Catch Bonds Nonlinearly Control CD8 Cooperation to Shape T Cell Specificity

T cell receptors (TCRs) play a crucial role in the immune system by recognizing antigen peptides presented by major histocompatibility complexes (MHCs), thereby initiating immune responses against pathogens and tumor cells. However, the specificity of TCRs—their ability to distinguish self-antigens from non-self antigens—is central to the effective...

Significance in Scale Space for Hi-C Data Analysis

In the field of genomics, understanding the spatial organization of the genome is crucial for uncovering gene regulatory mechanisms. Hi-C technology, as a genome-wide chromosome conformation capture technique, can reveal the three-dimensional structure of the genome, particularly the key role of chromatin loops in gene regulation. However, existing...

Multi-Modal Interpretable Representation for Non-Coding RNA Classification and Class Annotation

Non-coding RNAs (ncRNAs) play critical roles in cellular processes and disease development. Although genome sequencing projects have revealed a vast number of non-coding genes, the functional classification of ncRNAs remains a complex and challenging issue. The diversity, complexity, and functionality of ncRNAs make them important subjects in biome...

Privacy-Preserving Framework for Genomic Computations via Multi-Key Homomorphic Encryption

Privacy-Preserving Framework for Genomic Analysis: A Study Based on Multi-Key Homomorphic Encryption Academic Background With the reduction in the cost of genome sequencing, the widespread availability of genomic data has opened up new possibilities for personalized medicine (also known as genomic medicine). However, genomic data contains a vast am...

EPICPred: Predicting Phenotypes Driven by Epitope-Binding TCRs Using Attention-Based Multiple Instance Learning

T-cell receptors (TCRs) play a crucial role in the adaptive immune system by recognizing pathogens through binding to specific antigen epitopes. Understanding the interactions between TCRs and epitopes is essential for uncovering the biological mechanisms of immune responses and developing T cell-mediated immunotherapies. However, although the impo...