Damon May

Immune signatures of common exposures through co-occurrence of T-cell receptors in tens of thousands of donors

The paper identifies immune exposure signatures by clustering T-cell receptors co-occurring across donors, linking them to specific pathogens and HLA alleles.

IMMREP25: Unseen Peptides

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

Multi-centered T cell repertoire profiling identifies novel alterations in the immune repertoire of individuals with inflammatory bowel disease and validates previous findings

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.

A Fundamental Relationship between TCR Diversity, Repertoire Size and Systemic Clonal Expansion: Insights from 30,000 TCRβ Repertoires

The paper analyzes TCRβ repertoires from 30,000 individuals to show that TCR diversity is primarily determined by repertoire size and the frequency of the 1,000 most abundant clones, explaining 96% of variance in diversity.

Antigen-driven expansion of public clonal T cell populations in inflammatory bowel diseases

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.

A Catalog of the Public T-cell Response to Cytomegalovirus

The paper provides a catalog of public T-cell receptors specific to cytomegalovirus (CMV) and explores their antigen specificity and subgroup variations.

A learned embedding for efficient joint analysis of millions of mass spectra

This paper introduces a deep learning model called GLEAMS to embed mass spectra into a low-dimensional space for efficient clustering and analysis of large-scale proteomics data.

Detecting modifications in proteomics experiments with Param-Medic

The paper introduces a method to automatically detect modifications in proteomics experiments from mass spectra and provides open-source implementations.