Shengquan Chen

27 papers B 1Journal 26
YearRankTypeTitle / Venue / Authors
2025 J jnl
BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells.
Briefings Bioinform.
Lan Cao, Wenhao Zhang, Fan Yang, Shengquan Chen, Xiaobing Huang, Feng Zeng, Ying Wang
2025 J jnl
CASHeart: A database of single cells chromatin accessibility for the human heart.
Quant. Biol.
Qun jiang, Xiaoyang Chen, Zijing Gao, Jinmeng Jia, Shengquan Chen, Rui Jiang
2025 J jnl
Facilitating single-cell chromatin accessibility research with a user-friendly database.
Frontiers Comput. Sci.
Heyang Hua, Sijie Li, Haitian Liang, Shengquan Chen
2025 J jnl
Graph neural networks for single-cell omics data: a review of approaches and applications.
Briefings Bioinform.
Sijie Li, Heyang Hua, Shengquan Chen
2025 J jnl
Imputing not available values in single-cell DNA methylation data using the median is straightforward and effective.
Quant. Biol.
Songming Tang, Siyu Li, Shengquan Chen
2024 J jnl
Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yuhang Jia, Siyu Li, Rui Jiang, Shengquan Chen
2024 J jnl
Accurate cell type annotation for single-cell chromatin accessibility data via contrastive learning and reference guidance.
Quant. Biol.
Siyu Li, Songming Tang, Yunchang Wang, Sijie Li, Yuhang Jia, Shengquan Chen
2024 J jnl
Cofea: correlation-based feature selection for single-cell chromatin accessibility data.
Briefings Bioinform.
Keyi Li, Xiaoyang Chen, Shuang Song, Lin Hou, Shengquan Chen, Rui Jiang
2024 J jnl
Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity.
Nat. Comput. Sci.
Xuejian Cui, Xiaoyang Chen, Zhen Li, Zijing Gao, Shengquan Chen, Rui Jiang
2024 J jnl
EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data.
Bioinform.
Sijie Li, Yuxi Li, Yu Sun, Yaru Li, Xiaoyang Chen, Songming Tang, Shengquan Chen
2024 J jnl
Lockpicking LLMs: A Logit-Based Jailbreak Using Token-level Manipulation.
CoRR
Yuxi Li, Yi Liu, Yuekang Li, Ling Shi, Gelei Deng, Shengquan Chen, Kailong Wang
2024 J jnl
SCREEN: predicting single-cell gene expression perturbation responses via optimal transport.
Frontiers Comput. Sci.
Haixin Wang, Yunhan Wang, Qun jiang, Yan Zhang, Shengquan Chen
2024 J jnl
scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism.
Bioinform.
Qun jiang, Shengquan Chen, Xiaoyang Chen, Rui Jiang
2023 J jnl
ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data.
Bioinform.
Shengquan Chen, Rongxiang Wang, Wenxin Long, Rui Jiang
2023 J jnl
RefTM: reference-guided topic modeling of single-cell chromatin accessibility data.
Briefings Bioinform.
Zheng Zhang, Shengquan Chen, Zhixiang Lin
2023 J jnl
simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data.
Bioinform.
Chen Li, Xiaoyang Chen, Shengquan Chen, Rui Jiang, Xuegong Zhang
2022 J jnl
Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding.
Nat. Mach. Intell.
Xiaoyang Chen, Shengquan Chen, Shuang Song, Zijing Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang
2021 J jnl
DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers.
Genom. Proteom. Bioinform.
Shengquan Chen, Mingxin Gan, Hairong Lv, Rui Jiang
2021 J jnl
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions.
Nucleic Acids Res.
Shengquan Chen, Qiao Liu, Xuejian Cui, Zhan-Ying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang
2021 J jnl
SilencerDB: a comprehensive database of silencers.
Nucleic Acids Res.
Wanwen Zeng, Shengquan Chen, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Rui Jiang
2021 J jnl
Simultaneous deep generative modelling and clustering of single-cell genomic data.
Nat. Mach. Intell.
Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong
2021 J jnl
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics.
Bioinform.
Shengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang
2020 J jnl
EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes.
BMC Bioinform.
Xiaoyang Chen, Shengquan Chen, Rui Jiang
2020 B conf
Research and Improvement of Community Discovery Algorithm Based on Spark for Large Scale Complicated Networks.
TrustCom
Hui Kang, Shengquan Chen, Lingfeng Lu, Chenkun Meng
2019 J jnl
EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information.
Quant. Biol.
Shaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang
2019 J jnl
VPAC: Variational projection for accurate clustering of single-cell transcriptomic data.
BMC Bioinform.
Shengquan Chen, Kui Hua, Hongfei Cui, Rui Jiang
2017 J jnl
Predicting enhancers with deep convolutional neural networks.
BMC Bioinform.
Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang