Yuehua Cui's Homepage

Yuehua Cui, Ph.D.

Professor

C-432 Wells Hall

619 Red Cedar Rd.
Department of Statistics and Probability
Michigan State University
East Lansing, MI 48824

Phone: (517) 432-7098
Fax: (517) 432-1405
E-mail: cuiy@msu.edu

Education

Ph.D. (2005) Statistics, Department of Statistics, University of Florida
M.Stat. (2002) Statistics, Department of Statistics, University of Florida
M.S. (1998) Plant Biology, China Agricultural University, Beijing, China

Academic Appointment

Professor 2015 – pres, Department of Statistics & Probability, Michigan State University
Graduate Director 2019 – 2025, Department of Statistics & Probability, Michigan State University
Associate Professor 2010 – 2015, Department of Statistics & Probability, Michigan State University
Assistant Professor 2005 – 2010, Department of Statistics & Probability, Michigan State University
Research Scientist 1998 – 2000, Institute of Botany, Chinese Academy of Sciences

Research Interests

Statistical genetics: genetic association study, (e)QTL mapping, gene-gene and gene-environment interactions, Mendelian randomization, high-dimensional mediation analysis
Statistical genomics: scRNA-seq and spatial transcriptomics, gene network inference
Longitudinal data analysis; functional data analysis; mixture model
Statistical applications in biological sciences

Selected Editorial Services

· Senior Editorial Board: BMC Genomic Data (2021-)

· Academic Editor:

- PLoS Genetics (2026-)

- PLoS Computational Biology (2025-)

· Associate Editor:

- Statistical Applications in Genetics and Molecular Biology (2026-)

- Computational and Structural Biotechnology Journal (2023-)

- Frontiers in Systems Biology - Integrative Genetics and Genomics (2021-)

- Statistics and Probability Letters (2015-2026)

- BMC Genetics (2010-2016)

· Deputy Section Editor: BMC Genetics, Section on Statistical and Computational Genetics (2016-2020)

· Editorial Board Member:

- Journal of Computational Systems Biology (2014-)

- Computational and Structural Biotechnology Journal (2021-2023)

- The Scientific World Journal, Computational Biology Domain (2011-2017)

- Recent Patents on Biotechnology (2010-2014)

Selected Research Grants

PI (with P-S. Zhong, K. Klump and A. Burt), 05/19-04/22, NIH R21 HG010073.
Co-PI (with J. Wang and E. Andrechek), 09/18-05/23, NIH 1R01GM131398.
Co-PI (with C.R. Robin, J. Jiang, D. Douches and R. Veilleux), 10/12-09/17, NSF (IOS-1237969)
PI (with P-S. Zhong), 06/12-06/16, NSF DMS-1209112
Co-PI (with N. Jiang, C.R. Buell and J. Jiang), 09/11-09/16, NSF (MCB-1121650)
Sole-PI, 01/10-10/10, NIH subcontract
Sole-PI, 06/07-05/11, National Science Foundation, DMS-0707031
Sole-PI, 12/06-12/08, MSU Intramural Research Grant (06-IRGP-789)

Honors and Awards

Elected Fellow, American Statistical Association (ASA), 2022
Elected member, International Statistics Institute (ISI), 2010
Sigma Xi full membership, The Scientific Research Society, 2008-
Junior Faculty Award, Michigan State University Chapter of Sigma Xi Honorary Scientific Society, 2008
William L. Harkness Instructional Innovation Award, Department of Statistics and Probability, Michigan State University, 2007

Selected Publications

· Ma, S.J., L.J. Yang, R. Romero, and Y.H. Cui*. (2011) Varying coefficient model for gene-environment interaction: a non-linear look. Bioinformatics 27(15): 2119-2126.

· Li, S.Y. and Y.H. Cui*. (2012) Gene-centric gene-gene interaction: a model-based kernel machine method. Annals of Applied Statistics 6(3): 1134-1161.

· Gao, B. and Y.H. Cui*. (2015) Learning directed graphical structures with genetical genomics data. Bioinformatics 31(24): 3953-60.

· Liu, X., Y.H. Cui* and R. Li. (2016) Partial linear varying multi-index coefficient model for integrative gene-environment interactions. Statistica Sinica 26: 1037-1060.

· Gao, B., X. Liu, H. Li and Y.H. Cui*. (2019) Integrative analysis of genetical genomics data incorporating network structures. Biometrics 75(4): 1063-1075.

· Shi, R., L. Wang, S. Burgess and Y.H. Cui*. (2024) MR-SPLIT: a novel method to address selection and weak instrument bias in one-sample Mendelian randomization studies. PloS Genetics 20: e1011391.

· Su, H., Y. Wu, B. Chen, Y.H. Cui*. (2025) STANCE: a unified statistical model to detect cell-type-specific spatially variable genes in spatial transcriptomics. Nature Communications 16(1): 1793.

Das Adhikari, S., N.G. Steele, B. Theisen, J. Wang*, and Y.H. Cui*. (2025) SPACE: Spatially variable gene clustering adjusting for cell type effect for improved spatial domain detection. Nucleic Acids Research 53(18): gkaf936.

· Su, H. and Y.H. Cui*. (2025) Rotation-invariance is essential for accurate detection of spatially variable genes in spatial transcriptomics. Nature Communications 16(1), 7122.

Xie, A., N.G. Steele and Y.H. Cui*. (2025) gwSPADE: gene-frequency weighted reference-free deconvolution in spatial transcriptomics. Nucleic Acids Research 53 (18), gkaf966.
Cao, H*, G. Liu, J. Xia, R. Chen, T. Wang, X. Yang, R. Fang, Y. Luo, P. Zeng, H. Yu, Y. Zhang, and Y.H. Cui*. (2026) SpatialESD: Spatial ensemble domain detection in spatial transcriptomics. Advanced Science, e20912.

· Vo, P. and Y.H. Cui*. (2026) Spatially informed reference-free cell type deconvolution for spatial transcriptomics with SpatialCD. Genome Research (accepted in principle)

Research Highlight

Our work on Gene-centric genetic association study (Cui et al. 2008, Genetics) was highlighted in Nature Reviews Genetics Vol. 9 No. 6 (2008).