Aya K.H. Mahdy

This study profiles the B cell repertoire in treatment-naive Crohn's disease patients and controls, finding reduced diversity, increased clonality, and altered immunoglobulin clonotype expansions.

This study maps immune responses to fungal antigens in IBD using T cell repertoire sequencing and PhIP-Seq, identifying T cell clonotypes and antibody responses against S. cerevisiae proteins.

The paper uses statistical learning to decode T cell receptor associations with HLA alleles using a large dataset, identifying clonotypes linked to specific HLA alleles and infections.

The paper profiles T cell receptor alpha repertoires in IBD patients across multiple cohorts, identifies disease-associated clonotypes, and validates findings in an independent dataset.

This study evaluates how methodological choices in bulk TCR-Seq affect T cell repertoire profiling, finding that RNA/DNA quality significantly impacts results and that low quantities can be partially compensated by increasing PCR cycles.

The paper identifies and validates T cell receptor clonotypes associated with Crohn's disease and ulcerative colitis, suggesting they are potential therapeutic targets.