Matthew McCoy

Impact of Trastuzumab and Pertuzumab on HER2 Localization and the Estrogen Receptor Cistrome in ER+/HER2+ Breast Cancer

This study examines how anti-HER2 therapy affects HER2 localization and ER genomic binding in ER+/HER2+ breast cancer, finding ER redistribution correlates with treatment resistance.

Hidden State Genomics: Graph-Based Analysis of Sparse Auto-Encoder Feature Activity in Genomic Language Models

The paper investigates genomic language model representations by analyzing sparse auto-encoder features, finding they encode granular sequence syntax and conservation patterns rather than complex regulatory logic.

Probability Distribution for Rare Neutral Mutations in Cancers and Application to Dynamic Precision Medicine of Cancer

The paper develops a probability distribution for rare subclones in cancer and applies it to simulate dynamic precision medicine to improve treatment outcomes despite sequencing limitations.

Personalized cancer treatment strategies incorporating irreversible and reversible drug resistance mechanisms

This study enhances a personalized cancer treatment strategy by incorporating both irreversible and reversible drug resistance mechanisms, showing improved patient outcomes compared to current approaches.

SNP2SIM: A modular workflow for standardizing molecular simulation and functional analysis of protein variants

SNP2SIM provides a modular workflow for generating molecular simulations of protein variants to support functional analysis and drug development.

Clingen Cancer Somatic Working Group: standardizing and democratizing access to cancer molecular diagnostic data to drive translational research

The paper describes the development of standards for cancer variant interpretation and sharing through the ClinGen Cancer Somatic Working Group.