S. Thomas Kelly

UniverSC is a single-cell RNA-sequencing processing pipeline that supports UMI-based platforms, enabling consistent integration and comparison across diverse data sources.

HiCUP-Plus improves Hi-C data processing by integrating HiSAT2 and Dragen aligners, enhancing speed and accuracy while maintaining compatibility with Bowtie2.

This study introduces a new genomic DNA library preparation method that reduces GC bias and improves coverage breadth compared to existing protocols.

The paper introduces graphsim, an R package that simulates gene expression data from biological pathway graphs to aid in method validation.

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.