Kelly Cochran

Directionality of Transcriptional Regulatory Elements

This study compares divergent and unidirectional transcriptional regulatory elements, finding that unidirectional elements are younger and less constrained, with some transcription factors modulating their directionality.

The nascent transcriptome delineates the regulatory landscape in human health and disease

The paper presents a high-resolution atlas of transcriptional regulatory elements in human tissues and disease states using PRO-cap and deep learning models to prioritize noncoding variants.

Rewriting regulatory DNA to dissect and reprogram gene expression

The paper introduces Variant-FlowFISH to measure the effects of DNA sequence variants on gene expression, identifies regulatory mechanisms, and benchmarks predictive models.

The GENCODE CLS project: massively expanding the lncRNA catalog through capture long-read RNA sequencing

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

Dissecting the cis-regulatory syntax of transcription initiation with deep learning

The paper trains a deep learning model to predict transcription initiation from DNA sequences, revealing shared cis-regulatory logic and epistatic interactions across promoters and enhancers.

Domain adaptive neural networks improvecross-species prediction of transcription factor binding

This study improves cross-species prediction of transcription factor binding by addressing domain shifts caused by species-specific repeats using domain adaptive neural networks.