Shiyang Ma

EXPERIENCE

• Associate Director (2025/10-present), Institute of Clinical Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
• Associate Professor (2024/1-present), Institute of Clinical Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
  • Affiliated with School of Mathematical Sciences, Shanghai Jiao Tong University
• Assistant Professor (2022/11-2023/12), Institute of Clinical Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
• Postdoctoral Research Scientist (2019/10-2022/09), Department of Biostatistics, Columbia University, New York, NY
  • Supervisor: Prof. Iuliana Ionita-Laza

EDUCATION

• Ph.D. in Statistics (2019), Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY
  • Advisors: Prof. Michael P. McDermott and Prof. David Oakes
  • Dissertation: Methods for Improving Efficiency in Clinical Trials
• M.A. in Statistics (2016), Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY
• B.S. in Mathematics (2014), Department of Mathematics, Sichuan University, Chengdu, China

RESEARCH INTEREST

• statistical genetics
  • developing statistical and computational methods for the analysis of high-dimensional genetic and genomic data
• biostatistics
  • clinical trials, adaptive designs and repeated measures designs

SELECTED PUBLICATIONS

• Hu, L., Yang, C., Tang, Z., Yan, J., Cheng, H., Bao, L., Ji, J.*, Ma, S.* and Zhang, T.* (2025). Cox-MK: a model-X knockoff method for genome-wide survival association analysis. *Co-corresponding author.

• Hu, L., Chang, Z., Tang, Z., Yang, C., Ma, S. and Zhang, T. (2025). Independent and joint association of smoking status and obesity with accelerated aging.

• Chen, M., Hu, L., Ma, S.* and Zhang, T.* (2025) A two-stage pooled propensity score model of causal inference for multilevel data. *Co-corresponding author.

• Chen, M., Chang, Z., Gong, P., Tang, Z., Hu, L., Zhang, X., Ma, S., Liao, J., Jiang, X., Li, J., and Zhang, T. (2025). Introduction to Secure Data Sharing in Primary Care Using the Federated Causal Learning Models.

• Huang, S., Ran, Q., Wang, X., Tang, J., Xi, J., Ma, S.* and Xi, R.* (2025). SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data. *Co-corresponding author.

• Cui, Y.#, Ma, S.#, Yuan, Y., Zhu, N., Chen, H., Wei, T., Li, Z., Li, X. and Yu, Z. (2025) SurvSTAAR: A powerful statistical framework for rare variant analysis of time-to-event traits in large-scale whole-genome sequencing studies. Journal of the American Statistical Association. #Co-first author.

• Ma, S., Wang, F., Border, R., Buxbaum, J., Zaitlen, N. and Ionita-Laza, I. (2024) Local genetic correlation via knockoffs reduces confounding due to cross-trait assortative mating. The American Journal of Human Genetics, 111, 2839-2848.

• Cui, Y., Lin, Q., Zhou, J., Yuan, X., Ma, S.* and Yu, Z.* (2024) High-dimensional mediation analysis for longitudinal data. Briefings in Bioinformatics, 25, bbae496. *Co-corresponding author.

• Sun, X.#, Ma, S.#, Guo, Y.,#, Chen, C., Pan, L., Cui, Y., Chen, Z., Dijkhuizen, R. M., Zhou, Y., Boltze, J., Yu, Z. and Li, P. (2024) The association between air pollutant exposure and cerebral small vessel disease with modifying effects of PRS-defined genetic susceptibility. Ecotoxicology and Environmental Safety, 281, 116638. #Co-first author.

• Yuan, X., Ma, Y., Gao, R., Cui, S., Wang, Y., Fa, B., Ma, S., Wei, T., Ma, S. and Yu, Z. (2024) HEARTSVG: a fast and accurate method for spatially variable gene identification in large-scale spatial transcriptomic data. Nature Communications, 15, 5700.

• Ma, S. and Wang, T. (2023). The optimal pre-post allocation for randomized clinical trials. BMC Medical Research Methodology, 23, 72.

• Ma, S., Wang, C., Khan, A., Liu, L., Dalgleish, J., Kiryluk, K., He, Z. and Ionita-Laza, I. (2023). BIGKnock: fine-mapping gene-based associations via knockoff analysis of biobank-scale data. Genome Biology, 24, 24.

• He, Z., Liu, L., Belloy, M. E., Guen, Y. L., Sossin, A., Liu. X., Qi. X, Ma, S., Gyawali, P. K., Wyss-Coray, T., Tang, H., Sabatti, C., Candès, E., Greicius, M. D. and Ionita-Laza, I. (2022) GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies. Nature Communications, 13, 7209.

• Ma, S.* and McDermott, M. P. (2022). Adaptive dose-response studies to establish proof-of-concept in learning-phase clinical trials. Biometrical Journal, 64, 146-164. *Corresponding author.

• Ma, S., Dalgleish, J., Lee, J., Wang, C., Liu, L., Gill, R., Buxbaum, J. D., Chung, W. K., Aschard, H., Silverman, E. K., Cho, M. H., He, Z. and Ionita-Laza, I. (2021). Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes. Proceedings of the National Academy of Sciences of the United States of America, 118, e2105191118.

• He, Z., Guen, Y. L., Liu, L., Lee, J., Ma, S., Yang, A. C., Liu. X., Rutledge, J., Losada, P. M., Song, B., Belloy, M. E., Butler, R. R., Longo, F. M., Tang, H., Mormino, E. C., Wyss-Coray, T., Greicius, M. D. and Ionita-Laza, I. (2021) Genome-wide analysis of common and rare variants via multiple knockoffs at biobank scale, with an application to Alzheimer disease genetics. The American Journal of Human Genetics, 108, 2336-2353.

• Ma, S.* and McDermott, M. P. (2020). Generalized multiple contrast tests in dose-response studies. Statistics in Medicine, 39, 757-772. *Corresponding author.

• Schobel, S. A., Palermo, G., Auinger, P., Long, J. D., Ma, S., Khwaja, O. S., Trundell, D., Cudkowicz, M., Hersch, S., Sampaio, C., Dorsey, E. R., Leavitt, B. R., Kieburtz, K. D., Sevigny, J. J., Langbehn, D. R., Tabrizi, S. J.; TRACK-HD, COHORT, CARE-HD, and 2CARE Huntington Study Group Investigators. (2017) Motor, cognitive, and functional declines contribute to a single progressive factor in early HD. Neurology, 89, 2495-2502.

FUNDING (as PI)

• Shanghai Municipal Commission of Education, JWAIYB-3, (2024-2025).
• The National Natural Science Foundation of China Excellent Young Scholars Fund (Overseas), (2024-2026).
• Shanghai Rising-Star Program, 23YF1421000, (2023-2026).
• Clinical Research Project of Shanghai Municipal Health Commission in Health Industry, 20234Y0285, (2023-2026).
• Fundamental Research Funds for the Central Universities, YG2023QNA01, (2023-2025).

TEACHING

• Survival analysis (MATH4705), School of Mathematical Sciences, Shanghai Jiao Tong University (Fall 2025)
• Biostatistics (STAT6138), School of Mathematical Sciences, Shanghai Jiao Tong University (Fall 2024)
• Introduction to Clinical Research Methods, Shanghai Jiao Tong University School of Medicine (Fall 2025, Guest lecturer)
• Introduction to Clinical Research Methods, Shanghai Jiao Tong University School of Medicine (Fall 2024, Guest lecturer)
• Medical Statistics and Clinical Research, Shanghai Jiao Tong University School of Medicine (Spring 2024, Guest lecturer)
• Introduction to Clinical Research Methods, Shanghai Jiao Tong University School of Medicine (Fall 2023, Guest lecturer)

SOFTWARE DEVELOPED

• LAVAKnock: An R package to conduct local genetic correlation analysis via knockoffs.
• BIGKnock: An R package of performing biobank-scale gene-based association test via knockoffs.
• GeneScan3DKnock: An R package for performing improved gene-based testing by integrating long-range chromatin interactions, along with knockoff-enhanced tests.
• GeneScan3D - UK Biobank Gene-based Results: Browser of the GeneScan3D gene-based results for 1,403 UK biobank binary phecodes, 42 BioBank Japan binary phenotypes and 5 psychiatric phenotypes.

Journal Review

Journal of the American Statistical Association; Briefings in Bioinformatics; BMC Medical Research Methodology; Statistics in Biopharmaceutical Research; Epidemiology and Infection; F1000Research; Journal of Applied Statistics; Clinical Trials: Journal of the Society for Clinical Trials; Journal of Digestive Diseases; Biostatistics and Epidemiology

INVITED TALKS

• Shanghai Society for Bioinformatics, Fudan University, Shanghai, China (2025/11).
• The 3rd Conference on Causal Inference, Xinjiang University, Urumqi, China (2025/07).
• The 3rd Joint Conference on Statistics and Data Science in China (JCSDS 2025), Hangzhou, China (2025/07).
• 2025 ICSA China Conference, Zhuhai, China (2025/06).
• AI for Science, Fudan University, Shanghai, China (2025/06).
• Fuwai Hospital, Chinese Academy of Medical Sciences, Beijing, China (2025/04).
• School of Mathematics, Northwest University, Xi’an, China (2025/04).
• Open Mendel Meeting, University of California Los Angeles, USA (2025/01).
• Center of Statistical Research, Southwestern University of Finance and Economics, Chengdu, China (2024/12).
• Center for Data Science, Zhejiang University, Hangzhou, China (2024/12).
• The School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, China (2024/12).
• The 22nd Conference on International Exchange of Professionals, Mathematics and Life Health, Shanghai, China (2024/11).
• School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming, China (2024/10).
• School of Mathematical Sciences, Tongji University, Shanghai, China (2024/10).
• Institute of Statistics and Big Data, Renmin University of China, Beijing, China (2024/10).
• The 7th International Conference on Econometrics and Statistics (EcoSta 2024), Beijing, China (2024/07).
• The 2nd Joint Conference on Statistics and Data Science in China (JCSDS 2024), Kunming, China (2024/07).
• School of Mathematics and Statistics, Northeast Normal University, Changchun, China (2024/06).
• Institute of Statistics and Big Data, Renmin University of China, Beijing, China (2024/05).
• 12th International Conference on Bioinformatics and Computational Biology (ICBCB 2024), Tokyo, Japan (2024/03).
• Tianyuan Mathematics Research Center, Kunming, China (2024/01).
• 16th International Conference of the ERCIM WG on Computational and Methodological Statistics, Berlin, Germany (2023/12).
• Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China (2023/11).
• Department of Biostatistics, Peking University, Beijing, China (2023/11).
• Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China. (2023/10).
• Joint Conference on Statistics and Data Science in China 2023, Beijing, China (2023/07).
• The Second International Workshop on Statistical Theory and Related Fields, Tianjin, China (2023/07).
• ICSA 2023 China Conference, Chengdu, China (2023/06).
• Center for Statistical Science, Tsinghua University, Beijing, China (2023/05).
• School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai, China (2023/03).
• Department of Biostatistics, City University of Hong Kong, China (2022/11).
• Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, China (2022/06).
• The 34th New England Statistics Symposium, Hybrid conference, USA (2021/10).

PhD Students

• Changle Liu, Ph.D. student, Joint supervised with Prof. Tao Wang (2026/9 – present)
• Bonan Ding, M.D. student (2025/9 – present)

CONTACT

Room 709, East 2nd building, 227 South Chongqing Road, Shanghai, 200025, China

Email: mashiyang1991@sjtu.edu.cn

I am recruiting highly motivated PhD students and postdoctoral researchers. Please email me if you are interested.