Vadim K Karnaukhov

IMMREP25: Unseen Peptides

IMMREP25 evaluates TCR:pMHC binding prediction for unseen peptides, showing improved performance with structural modeling but still below random guessing.

Analysis of intratumoral immune heterogeneity reveals spatial organisation of immunosuppression in breast cancer

This study maps spatial immune heterogeneity in luminal breast cancer, showing progressive immunosuppression from tumor margins to core.

Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features.

The paper uses template-based modeling to generate TCR:antigen:MHC structures and identifies amino acid contact features that influence antigen recognition.

Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

The paper benchmarks 23 TCR-epitope prediction models, finding that using paired-chain alpha-beta and CDR1/2/V/J data improves performance, and simple distance-based methods can be competitive.

HLA binding of self-peptides is biased towards proteins with specific molecular functions

The paper shows HLA alleles preferentially present peptides from proteins with specific molecular functions, linking these preferences to HLA allele differences and disease susceptibility.