Joel S. Parker

Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling

This study identifies regulatory elements that switch from silencers to enhancers in breast cancer cells using single-cell ATAC-seq and RNA-seq data.

An Integrated Model for Predicting KRAS Dependency

The paper develops a model to predict KRAS dependency using molecular profiles from cell lines, achieving high accuracy in validation and external datasets.

A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels

The paper analyzes DNA alterations across cell cycle activity levels in 9,515 cancer patients, finding that mutation frequencies vary with cell cycle activity and that cell cycle activity is a prognostic factor.

FastPG: Fast clustering of millions of single cells

FastPG improves single-cell clustering speed by 27x while maintaining accuracy over existing methods like FlowSOM and PARC.

An Integrative Boosting Approach for Predicting Survival Time With Multiple Genomics Platforms

This paper introduces I-Boost, a method that improves survival time prediction by integrating multiple genomics data types with clinical variables, showing better accuracy than existing methods.