Hashem Koohy

This paper identifies barriers to generalisable TCR:pMHC prediction and proposes solutions through data analysis, evaluation setup, and metric alignment.

This study identifies distinct transcriptional states of T cells in draining lymph nodes after influenza vaccination in individuals with African or Asian ancestry using scRNA-seq.

This study evaluates AlphaFold 3's ability to predict T cell antigen specificity using structural models and finds that binding scores correlate with TCR positioning over pMHC, not chemical interactions.

The paper defines the developmental circuits and mechanisms underlying postnatal intestinal epithelial immune competency using single-cell multi-omics and spatial transcriptomics.

This study examines immune responses in ancestrally diverse individuals after influenza vaccination, finding that draining lymph nodes show rapid activation and specific cellular changes.

This study quantifies conformational changes in the TCR:pMHC-I binding interface using a dataset of 358 structures, showing that CDR3 and CDR3β loops modify their shape upon binding and peptides undergo conformational changes dependent on their anchoring in the MHC groove.

This paper introduces TRAP, a deep learning platform for predicting CD8+ T-cell epitopes, which outperforms existing methods in cancer and pathogenic settings.

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