以第一、通讯（含共同）作者身份在Nature Methods、Nature Machine Intelligence、Science Advances发表多篇论文：
“#”符号表示共同第一作者，“*” 符号表示通讯作者
[1] Chen X, Li K, Cui X, Wang Z, Jiang Q, Lin J, Li Z, Gao Z, Lv H, and Jiang R*, EpiAgent: Foundation model for single-cell epigenomics, Nature Methods, 2025, 22(11): 2316-2327.
[2] Chen X and Jiang R, Deciphering single-cell epigenomic language with a foundation model, Nature Methods, 2025, 22(11): 2239-2240. Note: This is an invited Research Briefing by the editors, written to highlight the findings of work [1].
[3] Chen X#, Chen S#, Song S, Gao Z, Hou L, Zhang X, Lv H, and Jiang R*, Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding, Nature Machine Intelligence, 2022, 4(2), 116–126.
[4] Wu X, Wang Z, Jiang R*, and Chen X*. Hi-Cformer enables multi-scale chromatin contact map modeling for single-cell Hi-C data analysis, Science Advances, 2026, Accepted.
[5] Chen X#, Li K#, Wu X, Li Z, Jiang Q, Cui X, Gao Z, Wu Y, and Jiang R*, Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations, Genome Biology, 2024, 25(1), 322.
[6] Chen X#, Gao Z#, Li K#, Wang Z#, Jiang Q, Cui X, Li Z, and Jiang R*, Human-scATAC-Corpus: a comprehensive database of scATAC-seq data, Nucleic Acids Research, 2026, 54(D1): D175-D183.
[7] Chen X, Chen S, and Jiang R*, EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes, APBC2020 & BMC Bioinformatics, 2020, 21(Supplement_13), 392.
[8] Li K#, Chen X#, Song S, Hou L, Chen S*, and Jiang R*, Cofea: correlation-based feature selection for single-cell chromatin accessibility sequencing data, Briefings in Bioinformatics, 2024, 25(1), bbad458.
[9] Li C#, Chen X#, Chen S, Jiang R*, and Zhang X*, simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data, Bioinformatics, 2023, 39(8), btad453.
[10] Gao Z#, Chen X#, Li Z#, Cui X#, Jiang Q, Li K, Chen S*, and Jiang R*, scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data, Journal of Genetics and Genomics, 2024, 51(4), 462–465.
[11] Cui X, Chen X, Li Z, Gao Z, Chen S, and Jiang R*, Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity, Nature Computational Science, 2024, 4(5), 346–359.
[12] Li Z, Chen X, Zhang X, Jiang R, and Chen S*, Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics, Genome Research, 2023, 33(10), 1757–1773.
[13] Li Z, Cui X, Chen X, Gao Z, Liu Y, Pan Y, Chen S, Lv H, Zhai L*, and Jiang R*, Cross-modality representation and multi-sample integration of spatially resolved omics data, Briefings in Bioinformatics, 2026, 27(3): bbag214.
[14] Liu Y#, Li Z#, Chen X, Cui X, Gao Z, and Jiang R*, INSTINCT: Multi-sample integration of spatial chromatin accessibility sequencing data via stochastic domain translation, Nature Communications, 2023, 33(10), 1757–1773.
[15] Cui X, Yin Q, Gao Z, Li Z, Chen X, Lv H, Chen S, Liu Q, Zeng W*, and Jiang R*, CREATE: cell-type-specific cis-regulatory element identification via discrete embedding, Nature Communications, 2025, 16(1), 4607.
[16] Chen S, Zhang B, Chen X, Zhang X, and Jiang R*, stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics, ISMB/ECCB & Bioinformatics, 2021, 37(Supplement_1), i299–i307.
[17] Jiang Q#, Chen S#, Chen X, and Jiang R*, scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism, Bioinformatics, 2024, 40(5), btae265.
[18] Zeng W#, Chen S#, Cui X#, Chen X, Gao Z, and Jiang R*, SilencerDB: a comprehensive database of silencers, Nucleic Acids Research, 2021, 49(D1), D221–D228.
[19] Li S, Li Y, Sun Y, Li Y, Chen X, Tang S, and Chen S*, EpiCarousel: memory-and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data, Bioinformatics, 2021, 40(4), btae191.
[20] Xi X#, Chen Y#, Wu X, Hao M, Li J, Bian H, Meng Q, Li F, Li C, Xiao C, Dong
X, You R, Xiong Y, Yang P, Gao Z, Cui X, Pan Y, Li Z, Li W, Li Z, Chen X, Cui Y, Lv H, Jiang R, Wei L*, and Zhang X*. hECA v2.0: an AI-ready ensemble cell atlas of single-cell RNA and ATAC sequencing data. Scientific Data, 2026, 13(1): 10.1038/s41597-025-06426-2.
[21] Jiang Q, Chen X, Gao Z, Jia J, Chen S, and Jiang R*, CASHeart: A database of single-cell chromatin accessibility for the human heart, Quantitative Biology, 2025, 13(2), e90.