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Nucleic Acids Research|May 15, 2016
TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysisZhicheng Ji, Hongkai JiMethods in Molecular Biology (Clifton, N.J.)|February 14, 2019
Pseudotime Reconstruction Using TSCANZhicheng Ji, Hongkai JiJournal of the American Statistical Association|November 8, 2021
Discussion of "Exponential-family Embedding with Application to Cell Developmental Trajectories for Single-cell RNA-seq Data"Zhicheng Ji, Hongkai JiBioinformatics (Oxford, England)|May 16, 2017
Single-cell regulome data analysis by SCRATZhicheng Ji, Weiqiang Zhou, Hongkai JiNucleic Acids Research|August 21, 2019
Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seqWeiqiang Zhou, Zhicheng Ji, Weixiang Fang, et al.Genome Biology|July 5, 2020
Single-cell ATAC-seq signal extraction and enhancement with SCATEZhicheng Ji, Weiqiang Zhou, Wenpin Hou, et al.Nucleic Acids Research|January 12, 2018
Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processesZheng Kuang, Zhicheng Ji, Jef D Boeke, et al.Genome Biology|August 29, 2020
A systematic evaluation of single-cell RNA-sequencing imputation methodsWenpin Hou, Zhicheng Ji, Hongkai Ji, et al.Nucleic Acids Research|September 10, 2015
Turning publicly available gene expression data into discoveries using gene set context analysisZhicheng Ji, Steven A Vokes, Chi V Dang, et al.Biorxiv : the Preprint Server for Biology|July 20, 2021
A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samplesWenpin Hou, Zhicheng Ji, Zeyu Chen, et al.Pageof 23