BioX Future Interdisciplinary Technology Mathematics Information Life Sciences
Welcome to Chen's Lab at Nankai University.X for Future, Interdisciplinary, and Technology.
We focus on the interrogation of cell heterogeneity and biological implication in single-cell omics data via mathematical methods and information technologies.
Impute missing data modalities and enhance highly noisy single-cell data via transfer learning.
Characterize cell heterogeneity in single-cell data via reference-based unsupervised learning.
Annotate cell types in single-cell data automatically via ensemble-based supervised learning.
Elucidate cell type-specific patterns in single-cell data via interpretable machine learning.
† first authors with equal contribution, * corresponding authors
Songming Tang, Siyu Li, Shengquan Chen*. Imputing not available values in single-cell DNA methylation data using the median is straightforward and effective.
Dongyue Yu, Shengquan Chen*, Wenjun Bu*. TransPro: integrating univariate and multivariate approaches for comprehensive gene functional enrichment analysis and visualization.
Shuchen Zhu†, Heyang Hua†, Shengquan Chen*. Rigorous integration of single-cell ATAC-seq data using regularized barycentric mapping.
Xuejian Cui, Qijin Yin, Zijing Gao, Zhen Li, Xiaoyang Chen, Shengquan Chen, Wanwen Zeng, Rui Jiang. CREATE: cell-type-specific cis-regulatory elements identification via discrete embedding.
Zhen Li, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Yuyao Liu, Yan Pan, Shengquan Chen, Rui Jiang*. Cross-modality representation and multi-sample integration of spatially resolved omics data.
Yuxi Li, Yi Liu, Yuekang Li, Ling Shi, Gelei Deng, Shengquan Chen, Kailong Wang. Lockpicking LLMs: a logit-based jailbreak using token-level manipulation.
Qiuchen Meng†, Xinze Wu†, Chen Li, Jiaqi Li, Xi Xi, Sijie Chen, Shengquan Chen, Jiaqi Li, Xiaowo Wang, Rui Jiang, Lei Wei*, Xuegong Zhang*. The full set of potential open regions (PORs) in the human genome defined by consensus peaks of ATAC-seq data.
[35] Siyu Li†, Xinhao Zhuang†, Songbo Jia†, Songming Tang, Liming Yan, Heyang Hua, Yuhang Jia, Xuelin Zhang, Yan Zhang, Qingzhu Yang*, Shengquan Chen*. MultiKano: an automatic cell type annotation tool for single-cell multi-omics data based on Kolmogorov-Arnold network and data augmentation. Protein & Cell, 2024, Accepted. [link, code]
[34] Qun Jiang, Xiaoyang Chen, Zijing Gao, Jinmeng Jia, Shengquan Chen, Rui Jiang*. CASHeart: a database of single-cells chromatin accessibility for the human heart. Quantitative Biology, 2024, Accepted. [link, code]
[33] Sicheng Feng, Siyu Li, Luonan Chen*, Shengquan Chen*. Unveiling potential threats: backdoor attacks in single-cell pretrained models. Cell Discovery, 2024, 10:122. [link, code]
[32] Ruike Song†, Xiaofeng Wang†, Jiahao Zhang, Shengquan Chen*, Jianyu Zhou*. GATDE: A graph attention network with diffusion-enhanced protein-protein interaction for cancer classification. Methods, 2024, Online. [link, code]
[31] Heyang Hua†, Wenxin Long†, Yan Pan†, Siyu Li, Jianyu Zhou*, Haixin Wang*, Shengquan Chen*. scCrab: a reference-guided ensemble method for cancer cell identification via Bayesian neural networks. Interdisciplinary Sciences: Computational Life Sciences, 2024, Online. [link, code]
[30] Zhihan Ruan, Weijun Zhou, Hong Liu, Jinmao Wei, Yichen Pan, Chaoyang Yan, Xiaoyi Wei, Wenting Xiang, Chengwei Yan, Shengquan Chen, Jian Liu*. Precise detection of cell-type-specific domains in spatial transcriptomics. Cell Reports Methods, 2024, 4(8):100841. [link, code]
[29] Qun Jiang†, Shengquan Chen†, Xiaoyang Chen, Rui Jiang*. scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism. Bioinformatics, 2024, btae265. [link, code]
[28] Zijing Gao, Rui Jiang, Shengquan Chen*. OpenAnnotateApi: Python and R packages to efficiently annotate and analyze chromatin accessibility of genomic regions. Bioinformatics Advances, 2024, vbae055. [link, code]
[27] Sijie Li, Yuxi Li, Yu Sun, Yaru Li, Xiaoyang Chen, Songming Tang, Shengquan Chen*. EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data. Bioinformatics, 2024, btae191. [link, code]
[26] Yichuan Cao, Xiamiao Zhao, Songming Tang, Qun Jiang, Sijie Li, Siyu Li, Shengquan Chen*. scButterfly: a versatile single-cell cross-modality translation method via dual-aligned variational autoencoders. Nature Communications, 2024, 15:2973. Editors' Highlights. [link, code]
[25] Xuejian Cui, Xiaoyang Chen, Zhen Li, Zijing Gao, Shengquan Chen*, Rui Jiang*. Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity. Nature Computational Science, 2024, 4:346-359. [link, code]
[24] Yuhang Jia†, Siyu Li†, Rui Jiang, Shengquan Chen*. Accurate annotation for differentiating and imbalanced cell types in single-cell chromatin accessibility data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2024, 21(3):461-471. [link, code]
[23] Songming Tang, Xuejian Cui, Rongxiang Wang, Sijie Li, Siyu Li, Xin Huang, Shengquan Chen*. scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data. Nature Communications, 2024, 15:1629. Editors' Highlights. [link, code]
[22] Haixin Wang†, Yunhan Wang†, Qun Jiang†, Yan Zhang*, Shengquan Chen*. SCREEN: predicting single-cell gene expression perturbation responses via optimal transport. Frontiers of Computer Science, 2024, 18:183909. [link, code]
[21] Keyi Li†, Xiaoyang Chen†, Shuang Song, Lin Hou, Shengquan Chen*, Rui Jiang*. Cofea: correlation-based feature selection for single-cell chromatin accessibility data. Briefings in Bioinformatics, 2024, bbad458. [link, code]
[20] Wenhao Zhang, Rui Jiang, Shengquan Chen*, Ying Wang*. scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data. Genome Biology, 2023, 24:225. [link, code]
[19] Zijing Gao†, Xiaoyang Chen†, Zhen Li†, Xuejian Cui†, Qun Jiang, Keyi Li, Shengquan Chen*, Rui Jiang*. scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data. Journal of Genetics and Genomics, 2023, 51(4):462-465. [link, tool]
[18] Zhen Li, Xiaoyang Chen, Xuegong Zhang, Rui Jiang, Shengquan Chen*. Latent feature extraction with a Prior-based self-Attention framework for Spatial Transcriptomics. Genome Research, 2023, 33:1757-1773. [link, code]
[17] Chen Li†, Xiaoyang Chen†, Shengquan Chen, Rui Jiang*, Xuegong Zhang*. simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. Bioinformatics, 2023, btad453. [link, code]
[16] Siyu Li, Songming Tang, Yunchang Wang, Sijie Li, Yuhang Jia, Shengquan Chen*. Accurate cell type annotation for single-cell chromatin accessibility data via contrastive learning and reference guidance. Quantitative Biology, 2023, 12(1):85-99. [link, code]
[15] Rui Jiang, Zhen Li, Yuhang Jia, Siyu Li, Shengquan Chen*. SINFONIA: scalable identification of spatially variable genes for deciphering spatial domains. Cells, 2023, 12(4):604. [link, code]
[14] Shengquan Chen*, Rongxiang Wang, Wenxin Long, Rui Jiang*. ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data. Bioinformatics, 2022, btac842. [link, code]
[13] Zheng Zhang, Shengquan Chen, Zhixiang Lin*. RefTM: reference-guided topic modeling of single-cell chromatin accessibility data. Briefings in Bioinformatics, 2022, bbac540. [link, code]
[12] Xiaoyang Chen†, Shengquan Chen†, Shuang Song, Zijing Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang*. Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding. Nature Machine Intelligence, 2022, 4:116-126. [link, code]
[11] Xi Xi, Haochen Li, Shengquan Chen, Tingting Lv, Tianxing Ma, Rui Jiang, Ping Zhang, Wing Hung Wong*, Xuegong Zhang*. Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling. iScience, 2022, 25(8):104790. [link, code]
[10] Shengquan Chen†, Guanao Yan†, Wenyu Zhang, Jinzhao Li, Rui Jiang*, Zhixiang Lin*. RA3 is a reference-guided approach for epigenetic characterization of single cells. Nature Communications, 2021, 12:2177. [link, code]
[9] Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang*. OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. Nucleic Acids Research, 2021, 49(W1):W483-W490. [link, tool]
[8] Wanwen Zeng†, Shengquan Chen†, Xuejian Cui†, Xiaoyang Chen, Zijing Gao, Rui Jiang*. SilencerDB: a comprehensive database of silencers. Nucleic Acids Research, 2021, 49(D1):D221-D228. [link, tool]
[7] Shengquan Chen, Mingxin Gan, Hairong Lv, Rui Jiang*. DeepCAPE: a deep convolutional neural network for the accurate prediction of enhancers. Genomics, Proteomics & Bioinformatics, 2021, 19(4):565-577. [link, code]
[6] Shengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang*. stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. ISMB/ECCB 2021, Bioinformatics, 2021, 37(S1):i299-i307. [link, tool]
[5] Qiao Liu, Shengquan Chen, Rui Jiang*, Wing Hong Wong*. Simultaneous deep generative modeling and clustering of single cell genomic data. Nature Machine Intelligence, 2021, 3:536-544. [link, code]
[4] Xiaoyang Chen, Shengquan Chen, Rui Jiang*. EnClaSC: A novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes. BMC Bioinformatics, 2020, 21(13):1-16. [link, code]
[3] Shengquan Chen, Kui Hua, Hongfei Cui, Rui Jiang*. VPAC: Variational projection for accurate clustering of single-cell transcriptomic data. BMC Bioinformatics, 2019, 20(7):139-151. [link, code]
[2] Shaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang*. EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information. Quantitative Biology, 2019, 7(3):233-243. [link, tool]
[1] Xu Min†, Wanwen Zeng†, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang*. Predicting enhancers with deep convolutional neural networks. BMC Bioinformatics, 2017, 18(13):478. [link, code]
School of Mathematical Sciences
Associate Prof., Nankai U. (2022.1-)
Ph.D., Tsinghua U. (2017.9-2021.12)
B.Eng., Xiamen U. (2013.9-2017.7)
Read MoreChern Class of Nankai Mathematics
Ph.D. Student, Nankai U. (2025.9-)
B.Sc., Nankai U. (2021.9-2025.7)
Read MoreSchool of Mathematical Sciences
Ph.D. Student, Nankai U. (2025.9-)
M.Phil., Hunan U. (2022.9-2025.7)
B.Sc., CAUC. (2018.9-2022.7)
Read MoreSchool of Aerospace Engineering
Ph.D. Student, Xiamen U. (2024.9-)
M.Phil., Xiamen U. (2021.9-2024.7)
B.Eng., Xiamen U. (2016.9-2020.7)
Read MoreSchool of Mathematical Sciences
M.Phil. Student, Nankai U. (2022.9-)
B.Sc., Nankai U. (2018.9-2022.7)
Read MoreSchool of Mathematical Sciences
M.Phil. Student, Nankai U. (2023.9-)
B.Sc., SCUT. (2019.9-2023.7)
Read MoreSchool of Mathematical Sciences
M.Phil. Student, Nankai U. (2023.9-)
B.Sc., NWAFU. (2019.9-2023.7)
Read MoreSchool of Mathematical Sciences
M.Phil. Student, Nankai U. (2024.9-)
Visiting Student, Department of Statistics, The Chinese University of Hong Kong. (2024.1-2024.6)
B.Sc., Nankai U. (2020.9-2024.7)
Read MoreSchool of Mathematical Sciences
M.Phil. Student, Nankai U. (2024.9-)
Visiting Student, Shenzhen Institute of Advanced Technology, CAS. (2023.10-2024.6)
B.Sc., Nankai U. (2020.9-2024.7)
Read MoreSchool of Mathematical Sciences
M.Phil. Student, Nankai U. (2024.9-)
B.Sc., Chern Class of Nankai Mathematics (2020.9-2024.7)
Read MoreChern Class of Nankai Mathematics
M.Phil. Student, Nankai U. (2024.7-)
B.Sc., Nankai U. (2021.9-2024.7)
Read MoreCollege of Computer Science
B.Eng., Nankai U. (2021.9-)
Visiting Student, School of Engineering, Westlake University (2024.7-)
Next position: M.Phil. Student, School of Mathematical Sciences, Nankai University
Read MoreSchool of Mathematical Sciences
B.Sc., Nankai U. (2023.9-)
Read MoreYichuan Cao, Undergraduate student, 2022.7-2023.7 Next position: PhD in Academy of Mathematics and Systems Science, Chinese Academy of Sciences
Xiamiao Zhao, Undergraduate student, 2022.7-2023.7 Next position: PhD in School of Mathematical Sciences, Tsinghua University
Yunhan Wang, Undergraduate student, 2022.11-2023.7 Next position: MS in School of Statistics, Renmin University of China
Yuxi Li, Undergraduate student, 2022.7-2023.7 Next position: MS in School of Cyber Science and Engineering, Huazhong University of Science and Technology
Wenhao Zhang, Postgraduate student, 2022.7-2023.10 Next position: PhD in School of Aerospace Engineering, Xiamen University
Xiaoyang Chen, Postgraduate student, 2022.2-2024.1 Next position: PhD in Department of Automation, Tsinghua University
Zijing Gao, Postgraduate student, 2023.1-2024.4 Next position: PhD in Department of Automation, Tsinghua University
Xuejian Cui, Postgraduate student, 2022.8-2024.5 Next position: PhD in Department of Automation, Tsinghua University
Qun Jiang, Postgraduate student, 2023.5-2024.5 Next position: MS in Department of Automation, Tsinghua University
Yuhang Jia, Undergraduate student, 2022.4-2024.7 Next position: MS in School of Mathematical Sciences, Nankai University
Siyu Li, Undergraduate student, 2022.4-2024.7 Next position: MS in School of Mathematical Sciences, Nankai University
Wenxin Long, Undergraduate student, 2022.5-2024.7 Next position: PhD in Statistics, Eberly College of Science, Penn State University
Shuchen Zhu, Undergraduate student, 2022.10-2024.7 Next position: PhD in Academy for Advanced Interdisciplinary Studies, Peking University
Yifan Xu, Undergraduate student, 2023.9-2024.7 Next position: MS in Financial Engineering, New York University
Hongyang Pang, Undergraduate student, 2023.12-2024.7 Next position: MS in Department of Statistics and Data Science, Northwestern University
Rufeng Li, Postgraduate student, 2024.3-2024.9 Next position: PhD in School of Basic Medical Sciences, Xi’an Jiaotong University
Yufei Yao, Postgraduate student, 2024.3-2024.10 Next position: PhD in School of Basic Medical Sciences, Xi’an Jiaotong University
Zhen Li, Postgraduate student, 2022.11-2024.11 Next position: PhD in Department of Automation, Tsinghua University
Yan Pan, Postgraduate student, 2023.5-2024.11 Next position: MS in Department of Automation, Tsinghua University
We are now looking for self-motivated graduate/undergraduate students.If you are interested in and want to join BioX at NKU, feel free to contact us.
Dr. Shengquan Chen
shengquan[dot]chenl[at]gmail[dot]com
Room 423, Department of Informatics Theory and Data Science
School of Mathematical Sciences, Nankai University, Tianjin, China