Shiyang Ma

EXPERIENCE

• Associate Professor (2024-present), School of Medicine, School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai, China
• Assistant Professor (2022-2023), School of Medicine, Shanghai Jiao Tong University, Shanghai, China
• Postdoctoral Research Scientist (2019-2022), 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 data
• clinical trials
  • dose-response studies, adaptive designs, repeated measures designs

SELECTED PUBLICATIONS

• 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. American Journal of Human Genetics, 111, 1-10.

• 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.

• 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. 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.

FUNDING (as PI)

• 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).
• Startup Fund for Young Faculty at Shanghai Jiao Tong University School of Medicine, (2024-2028).

TEACHING

• Biostatistics (STAT6138), School of Mathematical Sciences, Shanghai Jiao Tong University (Fall 2024)
• Medical Statistics and Clinical Research, 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; Journal of Applied Statistics; Clinical Trials: Journal of the Society for Clinical Trials; Statistics in Biopharmaceutical Research; Biostatistics and Epidemiology; F1000Research; Journal of Digestive Diseases, Epidemiology and Infection

INVITED TALKS

• The 22nd Conference on International Exchange of Professionals, Mathematics and Life Health, Shanghai, China (11/2024).
• School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming, China (10/2024).
• School of Mathematical Sciences, Tongji University, Shanghai, China (10/2024).
• Institute of Statistics and Big Data, Renmin University of China, Beijing, China (10/2024).
• The 7th International Conference on Econometrics and Statistics (EcoSta 2024), Beijing, China (07/2024).
• The 2nd Joint Conference on Statistics and Data Science in China (JCSDS 2024), Kunming, China (07/2024).
• School of Mathematics and Statistics, Northeast Normal University, Changchun, China (06/2024).
• Institute of Statistics and Big Data, Renmin University of China, Beijing, China (05/2024).
• 12th International Conference on Bioinformatics and Computational Biology (ICBCB 2024), Tokyo, Japan (03/2024).
• Tianyuan Mathematics Research Center, Kunming, China (01/2024).
• 16th International Conference of the ERCIM WG on Computational and Methodological Statistics, Berlin, Germany (12/2023).
• Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China (11/2023).
• Department of Biostatistics, Peking University, Beijing, China (11/2023).
• Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China. (10/2023).
• Joint Conference on Statistics and Data Science in China 2023, Beijing, China (07/2023).
• The Second International Workshop on Statistical Theory and Related Fields, Tianjin, China (07/2023).
• ICSA 2023 China Conference, Chengdu, China (06/2023).
• Center for Statistical Science, Tsinghua University, Beijing, China (05/2023).
• School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai, China (03/2023).
• Department of Biostatistics, City University of Hong Kong, China (11/2022).
• Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, China (06/2022).
• The 34th New England Statistics Symposium, Hybrid conference, USA (10/2021).

CONTACT

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

Email: mashiyang1991@sjtu.edu.cn