Parallel Implementation of SEMPHY - a Structural EM Algorithm for Phylogenetic Reconstruction. - Eric Q. Li; Zhengqing Ouyang; Xi Deng; Yimin Zhang 002; Wenguang Chen (PARCO, 2005)

Multi-track Modeling for Genome-Scale Reconstruction of 3D Chromatin Structure from Hi-C Data. - Chenchen Zou; Yuping Zhang; Zhengqing Ouyang (RECOMB, 2016)

LISA: Accurate reconstruction of cell trajectory and pseudo-time for massive single cell RNA-seq data. - Yang Chen; Yuping Zhang; Zhengqing Ouyang (PSB, 2019)

Text Mining and Machine Learning for Precision Medicine. - Graciela Gonzalez 001; Zhiyong Lu; Robert Leaman; Davy Weissenbacher; Mary Regina Boland; Yong Chen 016; Jingcheng Du; Juliane Fluck; Casey S. Greene; John H. Holmes; Aditya Kashyap; Rikke Linnemann Nielsen; et al. (PSB, 2019)

PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks. - Jianan Lin; Yuping Zhang; Wayne N. Frankel; Zhengqing Ouyang (PLoS Comput. Biol., 2019)

PATH: An interactive web platform for analysis of time-course high-dimensional genomic data. - Yuping Zhang; Yang Chen 004; Zhengqing Ouyang (Int. J. Comput. Biol. Drug Des., 2020)

Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins. - Jianan Lin; Zhengqing Ouyang (Quant. Biol., 2020)

Differential RNA methylation using multivariate statistical methods. - Deepak Nag Ayyala; Jianan Lin; Zhengqing Ouyang (Briefings Bioinform., 2022)

Deciphering the role of RNA structure in translation efficiency. - Jianan Lin; Yang Chen 004; Yuping Zhang; Haifan Lin; Zhengqing Ouyang (BMC Bioinform., 2022)