The first evidence showing direct CTCF regulation of global transcription and chromatin accessibility in vertebrates. 

Chen D*, Keremane S^, Wang S, and Lei EP*, 2025

CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development. PNAS

This paper elucidates tinamou egg coloration as mating signals that diverged as character displacement.

Li Q., D. Chen and S. Wang*, 2023

Character displacement of egg colors during tinamou speciation. Evolution

This paper elucidates the highly compacted genome and dosage compensation mechanisms in silkmoths. 

​Rosin. F. L.*, D. Chen, Y. Chen and E. P. Lei*, 2022 

Dosage compensation in Bombyx mori is achieved by partial repression of both Z chromosomes in males. PNAS

This paper reports for the first time that proper chromatin 3D structure plays a key role in regulating neuronal remodeling.  

​Chen, D., C. E. McManus, B. Radmanesh, L. Matzat and E. P. Lei*, 2021

Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling. Nat. Commun.

This review summarizes key recent findings about regulation of chromatin 3D structure.

Chen, D., and E. P. Lei*, 2019

Function and Regulation of Chromatin Insulators in Dynamic Genome Organization. Curr Opin Cell Biol

This paper identifies key residues of a neural-specific antagonist of chromatin insulators.

Chen, D., M. Brovkina^, L. H. Matzat and E. P. Lei*, 2019

Shep RNA-Binding Capacity Is Required for Antagonism of gypsy Chromatin Insulator Activity. G3 (Bethesda)

​This paper elucidates the first neuron-specific transcriptome dynamics during normal and dysregulated neuronal remodeling.

Chen, D., R. K. Dale and E. P. Lei*, 2018

Shep Regulates Drosophila Neuronal Remodeling by Controlling Transcription of Its Chromatin Targets. Development

This paper describes behavior-based efficient screens to identify essential genes for neuronal remodeling

Chen, D., T. Gu, T. N. Pham^, M. J. Zachary^ and R. S. Hewes*, 2017

Regulatory Mechanisms of Metamorphic Neuronal Remodeling Revealed Through a Genome-Wide Modifier Screen in Drosophila melanogaster. Genetics

This paper elucidates specific Shep regulation of neuronal remodeling.

Chen, D., C. Qu, S. M. Bjorum, K. M. Beckingham and R. S. Hewes*, 2014 

Neuronal Remodeling During Metamorphosis Is Regulated by the alan shepard (shep) Gene in Drosophila melanogaster. ​

Genetics |   Highlight in Journal.