Related papers: Diversity in immunogenomics: the value and the cha…
How does immune system evolve functional proteins - potent antibodies - in such a short time? We address this question using a microscopic, protein-level, sequence-based model of humoral immune response with explicitly defined interactions…
According to Jerne's idiotypic network hypothesis, the adaptive immune system is regulated by interactions between the variable regions of antibodies, B cells, and T cells.1 The symmetrical immune network theory2,3 is based on Jerne's…
Genomic approaches have revolutionized medical research, providing valuable insights into human physiology and disease. Despite major benefits from large collections of genomes, the lack of diversity in genomic data represents a significant…
Serology testing can identify past infection by quantifying the immune response of an infected individual providing important public health guidance. Individual immune responses are time-dependent, which is reflected in antibody…
The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial…
Generative artificial intelligence (AI) has brought revolutionary innovations in various fields, including medicine. However, it also exhibits limitations. In response, retrieval-augmented generation (RAG) provides a potential solution,…
Subclasses of lymphocytes carry different functional roles to work together to produce an immune response and lasting immunity. Additionally to these functional roles, T and B-cell lymphocytes rely on the diversity of their receptor chains…
Insurance application processes often rely on lengthy and standardized questionnaires that struggle to capture individual differences. Moreover, insurers must blindly trust users' responses, increasing the chances of fraud. The ARQuest…
Immune repertoires rely on diversity of T-cell and B-cell receptors to protect us against foreign threats. The ability to recognize a wide variety of pathogens is linked to the number of different clonotypes expressed by an individual. Out…
Adaptive Retrieval-Augmented Generation (RAG) promises accuracy and efficiency by dynamically triggering retrieval only when needed and is widely used in practice. However, real-world queries vary in surface form even with the same intent,…
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…
Computational protein design, i.e. inferring novel and diverse protein sequences consistent with a given structure, remains a major unsolved challenge. Recently, deep generative models that learn from sequences alone or from sequences and…
Despite the extreme diversity of T cell repertoires, many identical T-cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely-shared sequences, often referred to as `public', have been suggested…
The future of ART in head and neck cancer is just beginning. Novel technologies have pushed the boundary of what is possible in terms of techniques to identify biomarkers for adaptation as well as innovative devices specialized to respond…
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…
Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise…
Machine learning techniques are steadily becoming more important in modern biology, and are used to build predictive models, discover patterns, and investigate biological problems. However, models trained on one dataset are often not…
While generative modeling has become prevalent across numerous research fields, its integration into the realm of image retrieval remains largely unexplored and underjustified. In this paper, we present a novel methodology, reframing image…
Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency.…
In the past, the development of vaccines and immunotherapeutics relied heavily on trial-and-error experimentation and extensive in vivo testing, often requiring years of pre-clinical and clinical trials. Today, artificial intelligence (AI)…