanding how T cell receptors (TCRs) discriminate…

The human adaptive immune response is known to weaken in advanced age, resulting in increased severity of pathogen-born illness, poor vaccine efficacy, and a higher prevalence of cancer in the elderly. Age-related erosion of the T-cell…

The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ…

In this paper, we present a nonparametric method to estimate the heterogeneity of a random medium from the angular distribution of intensity transmitted through a slab of random material. Our approach is based on the modeling of forward…

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…

We study nonparametric methods for the setting where multiple distinct networks are observed on the same set of nodes. Such samples may arise in the form of replicated networks drawn from a common distribution, or in the form of…

The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…

The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…

Imaging demonstrates that preclinical and human tumors are heterogeneous, i.e. a single tumor can exhibit multiple regions that behave differently during both normal development and also in response to treatment. The large variations…

In recent years, advances in high throughput sequencing technology have led to a need for specialized methods for the analysis of digital gene expression data. While gene expression data measured on a microarray take on continuous values…

This paper deals with a new model for clonal network dynamics. We describe in detail this model and derive special equations governing immune system dynamics based on the general gradient type principles that can be inherent to a wide class…