Stephen Martis

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.

This study uses spatial transcriptomics and single-cell analysis to reveal how MDS bone marrow microenvironments are altered, showing TGFβ dysregulation in malignant cells and immune escape mechanisms.

The paper analyzes the evolutionary trajectories of high-level copy-number amplifications in cancer cell genomes to distinguish between extrachromosomal and intrachromosomal amplification mechanisms.

The paper quantifies viral mimicry in genomes across species and shows how repetitive elements maintain pathogen-like features under selection.

The paper shows that mutation tempo and mode affect eco-evolutionary system behavior, challenging classical population genetic assumptions through a consumer-resource model.