Computational immunogenomic approaches to predict response to cancer immunotherapies

V Addala, F Newell, JV Pearson, A Redwood… - Nature Reviews …, 2024 - nature.com
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The
establishment of large-scale genomic collaborative efforts along with the development of …

Artificial intelligence applied in neoantigen identification facilitates personalized cancer immunotherapy

Y Cai, R Chen, S Gao, W Li, Y Liu, G Su, M Song… - Frontiers in …, 2023 - frontiersin.org
The field of cancer neoantigen investigation has developed swiftly in the past decade.
Predicting novel and true neoantigens derived from large multi-omics data became difficult …

IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing

Y Pan, JW Phillips, BD Zhang… - Proceedings of the …, 2023 - National Acad Sciences
Alternative splicing (AS) is prevalent in cancer, generating an extensive but largely
unexplored repertoire of novel immunotherapy targets. We describe I soform peptides from …

Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy

G Li, S Mahajan, S Ma, ED Jeffery, X Zhang… - Science Translational …, 2024 - science.org
Immunotherapy has emerged as a crucial strategy to combat cancer by “reprogramming” a
patient's own immune system. Although immunotherapy is typically reserved for patients with …

Comprehensive analysis of neoantigens derived from structural variation across whole genomes from 2528 tumors

Y Shi, B **g, R ** - Genome biology, 2023 - Springer
Background Neoantigens are critical for anti-tumor immunity and have been long-
envisioned as promising therapeutic targets. However, current neoantigen analyses mostly …

LENS: landscape of effective neoantigens software

SP Vensko, K Olsen, D Bortone, CC Smith… - …, 2023 - academic.oup.com
Motivation Elimination of cancer cells by T cells is a critical mechanism of anti-tumor
immunity and cancer immunotherapy response. T cells recognize cancer cells by …

[HTML][HTML] Quantifying tumor specificity using Bayesian probabilistic modeling for drug and immunotherapeutic target discovery

G Li, D Schnell, A Bhattacharjee, M Yarmarkovich… - Cell Reports …, 2024 - cell.com
In diseases such as cancer, the design of new therapeutic strategies requires extensive,
costly, and unfortunately sometimes deadly testing to reveal life threatening off-target effects …

Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources

Y Wang, J Wengler, Y Fang, J Zhou… - Genomics …, 2025 - academic.oup.com
Tumor-specific antigens, also known as neoantigens, have potential utility in anti-cancer
immunotherapy, including immune checkpoint blockade (ICB), neoantigen-specific T cell …

Neoantigen identification: Technological advances and challenges

T Pu, A Peddle, J Zhu, S Tejpar, S Verbandt - Methods in Cell Biology, 2024 - Elsevier
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as
cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and …

Advances in CAR T cell therapy: antigen selection, modifications, and current trials for solid tumors

SH Khan, Y Choi, M Veena, JK Lee… - Frontiers in …, 2025 - frontiersin.org
Chimeric antigen receptor (CAR) T cell therapy has revolutionized the treatment of
hematologic malignancies, achieving remarkable clinical success with FDA-approved …