Related papers: T-Cell Receptor Optimization with Reinforcement Le…
T cell receptor (TCR) repertoires encode critical immunological signatures for autoimmune diseases, yet their clinical application remains limited by sequence sparsity and low witness rates. We developed EAMil, a multi-instance deep…
Antigen-specific T cells play an essential role in immunoregulation and diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the antigenic determinants of…
Designing full-length, epitope-specific TCR {\alpha}\b{eta} remains challenging due to vast sequence space, data biases and incomplete modeling of immunogenetic constraints. We present LSMTCR, a scalable multi-architecture framework that…
T-cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed a statistical…
B cell receptors (BCRs) play a crucial role in recognizing and fighting foreign antigens. High-throughput sequencing enables in-depth sampling of the BCRs repertoire after immunization. However, only a minor fraction of BCRs actively…
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…
To ensure faithful information transmission, cells utilize nonequilibrium drives to reduce errors. Kinetic proofreading is a classic mechanism known to sharpen ligand discrimination by T lymphocytes. It remains an open question whether the…
Physicochemically informed biological sequence generation has the potential to accelerate computer-aided cellular therapy, yet current models fail to \emph{jointly} ensure novelty, diversity, and biophysical plausibility when designing…
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such…
Traditional vaccines against viruses are designed to target their surface proteins, i.e., antigens, which can trigger the immune system to produce specific antibodies to capture and neutralize the viruses. However, viruses often evolve…
T cells form intriguing patterns during adhesion to antigen-presenting cells. The patterns at the cell-cell contact zone are composed of two types of domains, which either contain short TCR/MHCp receptor-ligand complexes or the longer…
The adaptive immune system constantly remodels its lymphocyte repertoire for better protection against future pathogens. Its ability to improve antigen recognition on the fly relies on somatic mutation and selective expansion of B…
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…
Artificial intelligence (AI) is accelerating progress in modeling T and B cell receptors by enabling predictive and generative frameworks grounded in sequence data and immune context. This chapter surveys recent advances in the use of…
One primary goal of precision medicine is to estimate the individualized treatment rules (ITRs) that optimize patients' health outcomes based on individual characteristics. Health studies with multiple treatments are commonly seen in…
Following antigen stimulation, the net outcomes of a T cell response are shaped by integrated signals from both positive co-stimulatory and negative regulatory molecules. Recently, the blockade of negative regulatory molecules (i.e. immune…
The study of cells and their responses to genetic or chemical perturbations promises to accelerate the discovery of therapeutic targets. However, designing adequate and insightful models for such data is difficult because the response of a…
Diverse repertoires of hypervariable immunoglobulin receptors (TCR and BCR) recognize antigens in the adaptive immune system. The development of immunoglobulin receptor repertoire sequencing methods makes it possible to perform…
CD8+ "killer" T cells and CD4+ "helper" T cells play a central role in the adaptive immune system by recognizing antigens presented by Major Histocompatibility Complex (pMHC) molecules via T Cell Receptors (TCRs). Modeling binding between T…
Purpose: MRI cell tracking can be used to monitor immune cells involved in the immunotherapy response, providing insight into the mechanism of action, temporal progression of tumour growth and individual potency of therapies. To evaluate…