| Predicting enhancers with deep convolutional neural networks X Min, W Zeng, S Chen, N Chen, T Chen, R Jiang BMC bioinformatics 18, 35-46, 2017 | 99 | 2017 |
| Simultaneous deep generative modelling and clustering of single-cell genomic data Q Liu, S Chen, R Jiang, WH Wong Nature machine intelligence 3 (6), 536-544, 2021 | 79 | 2021 |
| stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics S Chen, B Zhang, X Chen, X Zhang, R Jiang Bioinformatics 37 (Supplement_1), i299-i307, 2021 | 65 | 2021 |
| RA3 is a reference-guided approach for epigenetic characterization of single cells S Chen, G Yan, W Zhang, J Li, R Jiang, Z Lin Nature communications 12 (1), 2177, 2021 | 54 | 2021 |
| Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding X Chen, S Chen, S Song, Z Gao, L Hou, X Zhang, H Lv, R Jiang Nature Machine Intelligence 4 (2), 116-126, 2022 | 51 | 2022 |
| SilencerDB: a comprehensive database of silencers W Zeng, S Chen, X Cui, X Chen, Z Gao, R Jiang Nucleic acids research 49 (D1), D221-D228, 2021 | 42 | 2021 |
| OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions S Chen, Q Liu, X Cui, Z Feng, C Li, X Wang, X Zhang, Y Wang, R Jiang Nucleic Acids Research 49 (W1), W483–W490, 2021 | 23* | 2021 |
| DeepCAPE: a deep convolutional neural network for the accurate prediction of enhancers S Chen, M Gan, H Lv, R Jiang Genomics, Proteomics and Bioinformatics 19 (4), 565-577, 2021 | 21 | 2021 |
| SINFONIA: scalable identification of spatially variable genes for deciphering spatial domains R Jiang, Z Li, Y Jia, S Li, S Chen Cells 12 (4), 604, 2023 | 15 | 2023 |
| Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics Z Li, X Chen, X Zhang, R Jiang, S Chen Genome Research 33 (10), 1757-1773, 2023 | 12 | 2023 |
| scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data Z Gao, X Chen, Z Li, X Cui, S Chen, R Jiang bioRxiv, 2023.04. 27.538652, 2023 | 11 | 2023 |
| ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data S Chen, R Wang, W Long, R Jiang Bioinformatics 39 (1), btac842, 2023 | 10 | 2023 |
| VPAC: Variational projection for accurate clustering of single-cell transcriptomic data S Chen, K Hua, H Cui, R Jiang BMC bioinformatics 20, 139-151, 2019 | 9 | 2019 |
| EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes X Chen, S Chen, R Jiang BMC bioinformatics 21, 1-16, 2020 | 6 | 2020 |
| Lockpicking LLMs: A Logit-Based Jailbreak Using Token-level Manipulation Y Li, Y Liu, Y Li, L Shi, G Deng, S Chen, K Wang arXiv preprint arXiv:2405.13068, 2024 | 3 | 2024 |
| scButterfly: a versatile single-cell cross-modality translation method via dual-aligned variational autoencoders Y Cao, X Zhao, S Tang, Q Jiang, S Li, S Li, S Chen Nature Communications 15 (1), 2973, 2024 | 3 | 2024 |
| scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data S Tang, X Cui, R Wang, S Li, S Li, X Huang, S Chen Nature Communications 15 (1), 1629, 2024 | 2 | 2024 |
| scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data W Zhang, R Jiang, S Chen, Y Wang Genome Biology 24 (1), 225, 2023 | 2 | 2023 |
| RefTM: reference-guided topic modeling of single-cell chromatin accessibility data Z Zhang, S Chen, Z Lin Briefings in Bioinformatics 24 (1), bbac540, 2023 | 2 | 2023 |
| EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information S Song, H Cui, S Chen, Q Liu, R Jiang Quantitative Biology 7 (3), 233-243, 2019 | 2 | 2019 |
Rui JiangTsinghua UniversityVerified email at tsinghua.edu.cn
