Publications

Sorted by domains and years.

Computational Biology (Statistical Genetics, Single-cell Genomics, etc.)

• Sun, J., Liang, C., Wei, R., Zheng, P., Yan, H., Bai, L., Zhang, K., Ouyang, W. and Ye, P.* (2025). Scalable integration and prediction of unpaired single-cell and spatial multi-omics via regularized disentanglement. bioRxiv.
  bioRxiv | Codes | Package Document

• Sun, J., Stojanov, P., Zhang, K.* (2025). Single-cell disentangled representations for perturbation modeling and treatment effect estimation. bioRxiv.
  bioRxiv | Codes | Package Document

• Sun, J., Liang, C., Wei, R., Zheng, P., Bai, L., Ouyang, W., Yan, H. & Ye, P.* (2025). scMRDR: A scalable and flexible framework for unpaired single-cell multi-omics data integration. The Thirty-Ninth Annual Conference on Neural Information Processing Systems (NeurIPS). (Spotlight)
  Paper | Codes | Package Document

• Sun, J., Dong Q., Wei, J., Gao, Y., Yu, Z., Hu, X.*, Zhang, Y.* (2025). ti-scMR: Trajectory-inference-based dynamic single-cell Mendelian randomization identifies causal genes underlying phenotypic differences. NAR Genomics and Bioinformatics, 7(3), lqaf082.
  Paper | Codes

• 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, 143(9-10), 1081–1094.
  Paper | Supplementary materials | R package

• Gong, Y., Xu, J., Wu, M., Gao, R., Sun, J., Yu, Z.*, & Zhang, Y.* (2024). Single-Cell Biclustering for Cell-Specific Transcriptomic Perturbation Detection in AD Progression. Cell Reports Methods, 4(4), 100742.
  Paper | Python package

• 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.
  Paper | R package | Online tool

• 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.
  Paper | R package

General Methodology: Causal Inference, Machine Learning, etc.

• Dai, H., Ng, I., Sun, J., Tang, Z, Luo, G., Dong, X., Spirtes, P.*, Zhang, K.* (2025) When Selection meets Intervention: Additional Complexities in Causal Discovery. The Thirteenth International Conference on Learning Representations (ICLR). (Oral)
  Paper

• 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), 23354.
  Paper

Foundation Models in Biology

• Ran Wei #, Ziyao Zhang #, Jianle Sun #, Yongkang Sun #, Juan Meng, Peng Zheng, Chaoqi Liang, Fanyi Meng, Wanli Ouyang, Lei Bai*, Peng Ye*, Yidi Sun* (2025). scMOBA: A conversational single-cell Multi-Omics Brain Agent across species. bioRxiv. (co-first author)
  bioRxiv

• Liang, C.#, Ye, P.#, Yan, H.#, Zheng, P#, Sun, J., Wang, Y., Li, Y., Ren, Y., Jiang, Y., Xiang, J., Zhang, S., Jiang, L., Bai, W., Ma, X., Chen, T., Zuo, W.*, Bai, L.*, Ouyang, W.*, Li, J.* (2025). scDNAm-GPT Captures Genome-wide CpG Dependencies in Single-cell DNA methylomes to Revolutionize Epigenetic Analysis. bioRxiv.
  bioRxiv

• 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.
  bioRxiv

• 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.
  arXiv

Epidemiology

• Sun, J., Deng, L., Li, Q., Zhou, J., & Zhang, Y.* (2024). Dynamic relations between longitudinal morphological, behavioral, and emotional indicators and cognitive impairment: evidence from the Chinese Longitudinal Healthy Longevity Survey. BMC Public Health, 24(1), 3516.
  Paper | Supplementary materials | Codes

• 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.