Publications

Sorted by domains and years.

Methods in Statistical Genetics and Genomics

• Sun, J., Dong Q., Wei, J., Gao, Y., Yu, Z., Hu, X., Zhang, Y. ti-scMR: Trajectory-inference-based dynamic single-cell Mendelian randomization identifies causal genes underlying phenotypic differences. Under Review.
  Codes: https://github.com/sjl-sjtu/ti-scMR

• Sun, J., Zhou, J., Gong, Y., Pang, C., Ma, Y., Zhao, J., Yu, Z., & Zhang, Y. (2024). Bayesian network-based Mendelian randomization for variant prioritization and phenotypic causal inference. Human Genetics, 1-14.
  Read the paper: https://doi.org/10.1007/s00439-024-02640-x | PDF: BNMR
  R package: https://github.com/sjl-sjtu/bnmr2

• Gong, Y., Xu, J., Wu, M., Gao, R., Sun, J., Yu, Z., & Zhang, Y. Single-Cell Biclustering for Cell-Specific Transcriptomic Perturbation Detection in AD Progression. (2024). Cell Reports Methods, 4(4).
  Read the paper: https://doi.org/10.1016/j.crmeth.2024.100742 | PDF: scBC
  Python package: https://github.com/sjl-sjtu/scBC

• Sun, J., Lyu, R., Deng, L., Li, Q., Zhao, Y., & Zhang, Y. (2022). SMetABF: A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included. PLOS Computational Biology, 18(3), e1009948.
  Read the paper: https://doi.org/10.1371/journal.pcbi.1009948 | PDF: SMetABF
  R package: https://github.com/sjl-sjtu/GWAS_meta
  Online tool: https://sunjianle-sjtu.shinyapps.io/analycode/

• Lyu, R., Sun, J., Xu, D., Jiang, Q., Wei, C., & Zhang, Y. (2021). GESLM algorithm for detecting causal SNPs in GWAS with multiple phenotypes. Briefings in Bioinformatics, 22(6), bbab276.
  Read the paper: https://doi.org/10.1093/bib/bbab276 | PDF: GESLM
  R package: https://github.com/sjl-sjtu/GESLM

• Zhou, Y., Fa, B., Wei, T., Sun, J., Yu, Z., & Zhang, Y. (2021). Elastic Correlation Adjusted Regression (ECAR) scores for high dimensional variable importance measuring. Scientific Reports, 11(1), 1-12.
  Read the paper: https://doi.org/10.1038/s41598-021-02706-0 | PDF: ECAR

Foundation Models in Biology

• Ye, P., Bai, W., Ren, Y., Li, W., Qiao, L., Liang, C., Wang, L., Cai, Y., Sun, J., Yang, Z., Zheng, P., Dong, N., Chen, T., Wang, Z., Liu, X., Ma, X., Yan, H., Wang, Z., Wang, S. & Ouyang, W. (2024). Genomics-FM: Universal Foundation Model for Versatile and Data-Efficient Functional Genomic Analysis. bioRxiv.
  Read the paper: https://www.biorxiv.org/content/10.1101/2024.07.16.603653v1

• Liang, C., Qiao, L., Ye, P., Dong, N., Sun, J., Bai, W., Ren, Y., Ma, X., Yan, H., Song, C., Ouyang, W., & Zuo, W. (2023) Toward Understanding BERT-Like Pre-Training for DNA Foundation Models. arXiv.
  Read the paper: https://arxiv.org/abs/2310.07644

Epidemiology

• Sun, J., Deng, L., Li, Q., Zhou, J., & Zhang, Y. Dynamic relations between longitudinal morphological, behavioral, and emotional indicators and cognitive impairment: evidence from the Chinese Longitudinal Healthy Longevity Survey. Under Review
  Codes: https://github.com/sjl-sjtu/CLHLS

• Sun, J., Deng, L., Zhu, H., Liu, M., Lyu, R., Lai, Q., & Zhang, Y. (2021). Meta-analysis on the association between rs11868035, rs823144, rs3851179 and Parkinson’s disease. Meta Gene, 30, 100949.

You can also find my articles on Google Scholars, ResearchGate or ORCID.