BioX Future Interdisciplinary Technology Mathematics Information Life Sciences

Welcome to Chen's Lab at Nankai University.
X for Future, Interdisciplinary, and Technology.

Research

We focus on the interrogation of cell heterogeneity and biological implication in single-cell omics data via mathematical methods and information technologies.

#

Missing-data imputation

Impute missing data modalities and enhance highly noisy single-cell data via transfer learning.

Cell heterogeneity characterization

Characterize cell heterogeneity in single-cell data via reference-based unsupervised learning.

Cell type annotation

Annotate cell types in single-cell data automatically via ensemble-based supervised learning.

Cell type-specific pattern elucidation

Elucidate cell type-specific patterns in single-cell data via interpretable machine learning.

News


Publications

  • All
  • Preprints
  • 2024
  • 2023
  • 2022
  • 2017-2021

† 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]

Members

#

Principal Investigator

Shengquan Chen

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 More
#

Ph.D. Student

Heyang Hua

Chern Class of Nankai Mathematics

Ph.D. Student, Nankai U. (2025.9-)

B.Sc., Nankai U. (2021.9-2025.7)

Read More
#

Ph.D. Student

Lingyi Hu

School 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 More
#

Joint Ph.D. Student with Xiamen Univ.

Lan Cao

School 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 More
#

M.Phil. Student

Sijie Li

School of Mathematical Sciences

M.Phil. Student, Nankai U. (2022.9-)

B.Sc., Nankai U. (2018.9-2022.7)

Read More
#

M.Phil. Student

Songming Tang

School of Mathematical Sciences

M.Phil. Student, Nankai U. (2023.9-)

B.Sc., SCUT. (2019.9-2023.7)

Read More
#

M.Phil. Student

Yu Zhang

School of Mathematical Sciences

M.Phil. Student, Nankai U. (2023.9-)

B.Sc., NWAFU. (2019.9-2023.7)

Read More
#

M.Phil. Student

Siyu Li

School 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 More
#

M.Phil. Student

Yuhang Jia

School 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 More
#

M.Phil. Student

Yongkang Li

School of Mathematical Sciences

M.Phil. Student, Nankai U. (2024.9-)

B.Sc., Chern Class of Nankai Mathematics (2020.9-2024.7)

Read More
#

M.Phil. Student

Huangpei Qing

Chern Class of Nankai Mathematics

M.Phil. Student, Nankai U. (2024.7-)

B.Sc., Nankai U. (2021.9-2024.7)

Read More
#

B.Eng. Student

Sicheng Feng

College 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 More
#

B.Sc. Student

Shihan Xiang

School of Mathematical Sciences

B.Sc., Nankai U. (2021.9-)

Read More
#

Chern Class of Nankai Mathematics

Haitian Liang

School of Mathematical Sciences

B.Sc., Nankai U. (2023.9-)

Read More
#

B.Sc. Student

Yiming Lin

School of Mathematical Sciences

B.Sc., Nankai U. (2023.9-)

Read More
#

Encourager

Kaikai

School of Happiness

B.Sc., Home U. (2022.9-)

Read More

Alumni

Yichuan 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

Join us now

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.

Contact information

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