Accurate prediction of neoantigens and the subsequent elicited protective anti-tumor response are particularly important for the development of cancer vaccine and adoptive T-cell therapy. However, current algorithms for predicting neoantigens are lim...
High-throughput B-cell sequencing has opened up new avenues for investigating complex mechanisms underlying our adaptive immune response. These technological advances drive data generation and the need to mine and analyze the information contained in...
Proceedings of the National Academy of Sciences of the United States of America
33795515
Subclasses of lymphocytes carry different functional roles to work together and 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 to recogn...
BACKGROUND: Epitope prediction is a useful approach in cancer immunology and immunotherapy. Many computational methods, including machine learning and network analysis, have been developed quickly for such purposes. However, regarding clinical applic...
Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for immune-oncology. Still, the identification of non-tryptic peptides presents substantial computational...
Vaccination is one of the most significant inventions in medicine. Reverse vaccinology (RV) is a state-of-the-art technique to predict vaccine candidates from pathogen's genome(s). To promote vaccine development, we updated Vaxign2, the first web-bas...
Major histocompatibility complex (MHC) possesses important research value in the treatment of complex human diseases. A plethora of computational tools has been developed to predict MHC class I binders. Here, we comprehensively reviewed 27 up-to-date...
Generative machine learning (ML) has been postulated to become a major driver in the computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to confirm this hypothesis have been hindered by the infeasibility of testing ...
Antibodies are an established class of human therapeutics. Epitope characterization is an important part of therapeutic antibody discovery. However, structural characterization of antibody-antigen complexes remains challenging. On the one hand, X-ray...
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
36540990
Accurate prediction of TCR binding affinity to a target antigen is important for development of immunotherapy strategies. Recent computational methods were built on various deep neural networks and used the evolutionary-based distance matrix BLOSUM t...