Ruiqing Zheng

58 papers A* 1Journal 35Unranked 22
YearRankTypeTitle / Venue / Authors
2025 J jnl
A Flexible Data-Driven Framework for Correcting Coarsely Annotated scRNA-seq Data.
Big Data Min. Anal.
Ruiqing Zheng, Yongxin He, Jiawen Huang, Shichao Kan, Hui Wang, Edwin Wang, Min Li
2025 J jnl
ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration.
Genom. Proteom. Bioinform.
Xuhua Yan, Jinmiao Chen, Ruiqing Zheng, Min Li
2025 — conf
Contrastive Learning-Based Method for Single-Cell Multi-omics Data Clustering.
ISBRA (1)
Zhenlan Liang, Ruiqing Zheng, Huayu Tao, Yuxuan Chen, Min Li
2025 J jnl
DISHIC: An Effective Method for Identifying Differential Interaction in Single-Cell Hi-C.
IEEE Trans. Comput. Biol. Bioinform.
Yichao Zhao, Ruiqing Zheng, Li Tang, Pengzhen Jia, Min Li
2025 — conf
DP-GPT: GPT-Driven Gene Text Feature Embedding Fused with Gene Expression Data for Depression Prediction.
BIBM
Min Zeng, Junyu Gao, Qianpei Liu, Yiming Li, Fuhao Zhang, Ruiqing Zheng, Min Li
2025 — conf
DeepDICI: Accurately Predicting Drug-Ion Channel Interactions via Deep Learning with Dynamic Structural Features.
BIBM
Rui Tang, Zhangli Lu, Zhicun Zeng, Ruiqing Zheng, Min Zeng, Min Li
2025 A* conf
Dynamic Residual Encoding with Slide-Level Contrastive Learning for End-to-End Whole Slide Image Representation.
ACM Multimedia
Jing Jin, Xu Liu, Te Gao, Zhihong Shi, Yixiong Liang, Ruiqing Zheng, Hulin Kuang, Min Zeng, Shichao Kan
2025 J jnl
Dynamic Residual Encoding with Slide-Level Contrastive Learning for End-to-End Whole Slide Image Representation.
CoRR
Jing Jin, Xu Liu, Te Gao, Zhihong Shi, Yixiong Liang, Ruiqing Zheng, Hulin Kuang, Min Zeng, Shichao Kan
2025 — conf
GateFuseNet: An Adaptive 3D Multimodal Neuroimaging Fusion Network for Parkinson's Disease Diagnosis.
BIBM
Rui Jin, Chen Chen, Yin Liu, Peng Wu, Hongfu Sun, Ruiqing Zheng, Min Zeng, Min Li, Yang Gao
2025 J jnl
Leveraging protein language models for cross-variant CRISPR/Cas9 sgRNA activity prediction.
Bioinform.
Yalin Hou, Yiming Li, Ruiqing Zheng, Fuhao Zhang, Fei Guo, Min Li, Min Zeng
2025 J jnl
SpaNN: Spatial Transcriptomic Data Enhancement Using Deep Neural Network.
IEEE Trans. Comput. Biol. Bioinform.
Siqi Chen, Wenkang Wang, Ruiqing Zheng, Min Li
2025 J jnl
scHLens: a web server for hierarchically and interactively exploring single cell RNA-seq data.
Briefings Bioinform.
Jiazhi Xia, Zhiwei Deng, Chen He, Min Li, Ruiqing Zheng
2024 — conf
Aligning Multimodal Biomedical Images and Language via One Large Vision-Language Model.
BIBM
Haojie Zhang, Min Zeng, Jinfeng Ding, Yixiong Liang, Ruiqing Zheng, Zhe Qu, Min Li, Shichao Kan
2024 — conf
An Effective Tool for Differential Interaction Analysis in Single-Cell Hi-C Data.
BIBM
Yichao Zhao, Ruiqing Zheng, Li Tang, Pengzhen Jia, Min Li
2024 J jnl
CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification.
Briefings Bioinform.
Jin Liu, Weixing Zeng, Shichao Kan, Min Li, Ruiqing Zheng
2024 — conf
CellCom: A web server for prediction, visualization, and evaluation of cell-cell communication mediated by ligand-receptor pairs.
BCB
Jianing Wang, Jin A, Hanjun Pan, Ruiqing Zheng, Chaojin Wu, Min Li
2024 — conf
ComLMEss: Combining multiple protein language models enables accurate essential protein prediction.
BIBM
Xu Liu, Yiming Li, Fuhao Zhang, Ruiqing Zheng, Fei Guo, Min Li, Min Zeng
2024 — conf
DP-BERT: a pre-trained deep language model for depression prediction using microarray data.
BIBM
Junyu Gao, Min Zeng, Yiming Li, Fang Wang, Ruiqing Zheng, Jin Liu, Fei Guo, Min Li
2024 — conf
MSMK: Multiscale Module Kernel for Identifying Disease-Related Genes.
ISBRA (1)
Ju Xiang, Shengkai Chen, Xiangmao Meng, Ruiqing Zheng, Ying Zheng, Min Li
2024 — conf
Modeling Single-Cell ATAC-Seq Data Based on Contrastive Learning.
ISBRA (1)
Wei Lan, Weihao Zhou, Qingfeng Chen, Ruiqing Zheng, Yi Pan, Yi-Ping Phoebe Chen
2024 — conf
scCoRR: A Data-Driven Self-correction Framework for Labeled scRNA-Seq Data.
ISBRA (2)
Yongxin He, Jin Liu, Min Li, Ruiqing Zheng
2024 — conf
scGDCC: Graph-based Dual Contrastive Calibration for Single Cell MultiOmics Clustering.
BIBM
Huayu Tao, Xinliang Sun, Yuxuan Chen, Min Li, Ruiqing Zheng
2024 J jnl
scMAE: a masked autoencoder for single-cell RNA-seq clustering.
Bioinform.
Zhaoyu Fang, Ruiqing Zheng, Min Li
2024 J jnl
scMLC: an accurate and robust multiplex community detection method for single-cell multi-omics data.
Briefings Bioinform.
Yuxuan Chen, Ruiqing Zheng, Jin Liu, Min Li
2024 J jnl
scMoMtF: An interpretable multitask learning framework for single-cell multi-omics data analysis.
PLoS Comput. Biol.
Wei Lan, Tongsheng Ling, Qingfeng Chen, Ruiqing Zheng, Min Li, Yi Pan
2024 J jnl
stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics.
Briefings Bioinform.
Zhaoyu Fang, Teng Liu, Ruiqing Zheng, Jin A, Mingzhu Yin, Min Li
2023 — conf
A flexible gene regulatory network reconstruction method based on autoencoder and graph attention network.
BIBM
Ruiqing Zheng, Yanping Zeng, Weixing Zeng, Min Li
2023 J jnl
Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data.
Briefings Bioinform.
Siqi Chen, Xuhua Yan, Ruiqing Zheng, Min Li
2023 J jnl
CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity.
Bioinform.
Xuhua Yan, Ruiqing Zheng, Fang-Xiang Wu, Min Li
2023 J jnl
CellBRF: a feature selection method for single-cell clustering using cell balance and random forest.
Bioinform.
Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang
2023 J jnl
Inferring single-cell gene regulatory network by non-redundant mutual information.
Briefings Bioinform.
Yanping Zeng, Yongxin He, Ruiqing Zheng, Min Li
2023 J jnl
scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xiaolin Wang, Hongli Gao, Ren Qi, Ruiqing Zheng, Xin Gao, Bin Yu
2023 J jnl
scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization.
Bioinform.
Xuhua Yan, Ruiqing Zheng, Jinmiao Chen, Min Li
2022 — conf
A single cell potency inference method based on the local cell-specific network entropy.
BIBM
Ziwei Xu, Ruiqing Zheng, Yuxuan Chen, Edwin Wang, Min Li
2022 — conf
BayesImpute: a Bayesian imputation method for single-cell RNA-seq data.
BIBM
Siqi Chen, Ruiqing Zheng, Luyi Tian, Fang-Xiang Wu, Min Li
2022 J jnl
DPCMNE: Detecting Protein Complexes From Protein-Protein Interaction Networks Via Multi-Level Network Embedding.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xiangmao Meng, Ju Xiang, Ruiqing Zheng, Fang-Xiang Wu, Min Li
2022 J jnl
GLOBE: a contrastive learning-based framework for integrating single-cell transcriptome datasets.
Briefings Bioinform.
Xuhua Yan, Ruiqing Zheng, Min Li
2022 J jnl
KGANCDA: predicting circRNA-disease associations based on knowledge graph attention network.
Briefings Bioinform.
Wei Lan, Yi Dong, Qingfeng Chen, Ruiqing Zheng, Jin Liu, Yi Pan, Yi-Ping Phoebe Chen
2022 J jnl
NIMCE: A Gene Regulatory Network Inference Approach Based on Multi Time Delays Causal Entropy.
IEEE ACM Trans. Comput. Biol. Bioinform.
Haonan Feng, Ruiqing Zheng, Jianxin Wang, Fang-Xiang Wu, Min Li
2021 J jnl
An Ensemble Method to Reconstruct Gene Regulatory Networks Based on Multivariate Adaptive Regression Splines.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ruiqing Zheng, Min Li, Xiang Chen, Siyu Zhao, Fang-Xiang Wu, Yi Pan, Jianxin Wang
2021 — conf
DeepCI: a deep learning based clustering method for single cell RNA-seq data.
BIBM
Zhenlan Liang, Ruiqing Zheng, Siqi Chen, Xuhua Yan, Min Li
2021 J jnl
DeepDSC: A Deep Learning Method to Predict Drug Sensitivity of Cancer Cell Lines.
IEEE ACM Trans. Comput. Biol. Bioinform.
Min Li, Yake Wang, Ruiqing Zheng, Xinghua Shi, Yaohang Li, Fang-Xiang Wu, Jianxin Wang
2021 J jnl
Key residues influencing binding affinities of 2019-nCoV with ACE2 in different species.
Briefings Bioinform.
Senbiao Fang, Ruoqian Zheng, Chuqi Lei, Jianxin Wang, Ruiqing Zheng, Min Li
2021 — conf
MKG: a mutual information based method to infer single cell gene regulatory network.
BIBM
Yanping Zeng, Xuhua Yan, Zhenlan Liang, Ruiqing Zheng, Min Li
2021 J jnl
NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction.
Briefings Bioinform.
Ju Xiang, Jiashuai Zhang, Ruiqing Zheng, Xingyi Li, Min Li
2021 J jnl
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement.
Genom. Proteom. Bioinform.
Zhenlan Liang, Min Li, Ruiqing Zheng, Yu Tian, Xuhua Yan, Jin Chen, Fang-Xiang Wu, Jianxin Wang
2021 J jnl
scGMAI: a Gaussian mixture model for clustering single-cell RNA-Seq data based on deep autoencoder.
Briefings Bioinform.
Bin Yu, Cheng Chen, Ren Qi, Ruiqing Zheng, Patrick J. Skillman-Lawrence, Xiaolin Wang, Anjun Ma, Haiming Gu
2020 — conf
A robust single cell clustering method based on subspace learning and partial imputation.
BIBM
Ruiqing Zheng, Zhenlan Liang, Xiangmao Meng, Yu Tian, Min Li
2020 J jnl
Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network.
IEEE ACM Trans. Comput. Biol. Bioinform.
Min Li, Xiangmao Meng, Ruiqing Zheng, Fang-Xiang Wu, Yaohang Li, Yi Pan, Jianxin Wang
2020 J jnl
Network-based methods for predicting essential genes or proteins: a survey.
Briefings Bioinform.
Xingyi Li, Wenkai Li, Min Zeng, Ruiqing Zheng, Min Li
2019 J jnl
BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks.
Bioinform.
Ruiqing Zheng, Min Li, Xiang Chen, Fang-Xiang Wu, Yi Pan, Jianxin Wang
2019 J jnl
Identifying Interactions Between Kinases and Substrates Based on Protein-Protein Interaction Network.
J. Comput. Biol.
Qingfeng Chen, Canshang Deng, Wei Lan, Zhixian Liu, Ruiqing Zheng, Jin Liu, Jianxin Wang
2019 J jnl
MGT-SM: A Method for Constructing Cellular Signal Transduction Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Min Li, Ruiqing Zheng, Yaohang Li, Fang-Xiang Wu, Jianxin Wang
2019 J jnl
SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation.
Bioinform.
Ruiqing Zheng, Min Li, Zhenlan Liang, Fang-Xiang Wu, Yi Pan, Jianxin Wang
2018 — conf
KSIBW: Predicting Kinase-Substrate Interactions Based on Bi-random Walk.
ISBRA
Canshang Deng, Qingfeng Chen, Zhixian Liu, Ruiqing Zheng, Jin Liu, Jianxin Wang, Wei Lan
2018 — conf
PBMarsNet: A Multivariate Adaptive Regression Splines Based Method to Reconstruct Gene Regulatory Networks.
ISBRA
Siyu Zhao, Ruiqing Zheng, Xiang Chen, Yaohang Li, Fang-Xiang Wu, Min Li
2018 — conf
Using Deep Neural Network to Predict Drug Sensitivity of Cancer Cell Lines.
ICIC (2)
Yake Wang, Min Li, Ruiqing Zheng, Xinghua Shi, Yaohang Li, Fang-Xiang Wu, Jianxin Wang
2017 J jnl
Complex Brain Network Analysis and Its Applications to Brain Disorders: A Survey.
Complex.
Jin Liu, Min Li, Yi Pan, Wei Lan, Ruiqing Zheng, Fang-Xiang Wu, Jianxin Wang