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NAR Genomics and Bioinformatics|October 8, 2020
SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variationZhirui Hu, Songpeng Zu, Jun S LiuBioinformatics (Oxford, England)|March 31, 2015
Global optimization-based inference of chemogenomic features from drug-target interactionsSongpeng Zu, Ting Chen, Shao LiBioinformatics (Oxford, England)|June 30, 2016
Evaluating the molecule-based prediction of clinical drug responses in cancerZijian Ding, Songpeng Zu, Jin GuMolecular Biology and Evolution|March 10, 2019
Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic TreesZhirui Hu, Timothy B Sackton, Scott V Edwards, et al.Bioinformatics (Oxford, England)|March 15, 2020
VISAR: an interactive tool for dissecting chemical features learned by deep neural network QSAR modelsQingyang Ding, Siyu Hou, Songpeng Zu, et al.Molecular Biology and Evolution|September 4, 2023
PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree DiscordanceHan Yan, Zhirui Hu, Gregg W C Thomas, et al.Integrative and Comparative Biology|May 30, 2024
Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAccGregg W C Thomas, Patrick Gemmell, Subir B Shakya, et al.BMC Systems Biology|July 13, 2012
Novel Markov model of induced pluripotency predicts gene expression changes in reprogrammingZhirui Hu, Minping Qian, Michael Q ZhangSTAR Protocols|December 5, 2025
Protocol for inferring cell type relationships and linking genomic annotations to cell type hierarchies using CellWalker2Zhirui Hu, Pawel F Przytycki, Katherine S PollardBiorxiv : the Preprint Server for Biology|May 27, 2024
CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotationsZhirui Hu, Pawel F Przytycki, Katherine S PollardPageof 18