MaLab Shanghai Jiao Tong University
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Selected publications

20 publications
  1. 2026

    Deciphering spatial cellular organization through RNA-anchored multi-omics deconvolution.

    Bai, Y., Guan, X., Xiong, S., Guo, X., Wang, X., Yi, S., Ju, W., Ma, S., Dong, Q. and Liu, W.

    Full citation

    Bai, Y., Guan, X., Xiong, S., Guo, X., Wang, X., Yi, S., Ju, W., Ma, S., Dong, Q. and Liu, W. (2026). Deciphering spatial cellular organization through RNA-anchored multi-omics deconvolution.

  2. 2026

    MARV: MultivAriate exponential family-based SKAT and Burden tests for Rare Variant association analysis.

    Niu, T., Yu, K., Luo, S.* and Ma, S.*

    Full citation

    Niu, T., Yu, K., Luo, S.* and Ma, S.* (2026). MARV: MultivAriate exponential family-based SKAT and Burden tests for Rare Variant association analysis. *Co-corresponding author.

  3. 2026

    AI-enabled opportunistic screening of cerebral small vessel disease using large-scale routine clinical data.

    Wang, Y., Huang, D., Ma, S., Cui, Y., Yuan, X., Gao, R., Sun, X., Xia, Y., Zhang, Y., Li, P. and Yu, Z.

    Full citation

    Wang, Y., Huang, D., Ma, S., Cui, Y., Yuan, X., Gao, R., Sun, X., Xia, Y., Zhang, Y., Li, P. and Yu, Z. (2026). AI-enabled opportunistic screening of cerebral small vessel disease using large-scale routine clinical data.

  4. 2026

    KnockoffPipeline: A Unified R Workflow for Knockoff-Based Genome-Wide Association Analysis.

    Shen, Y., Wang, T.* and Ma, S.*

    Full citation

    Shen, Y., Wang, T.* and Ma, S.* (2026). KnockoffPipeline: A Unified R Workflow for Knockoff-Based Genome-Wide Association Analysis. *Corresponding author.

  5. 2026

    Cox-MK: a model-X knockoff method for genome-wide survival association analysis

    Hu, L., Yang, C., Tang, Z., Yan, J., Cheng, H., Bao, L., Ji, J.*, Ma, S.* and Zhang, T.*

    Genetics

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    Hu, L., Yang, C., Tang, Z., Yan, J., Cheng, H., Bao, L., Ji, J.*, Ma, S.* and Zhang, T.* (2026). Cox-MK: a model-X knockoff method for genome-wide survival association analysis. Genetics, 233, iyag123. *Co-corresponding author.

  6. 2026

    SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data

    Huang, S., Ran, Q., Wang, X., Tang, J., Xi, J., Ma, S.* and Xi, R.*

    Genome Biology

    Full citation

    Huang, S., Ran, Q., Wang, X., Tang, J., Xi, J., Ma, S.* and Xi, R.* (2026). SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data. Genome Biology, 27, 182. *Co-corresponding author.

  7. 2026

    Introduction to secure data sharing in primary care using the federated causal learning models

    Chen, M., Chang, Z., Gong, P., Tang, Z., Hu, L., Zhang, X., Ma, S., Liao, J., Jiang, X., Li, J., and Zhang, T.

    BMJ Health & Care Informatics

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    Chen, M., Chang, Z., Gong, P., Tang, Z., Hu, L., Zhang, X., Ma, S., Liao, J., Jiang, X., Li, J., and Zhang, T. (2026). Introduction to secure data sharing in primary care using the federated causal learning models. BMJ Health & Care Informatics 33, e101543.

  8. 2026

    SurvSTAAR: A powerful statistical framework for rare variant analysis of time-to-event traits in large-scale whole-genome sequencing studies

    Cui, Y.#, Ma, S.#, Yuan, Y., Zhu, N., Chen, H., Wei, T., Li, Z., Li, X. and Yu, Z.

    Journal of the American Statistical Association

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    Cui, Y.#, Ma, S.#, Yuan, Y., Zhu, N., Chen, H., Wei, T., Li, Z., Li, X. and Yu, Z. (2026) 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, 121, 905–916. #Co-first author.

  9. 2024

    Local genetic correlation via knockoffs reduces confounding due to cross-trait assortative mating

    Ma, S., Wang, F., Border, R., Buxbaum, J., Zaitlen, N. and Ionita-Laza, I.

    The American Journal of Human Genetics

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    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.

  10. 2024

    High-dimensional mediation analysis for longitudinal data

    Cui, Y., Lin, Q., Zhou, J., Yuan, X., Ma, S.* and Yu, Z.*

    Briefings in Bioinformatics

    Full citation

    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.

  11. 2024

    The association between air pollutant exposure and cerebral small vessel disease with modifying effects of PRS-defined genetic susceptibility

    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.

    Ecotoxicology and Environmental Safety

    Full citation

    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.

  12. 2024

    HEARTSVG: a fast and accurate method for spatially variable gene identification in large-scale spatial transcriptomic data

    Yuan, X., Ma, Y., Gao, R., Cui, S., Wang, Y., Fa, B., Ma, S., Wei, T., Ma, S. and Yu, Z.

    Nature Communications

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    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.

  13. 2023

    The optimal pre-post allocation for randomized clinical trials

    Ma, S. and Wang, T.

    BMC Medical Research Methodology

    Full citation

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

  14. 2023

    BIGKnock: fine-mapping gene-based associations via knockoff analysis of biobank-scale data

    Ma, S., Wang, C., Khan, A., Liu, L., Dalgleish, J., Kiryluk, K., He, Z. and Ionita-Laza, I.

    Genome Biology

    Full citation

    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.

  15. 2022

    GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies

    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.

    Nature Communications

    Full citation

    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.

  16. 2021

    Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes.

    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.

    Proceedings of the National Academy of Sciences of the United States of America

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    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 (direct submission), 118, e2105191118.

  17. 2021

    Genome-wide analysis of common and rare variants via multiple knockoffs at biobank scale, with an application to Alzheimer disease genetics.

    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.

    The American Journal of Human Genetics

    Full citation

    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.

  18. 2021

    “If the glove fits”: Hospital-wide universal gloving is associated with improved hand hygiene and may reduce Clostridioides difficile infection.

    Prasad, P., Brown, L., Ma, S., McDavid, A., Rudmann, A., Lent, D., Reagan-Webster, P., Valcin, K. E., Graman, P. and Apostolakos, M.

    Infection Control and Hospital Epidemiology

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    Prasad, P., Brown, L., Ma, S., McDavid, A., Rudmann, A., Lent, D., Reagan-Webster, P., Valcin, K. E., Graman, P. and Apostolakos, M. (2021) “If the glove fits”: Hospital-wide universal gloving is associated with improved hand hygiene and may reduce Clostridioides difficile infection. Infection Control and Hospital Epidemiology,, 42, 1351-1355.

  19. 2020

    Generalized multiple contrast tests in dose-response studies.

    Ma, S.* and McDermott, M. P.

    Statistics in Medicine

    Full citation

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

  20. 2017

    Motor, cognitive, and functional declines contribute to a single progressive factor in early HD.

    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.

    Neurology

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    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.