Dr. Xuekui Zhang

Dr. Xuekui Zhang

Associate Professor at UVic,
Tier 2 Canada Research Chair,
MSFHR Scholar

Publications (Selected)

Recently Published Papers

Trainees are underlined, and the last/corresponding authors are denoted by *. The impact factor (when provided) is 2023. A full list of publications can be found on my Google Scholar page.

Single Cell Genomics

  1. Kailun Bai, Belaid Moa, Xiaojian Shao, Xuekui Zhang*. scSorterDL: A Deep Neural Network-Enhanced Ensemble LDAs for Single Cell Classifications. 2025, Briefings in Bioinformatics (Accepted)
  2. Yao Dong, Chen Chen, Jin Shi, Yushan Hu, Xiaowen Cao, Yongfeng Dong and Xuekui Zhang*. MOH: a novel multilayer multi-omics heterogeneous graph for single-cell clustering. 2025, IEEE Journal of Biomedical and Health Informatics, 2025, (Accepted) Link to Paper
  3. Chang Bi, Kailun Bai, Xuekui Zhang*. HiCat: A Semi-Supervised Approach for Cell Type Annotation. 2025, Briefings in Bioinformatics, Link to Paper
  4. Kailun Bai, Belaid Moa, Xiaojian Shao, and Xuekui Zhang*. PCLDA: An interpretable cell annotation tool for single-cell RNA-sequencing data based on simple statistical methods. 2025, Computational and Structural Biotechnology Journal, Link to Paper
  5. Yao Dong, Jiaxue Zhang, Jin Shi, Yushan Hu, Xiaowen Cao, Yongfeng Dong, and Xuekui Zhang*. scAGCI: an anchor graph-based method for cell clustering from integrated scRNA-seq and scATAC-seq data. 2025, Briefings in Bioinformatics, Link to Paper and GitHub
  6. Yushan Hu, Xiaojian Shao, Li Xing, Xuan Li, Geoffrey M. Nonis, Graeme J. Koelwyn*, Xuekui Zhang*, Dong D. Sin*. Single Cell Sequencing of Lung Macrophages and Monocytes Reveals Novel Therapeutic Targets in COPD. 2023, Cells Link to Paper
  7. Xiangling Ji X, Danielle Tsao, Kailun Bai K, Min Tsao, Li Xing, and Xuekui Zhang*. scAnnotate: an automated cell type annotation tool for single-cell RNA-sequencing data. 2023, Bioinformatics Advance, Link to Paper and R package

Statistics, Bioinformatics, and Biomedicine

  1. Xiaowen Cao, Shuai You, Grace Y. Yi, Xuekui Zhang*, Li Xing*. Concurrent Prediction of Multiple Survival Outcomes with a Refined Stacking Algorithm. 2025, Journal of Computational and Graphical Statistics (Accepted)
  2. Bie Y, You S, Li X, Zhang X* and Lu T*, Essential Number of Principal Components and Nearly Training-Free Model for Spectral Analysis. 2024, IEEE Transactions on Pattern Analysis and Machine Intelligence, (Impact factor 20.8) Link to Paper
  3. Ning H, Boyes I, Numanagić I, Rott M*, Xing L*, Zhang X*. Diagnostics of viral infections using high-throughput genome sequencing data. 2024, Briefings in Bioinformatics Link to Paper and R package
  4. Luo W, Zhu Y, Zhang X, Lin L. A, Semi-parametric Estimation of Personalized Dose-response Function Using Instrumental Variables. 2024, Journal of Machine Learning Research , Link to Paper
  5. Zhang X, Huang X, and Xing L. ADSP: An Adaptive Sample Pooling Strategy for Diagnostic Testing. 2023, Journal of Biomedical Informatics, Link to Paper
  6. Cheng X, Liu Y, Wang J, Robertson G, Zhang X, Jones S, and Taubert S. cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines. 2022, Briefings in Bioinformatics (impact factor 9.5) Link to Paper
  7. Xing L, Zhang X, Burstyn I， Gustafson P. On logistic Box–Cox regression for flexibly estimating the shape and strength of exposure‐disease relationships. 2021，Canadian Journal of Statistics Link to Paper , （ Statistics Society of Canada 2022 CJS Award ）
  8. Xing L, Lesperance ML, Zhang X*. Simultaneous prediction of multiple outcomes using revised stacking algorithms. 2020， Bioinformatics Link to Paper and Software package

Environmental Research

  1. Liu Z, You S, Xing L, Durand G, Moccia P, Mercier V, Pan Y*, Zhang X*. OPMS - a web-based ocean pollution monitoring system, Marine Pollution Bulletin. 2025 Marine Pollution Bulletin (impact factor 5.8) Link to Paper
  2. You S, Xing L, Lesperance M, Pan Y*, Zhang X*. Temporal and Spatial Variation Patterns of Domoic Acid along Canada’s Coast. 2024 Science of the Total Environment (Impact Factor 9.8) Link to Paper
  3. You S, Xing L, Lesperance M, Pan Y*, Zhang X*. Longitudinal Study of Paralytic Shellfish Toxins along Canada’s Coast. 2024 Environmental Research (Impact Factor 8.3) Link to Paper
  4. You S, Huang X, Xing L, Lesperance M, LeBlanc C, Moccia P, Mercier V, Shao X, Pan Y*, Zhang X*. 2023, Dynamics of Fecal Coliform Bacteria along Canada’s Coast. Marine Pollution Bulletin (impact factor 5.8) Link to Paper

Design of adaptive clinical trials

  1. Cong Chen, Mo Huang, Xuekui Zhang*. Adaptive Phase 2/3 Design with Dose Optimization. 2025 Contemporary Clinical Trials Link to Paper
  2. Cong Chen, Mo Huang, Xuekui Zhang*. Adjustment for Inconsistency in Adaptive Phase 2/3 Designs with Dose Optimization. 2025 Pharmaceutical Statistics Link to Paper
  3. Cong Chen, Linda Sun, Xuekui Zhang. A promising biomarker adaptive Phase 2/3 design – explained and expanded. 2023, Contemporary Clinical Trials Communications Link to Paper
  4. Cong Chen, and Xuekui Zhang. From bench to bedside, 2-in-1 design expedites phase 2/3 oncology drug development. 2023, Frontiers in Oncology, Link to Paper
  5. Xuekui Zhang, Haijun Jia, Li Xing, and Cong Chen. Application of group sequential methods to the 2-in-1 design and its extensions for interim monitoring. 2023, Statistics in Biopharmaceutical Research, Link to Paper
  6. Yitao Lu, Julie Zhou, Li Xing, Xuekui Zhang*. The Optimal Design of Clinical Trials with Potential Biomarker Effects, A Novel Computational Approach. 2021， Statistics in Medicine Link to Paper and Software package

Economics

  1. Zhang X, Huang Y , Xu K, Xing L. Novel Modelling Strategies for High-frequency Stock Trading Data. 2023， Financial Innovation (impact factor 8.4) Link to Paper and GitHub code
  2. Xu K, Zheng X, Xing L, Zhang X. Stock Market Openness and Market Quality: Evidence from the Shanghai-Hong Kong Stock Connect Program. 2020， Journal of Financial Research Link to Paper

COVID-19 Research

  1. Li M, Esfahani F, Xing L, Zhang X*. Predicting the daily counts of COVID-19 infection using temporal convolutional networks. 2023, Journal of Global Health (impact factor 7.2), Link to Paper ( The first author is an intern high-school student in my lab, who lead programming and 1st draft preparation of this project.)
  2. Guo Y , Esfahani F, Shao X, Srinivasan V, Thomo A, Xing L, Zhang X*. Integrative COVID-19 Biological Network Inference with Probabilistic Core Decomposition. 2021， Briefings in Bioinformatics (impact factor 9.5) Link to Paper
  3. Huang X , Shao X, Xing L, Hu Y, Sin DD*, Zhang X*. The impact of lockdown timing on COVID-19 transmission across US counties. 2021， EClinicalMedicine (a journal published by the Lancet, impact factor 15.1) Link to Paper

Software

scAnnotate: An Automated Cell Type Annotation Tool for Single-Cell RNA-Sequencing Data. CRAN

DesignCTPB: Design Clinical Trials with Potential Biomarker Effect. CRAN

MTPS: Multi-Task Prediction using Stacking Algorithms. CRAN

GWASbyCluster: Identifying disease-associated significant SNPs using clustering approach. CRAN

PICS: Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. Bioconductor

PING: Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data. Bioconductor