Shengquan Chen

Nankai University — China

Biochemistry, Genetics and Molecular Biology · Life Sciences

17h-index1.1kcitations80works5.42yr avg
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Research Topics

Single-cell and spatial transcriptomics(52), Genomics and Chromatin Dynamics(21), Gene expression and cancer classification(17), Epigenetics and DNA Methylation(16), Cancer Genomics and Diagnostics(15)

Publications80 total

A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis
Nature Communications·2026Open Access
A unified framework combining linear and 3D molecular features for robust drug-protein interaction prediction
Cell Reports Methods·2026Open Access
DiTSim: A Diffusion-Transformers Based Single-Cell ATAC-seq Data Simulator
Interdisciplinary Sciences Computational Life Sciences·2025
Rigorous integration of single-cell ATAC-seq data using regularized barycentric mapping
Nature Machine Intelligence·2025· 2 cited
Triple-effect correction for Cell Painting data with contrastive and domain-adversarial learning
Nature Communications·2025· 1 citedOpen Access
MethAgingDB: a comprehensive DNA methylation database for aging biology
Scientific Data·2025· 3 citedOpen Access
MINGLE: a mutual information-based interpretable framework for automatic cell type annotation in single-cell chromatin accessibility data
Genome biology·2025· 1 citedOpen Access
CSFeatures improves identification of cell type-specific differential features in single-cell and spatial omics data
2025Open Access
CREATE: cell-type-specific cis-regulatory element identification via discrete embedding
Nature Communications·2025· 5 citedOpen Access
Facilitating single-cell chromatin accessibility research with a user-friendly database
Frontiers of Computer Science·2025· 2 cited
Imputing not available values in single‐cell DNA methylation data using the median is straightforward and effective
Quantitative Biology·2025Open Access
Graph neural networks for single-cell omics data: a review of approaches and applications
Briefings in Bioinformatics·2025· 22 citedOpen Access
A multistage, multitask transformer-based framework for multi-disease diagnosis and prediction using personal proteomes
2025· 2 citedOpen Access
CASHeart: A database of single cells chromatin accessibility for the human heart
Quantitative Biology·2025· 1 citedOpen Access
Triple-effect correction for Cell Painting data with contrastive and domain-adversarial learning
2025· 1 citedOpen Access
PHierT: A Privacy-Preserving Hierarchical Transformer Model for ICS Network Traffic Classification
Communications in computer and information science·2025· 1 cited
MultiKano: an automatic cell type annotation tool for single-cell multi-omics data based on Kolmogorov–Arnold network and data augmentation
Protein & Cell·2024· 4 citedOpen Access
Unveiling potential threats: backdoor attacks in single-cell pre-trained models
Cell Discovery·2024· 4 citedOpen Access
BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells
Briefings in Bioinformatics·2024· 2 citedOpen Access
Imputing not available values in single-cell DNA methylation data using the median is straightforward and effective
2024Open Access
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Frequent Co-authors

Rui Jiang(30), Xiaoyang Chen(12), Xuegong Zhang(9), Xuejian Cui(9), Zijing Gao(7), Zhen Li(7), Qiao Liu(6), Songming Tang(6), Siyu Li(5), Hairong Lv(4), Sijie Li(4), Yuhang Jia(4), Baosong Li(4), Ziwei Yuan(4), Wanwen Zeng(3), Wing Hung Wong(3), Xiaoyang Chen(3), Qun Jiang(3), Xiaowo Wang(3), Chen Li(3)