Year: 2026
Type: preprint
Abstract: Systems vaccinology approaches have identified factors affecting vaccine responses in multiple studies, but the ability of computational models to generalize these findings to unseen data remains unclear. We established a community resource to create and compare models predicting B. pertussis booster vaccination responses and put such modeling approaches to the test. We compiled multi-modal experimental training data from three independent cohorts (n=117 individuals), and asked investigators to predict vaccine responses in a cohort of 54 newly recruited individuals using only their pre-booster vaccination data. We benchmarked a total of 107 computational models. Top-performing models were characterized by workflows that prioritized rigorous data preprocessing, robust imputation of missing data, and the use of multi-omics integration or non-linear machine learning. We identified pre-existing antigen-specific antibody titers and baseline monocyte frequencies as the most consistent predictors of post-vaccination immunity, highlighting the dominant role of individual immune setpoints. We established the resulting datasets and evaluation framework as a community resource to advance predictive immunology and facilitate personalized vaccination strategies.
Authors: Pramod Shinde, Lisa Willemsen, Jiyeun Lee, Shelby Orfield, Ziyuan Ren, Minori Aoki, Nicola Thrupp, Aanya Gupta, Cheng-Chang Wu, Liran Mao, Chuxuan Li, Yuhao Tan, Tram Anh Nguyen, Ning-Shan Chang, Philipp S. L. Schäfer, Jian Xing, Cemil Can Ali Marandi, Burhan Sabuwala, CMI-PB Challenge Contestants, Joaquin Reyna, Jeremy P Gygi, Brendan Ha, James A. Overton, Tal Einav, Jason A. Greenbaum, Leying Guan, Mari Kojima, Ferhat Ay, Barry Grant, Steven H. Kleinstein, Bjoern Peters
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: Identifying mechanisms and correlates of long-lasting vaccine-induced immunity to whooping cough, Developing computational models to predict the immune response to B. pertussis booster vaccination, Human immune memory to COVID-19, vaccines, and respiratory pathogens, Towards a predictive understanding of influenza immunity through experimental data integration, iterative model development, and rigorous assessment of model quality
OpenAlex ID: W7204652166