相关论文: A Multi-Scale Model for Correlation in B Cell VDJ …

In the field of environmental toxicology, rapid and precise assessment of the inflammatory response to pollutants in biological models is critical. This study leverages the power of deep learning to enable automated assessments of…

The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors (TCRs). This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts…

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…

Collective behaviour in living systems is observed across many scales, from bacteria to insects, to fish shoals. Zebrafish have emerged as a model system amenable to laboratory study. Here we report a three-dimensional study of the…

Zebrafish have been used as a model organism in many areas of biology, including the study of pattern formation. The mean-field survival model is a coupled ODE system describing the expected evolution of chromatophores coordinating to form…

We quantify the VDJ recombination and somatic hypermutation processes in human B-cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the…

Zebrafish share a high degree of homology with human genes and are commonly used as model organism in biomedical research. For medical laboratories, counting zebrafish is a daily task. Due to the tiny size of zebrafish, manual visual…

Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM…

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…

Zebrafish are a common model organism used to identify new disease therapeutics. High-throughput drug screens can be performed on larval zebrafish in multi-well plates by observing changes in behaviour following a treatment. Analysis of…

Collective motion is one of the most ubiquitous behaviours displayed by social organisms and has led to the development of numerous models. Recent advances in the understanding of sensory system and information processing by animals impel…

Many events in the vertebrate immune system are influenced by some element of chance. The objective of the present work is to describe affinity maturation of B lymphocytes (in which random events are perhaps the most characteristic), and to…

In this paper we propose a "discrete in continuous" mathematical model for the morphogenesis of the posterior lateral line system in zebrafishes. Our model follows closely the results obtained in recent biological experiments. We rely on a…

Data-driven benchmarks have led to significant progress in key scientific modeling domains including weather and structural biology. Here, we introduce the Zebrafish Activity Prediction Benchmark (ZAPBench) to measure progress on the…

Living organisms are primarily made of cells. Identifying them and characterizing their geometry and spatial distribution is a first step towards building multi-scale models of these biomaterials. We propose a method to count cells using…

Many real-world data sets, especially in biology, are produced by complex nonlinear dynamical systems. In this paper, we focus on brain calcium imaging (CaI) of different organisms (zebrafish and rat), aiming to build a model of joint…

Social behavior across animal species ranges from simple pairwise interactions to thousands of individuals coordinating goal-directed movements. Regardless of the scale, these interactions are governed by the interplay between multimodal…

An inverse procedure is developed and tested to recover functional and structural information from global signals of brains activity. The method assumes a leaky-integrate and fire model with excitatory and inhibitory neurons, coupled via a…

We analyse a minimal model for the primary response in the adaptive immune system comprising three different players: antigens, T and B cells. We assume B-T interactions to be diluted and sampled locally from heterogeneous degree…

The vertebrate immune system is a wonder of modern evolution. Occasionally, however, correlations within the immune system lead to inappropriate recruitment of preexisting T cells against novel viral diseases. We present a random energy…