Nathaniel D. Tippens

This study evaluates multiple MPRA and STARR-seq datasets to identify enhancers, finding inconsistencies due to technical factors and proposing a unified pipeline to improve cross-assay agreement.

This study identifies YAP's role in controlling cell migration and invasion via a Rho-GTPase switch, with implications for glioblastoma progression.

The paper develops a dual reporter assay to measure promoter and enhancer potential, finding that they share regulatory logic and can function reciprocally.

This study introduces scGRO-seq, a single-cell nascent RNA sequencing method using click-chemistry, revealing coordinated transcription and enhancer-gene synchrony.

The paper identifies two types of eRNA QTLs associated with enhancer function and reveals a bipartite enhancer architecture through population-scale eRNA analysis.

The paper identifies fundamental enhancer units defined by transcription start sites and shows adjacent units operate non-cooperatively.

A precision run-on sequencing (PRO-seq) variant with one streptavidin bead binding and on-bead enzymatic steps yields adapter-ligated cDNA in about 10 h and libraries from 0.05–0.25 × 10^6 cells.

The paper introduces methyl-ATAC-seq (mATAC-seq) to simultaneously measure open chromatin and DNA methylation, eliminating the need for separate assays.

This study uses PRO-seq to analyze the rapid transcriptional response to celastrol in K562 cells, revealing two waves of transcriptional changes and identifying key transcription factors involved.