Publications by authors named "Zhirui Hu"

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Protocol for inferring cell type relationships and linking genomic annotations to cell type hierarchies using CellWalker2.
Zhirui Hu, Pawel F Przytycki, Katherine S Pollard

STAR Protoc· December 2025

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scATAnno: Automated Cell Type Annotation for Single-cell ATAC Sequencing Data.
Yijia Jiang, Zhirui Hu, Feng Lu, Allen W Lynch, Junchen Jiang, Alexander Zhu

Genomics Proteomics Bioinformatics· November 2025

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Human brain vascular multi-omics elucidates disease-risk associations.
Madigan M Reid, Shreya Menon, Hao Liu, Haoyue Zhou, Zhirui Hu

Neuron· October 2025

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In vivo three-dimensional kinematics of the upper cervical spine during upright head rotation in patients with atlantoaxial dislocation.
Jian He, Shilin Xue, Yang Luo, Zhirui Hu, Cheng Zhang

Eur Spine J· October 2025

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CellWalker2: Multi-omic discovery using hierarchical cell type relationships.
Zhirui Hu, Pawel F Przytycki, Katherine S Pollard

Cell Genom· July 2025

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Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc.
Gregg W C Thomas, Patrick Gemmell, Subir B Shakya, Zhirui Hu, Jun S Liu

Integr Comp Biol· November 2024

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[Prediction Spatial Distribution of Soil Organic Matter Based on Improved BP Neural Network with Optimized Sparrow Search Algorithm].
Zhi-Rui Hu, Wan-Fu Zhao, Yin-Xian Song, Fang Wang, Yan-Min Lin

Huan Jing Ke Xue· May 2024

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CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations.
Zhirui Hu, Pawel F Przytycki, Katherine S Pollard

bioRxiv· May 2024

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scATAnno: Automated Cell Type Annotation for single-cell ATAC Sequencing Data.
Yijia Jiang, Zhirui Hu, Allen W Lynch, Junchen Jiang, Alexander Zhu

bioRxiv· March 2024

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Deep flanking sequence engineering for efficient promoter design using DeepSEED.
Pengcheng Zhang, Haochen Wang, Hanwen Xu, Lei Wei, Liyang Liu, Zhirui Hu

Nat Commun· October 2023

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PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance.
Han Yan, Zhirui Hu, Gregg W C Thomas, Scott V Edwards, Timothy B Sackton

Mol Biol Evol· September 2023

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Joint Particle Swarm Optimization of Power and Phase Shift for IRS-Aided D2D Underlaying Cellular Systems.
Ruijie Wang, Xun Wen, Fangmin Xu, Zhijian Ye, Haiyan Cao, Zhirui Hu

Sensors (Basel)· June 2023

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[Spatiotemporal Pattern and Driving Force Analysis of Ecological Environmental Quality in Typical Ecological Areas of the Yellow River Basin from 1990 to 2020].
Fang Wang, Wen-Hui Li, Yan-Min Lin, Xiong-Xiong Nan, Zhi-Rui Hu

Huan Jing Ke Xue· May 2023

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Carbon Quantum Dot/Chitosan-Derived Hydrogels with Photo-stress-pH Multiresponsiveness for Wearable Sensors.
Xiaotong Wei, Jie Li, Zhirui Hu, Chen Wang, Zhiqiang Gao, Yingchun Li

Macromol Rapid Commun· April 2023

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[Spatial-temporal differentiation and driving factors of vegetation coverage in Ningxia Helan Mountain based on geodetector].
Yan-Min Lin, Wen-Hui Li, Xiong-Xiong Nan, Jun-Hua Zhang, Zhi-Rui Hu

Ying Yong Sheng Tai Xue Bao· December 2022

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Enhancing Strain-Sensing Properties of the Conductive Hydrogel by Introducing PVDF-TrFE.
Zhirui Hu, Jie Li, Xiaotong Wei, Chen Wang, Yang Cao, Yingchun Li

ACS Appl Mater Interfaces· October 2022

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Temperature-Stress Bimodal Sensing Conductive Hydrogel-Liquid Metal by Facile Synthesis for Smart Wearable Sensor.
Chen Wang, Jie Li, Zhaozhou Fang, Zhirui Hu, Xiaotong Wei, Yingchun Li

Macromol Rapid Commun· January 2022

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A RIPK1-regulated inflammatory microglial state in amyotrophic lateral sclerosis.
Lauren Mifflin, Zhirui Hu, Connor Dufort, Cynthia C Hession, Alec J Walker, Hong Zhu, Joshua Z Levin

Proc Natl Acad Sci U S A· March 2021

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SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation.
Zhirui Hu, Songpeng Zu, Jun S Liu

NAR Genom Bioinform· December 2020

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Reduction of mNAT1/hNAT2 Contributes to Cerebral Endothelial Necroptosis and Aβ Accumulation in Alzheimer's Disease.
Chengyu Zou, Lauren Mifflin, Zhirui Hu, Tian Zhang, Bing Shan, Huibing Wang, Hong Zhu, Joshua Z Levin, Chuan-Fa Liu

Cell Rep· December 2020

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Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees.
Zhirui Hu, Timothy B Sackton, Scott V Edwards, Jun S Liu

Mol Biol Evol· May 2019

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Convergent regulatory evolution and loss of flight in paleognathous birds.
Timothy B Sackton, Phil Grayson, Alison Cloutier, Zhirui Hu, Jun S Liu

Science· April 2019

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A novel epigenetic mini-circuitry contributes to t(8;21) leukaemogenesis.
Yonghui Li, Qiaoyang Ning, Jinlong Shi, Yang Chen, Mengmeng Jiang, Wenrong Huang, Sai Huang, Zhirui Hu

EMBO Mol Med· July 2017

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3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process.
Mohamed Nadhir Djekidel, Zhengyu Liang, Qi Wang, Zhirui Hu, Guipeng Li

Genome Biol· December 2015

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Small C-terminal Domain Phosphatase 3 Dephosphorylates the Linker Sites of Receptor-regulated Smads (R-Smads) to Ensure Transforming Growth Factor β (TGFβ)-mediated Germ Layer Induction in Xenopus Embryos.
Guanni Sun, Zhirui Hu, Zheying Min, Xiaohua Yan, Zhenpo Guan, Qinghua Tao

J Biol Chem· July 2015

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