Hesham ElAbd

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 identifies HLA-associated CDR3-QTLs that influence T-cell receptor composition in IBD and healthy controls, revealing disease-specific and universal effects on TRB repertoires.

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.

The paper identifies public TCRB sequences expanded in CD or UC, associated with HLA alleles and antigen-specific immune responses, showing differential expansion in CD compared to UC and healthy controls.

Seq2MAIT identifies MAIT cells from bulk TCR-sequencing data using a transformer-based model, achieving AUROC >0.80 across datasets.

The paper develops PIA-M, a multimodal transformer-based tool for predicting HLA-II peptide presentation, achieving higher accuracy and faster runtime than existing methods.

This study identifies a new susceptibility locus for severe COVID-19 through a detailed GWAS analysis in European populations, focusing on genetic variants associated with disease severity.

VCF2Prot generates personalized proteomes from VCF files by implementing a novel algorithm, improving runtime efficiency and enabling large-scale genomic-proteomic integration.

This study identifies shared and ethnicity-specific HLA associations with ulcerative colitis through trans-ethnic analysis of diverse populations.