COMBO-RATE identifies promiscuous HLA restrictions by analyzing immune response data, outperforming existing tools and revealing broader HLA allele coverage for T cell epitopes.

HLA · Oct 31, 2026Peer-reviewedImmunology

Peptide Driven Identification of TCRs (PDI-TCR) reveals dynamics and phenotypes of CD4 T cells in tuberculosis

Rashmi Tippalagama, Raphael Trevizani, Leila Y. Chihab, Ashu Chawla, Kai Fung, Jason Greenbaum, Kendall Kearns, Aruna Dharshan De Silva, Wathsala Gunasinghe, Judy Perera, Hansani Gunasekera, Darsha D. Senevirathne, Thomas J. Scriba, Alessandro Sette, Cecilia S. Lindestam Arlehamn, , Bjoern Peters

PDI-TCR identifies Mtb-specific TCRs and characterizes their phenotypes in TB patients and healthy individuals, revealing distinct dynamics of specific and unspecific T cell responses.

bioRxiv · May 6, 2025 · PreprintImmunology

Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes

Pramod S. Shinde, Lisa Willemsen, Michael Anderson, Minori Aoki, Saonli Basu, Julie G. Burel, Peng Cheng, Souradipto Ghosh Dastidar, Aidan Dunleavy, Tal Einav, Jamie Forschmiedt, Slim Fourati, Javier Garcia, William Gibson, Jason A Greenbaum, , Bjoern Peters

The paper benchmarks 49 algorithms for predicting B. pertussis vaccination outcomes, finding that purpose-built models outperform literature-based ones due to better handling of nonlinearities and data preprocessing.

PLoS Computational Biology · Mar 31, 2025Peer-reviewedImmunology