A compendium of RNA-binding motifs for decoding gene regulation. - Debashish Ray; Hilal Kazan; Kate B. Cook; Matthew T. Weirauch; Hamed S. Najafabadi; Xiao Li; Serge Gueroussov; Mihai Albu; Hong Zheng; Ally Yang; Hong Na; Manuel Irimia; et al. (Nat., 2013)

DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma. - Yang Chen 004; Shue Chen; Elissa P. Lei (Bioinform., 2022)

Deciphering the contribution of 3D interactions between cis-regulatory elements and promoters to regulate gene expression using graph neural networks. - Yang Chen 004; Elissa P. Lei (IEEE Big Data, 2024)