Zhirui Hu
Assistant Professor
Department of Statistics
Zhirui Hu
Assistant Professor
Department of Statistics
Current Research:
My current research focuses on developing statistical and machine learning methods for biological data analysis, with particular emphasis on integrating multi-omics single-cell data and modeling phenotypic evolution and genomic function across species.
Research Interests:
- Bayesian modeling and computational statistics for complex data analysis
- Computational biology: multi-omics integration and spatial-temporal modeling of single-cell data
- Phylogenetics and comparative genomics
- Deep learning for genome sequences and single-cell data
Teaching Responsibilities/Courses:
- ST 558D
- ST 552
Education
Bioinformatics Fellow, Gladstone Institutes & University of California, San Francisco, 2022-2025
Ph.D. in Statistics, Harvard University, 2014-2019
M.S. in Bioinformatics, Tsinghua University, 2011-2014
B.S. in Math and Physics, Tsinghua University, 2007-2011
Publications
- Zhirui Hu, Pawel F. Przytycki, Katherine S. Pollard. CellWalker2: Multi-omic discovery using hierarchical cell type relationships. Cell Genomics, 2025, 5(7), 100886.
- Han Yan*, Zhirui Hu*, Gregg W C Thomas*, Scott V Edwards, Timothy B Sackton, Jun S Liu. PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance. Molecular Biology and Evolution, 2023, 40(9): msad195.
- Zhirui Hu, Zheng Tracy Ke, Jun S. Liu. Measurement error models: from nonparametric methods to deep neural networks. Statist. Sci. 2022, 37(4): 473-493.
- Zhirui Hu, Songpeng Zu, Jun S Liu. SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation. NAR Genomics and Bioinformatics, 2020, 2(4): lqaa077.
- Zhirui Hu and Hyungsuk Tak. Modeling Stochastic Variability in Multiband Time-series Data. The Astronomical Journal, 2020, 160(6): 265.
- Zhirui Hu, Timothy B. Sackton, Scott V. Edwards, Jun S. Liu. Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees. Molecular Biology and Evolution 2019 36(5): 1086–1100.