Related papers: Quantifying lymphocyte receptor diversity
Some years ago a cellular automata model was proposed to describe the evolution of the immune repertoire of B cells and antibodies based on Jerne's immune network theory and shape-space formalism. Here we investigate if the networks…
Understanding how transient dynamics unfold in response to localized inputs is central to predicting and controlling signal propagation in network systems, including neural processing, epidemic intervention, and power-grid resilience.…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
Immune cells learn about their antigenic targets using tactile sense: during recognition, a highly organized yet dynamic motif, named immunological synapse, forms between immune cells and antigen-presenting cells (APCs). Via synapses,…
A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…
Knowledge of the time at which an HIV-infected individual seroconverts, when the immune system starts responding to HIV infection, plays a vital role in the design and implementation of interventions to reduce the impact of the HIV…
Humans can learn from very few samples, demonstrating an outstanding generalization ability that learning algorithms are still far from reaching. Currently, the most successful models demand enormous amounts of well-labeled data, which are…
T-cell receptor (TCR) interactions with antigenic peptides underpin adaptive immunity and are pivotal for personalized immunotherapy and vaccine development. Despite recent progress, computational modeling of TCR-peptide specificity remains…
The i.i.d. assumption is a useful idealization that underpins many successful approaches to supervised machine learning. However, its violation can lead to models that learn to exploit spurious correlations in the training data, rendering…
Pattern-diluted associative networks were introduced recently as models for the immune system, with nodes representing T-lymphocytes and stored patterns representing signalling protocols between T- and B-lymphocytes. It was shown earlier…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…
We derive and analyze a generic, recursive algorithm for estimating all splits in a finite cluster tree as well as the corresponding clusters. We further investigate statistical properties of this generic clustering algorithm when it…
T cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes is fundamental to adaptive immunity and central to the development of T cell-based immunotherapies. While transformer-based models have shown promise in predicting TCR-pMHC…
Accurate diagnostic tests are essential for effective screening and treatment. However, individual biomarkers often fail to provide sufficient diagnostic accuracy, as they typically capture only one aspect of the complex disease process.…
Cell type (e.g. pluripotent cell, fibroblast) is the end result of many complex processes that unfold due to evolutionary, developmental, and transformational stimuli. A cell's phenotype and the discrete, a priori states that define various…
Dynamic data selection accelerates training by sampling a changing subset of the dataset while preserving accuracy. We rethink two core notions underlying sample evaluation: representativeness and diversity. Instead of local geometric…
In this study, we develop consistent estimators for key parameters that govern the dynamics of tumor cell populations when subjected to pharmacological treatments. While these treatments often lead to an initial reduction in the abundance…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
We introduce a model for multi-agent interaction problems to understand how a heterogeneous team of agents should organize its resources to tackle a heterogeneous team of attackers. This model is inspired by how the human immune system…
The diverse repertoire of T-cell receptors (TCR) plays a key role in the adaptive immune response to infections. Previous studies show that secondary responses to the yellow fever vaccine - the model for acute infection in humans - are…