Jacob T. Stanley

Improving confidence of differential transcription calls in enhancers

The paper introduces two algorithms, Mu Counts and TFEA-LE, to improve the identification of differentially transcribed regulatory elements by integrating motif information and enhancing precision and recall.

Base Composition Influences the Position andPrecision of RNA Polymerase II Disassociation inBasal and Perturbed Conditions.

The paper identifies two types of Pol II disassociation regions, differing in base composition and sensitivity to cellular perturbations.

LIET Model: Capturing the kinetics of RNA polymerase from loading to termination

The paper introduces the LIET model to analyze RNA polymerase kinetics across transcription stages and applies it to human cell-types and perturbation experiments to detect changes in transcription dynamics.

Atlas of nascent RNA transcripts reveals enhancer to gene linkages

The paper identifies over 800,000 bidirectional transcription regions in human samples and links them to genes through correlated transcription, enriched for disease SNPs and supported by 3D data.

Transcription factor enrichment analysis (TFEA): Quantifying the activity of hundreds of transcription factors from a single experiment

TFEA quantifies transcription factor activity changes from perturbation data, identifying key regulators and temporal regulatory networks.