Zachary M. Sethna

This paper introduces CloneSearch, a method to identify expanding and contracting T cell clones from longitudinal TCR sequencing without requiring antigen-specific information.

The paper introduces enFoldX, a structure-based method for predicting TCR:pMHC binding using AlphaFold3 ensembles, achieving high accuracy for cognate vs. non-cognate classification.

GeneVector uses mutual information-based dimensionality reduction to identify transcriptional programs and classify cell types across single-cell RNA-seq datasets.

This paper introduces TCRi, an information theoretic framework to analyze TCR and gene expression data from cancer patients, showing improved characterization of clonotypes and their phenotypic changes post-therapy.

OLGA calculates amino acid sequence generation probabilities for B- and T-cell receptors using dynamic programming, showing agreement with published data and potential for vaccine design.