Ruiqing Zheng

发表

Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification

Fang-Xiang Wu, Jianxin Wang, Min Li, 2020, Frontiers in Genetics.

Prioritizing Disease Genes by Using Search Engine Algorithm

Fang-Xiang Wu, Jianxin Wang, Min Li, 2016 .

D3GRN: a data driven dynamic network construction method to infer gene regulatory networks

Fang-Xiang Wu, Jianxin Wang, Min Li, 2019, BMC Genomics.

Ecological Compensation Standard of a Water-Receiving Area in an Inter-Basin Water Diversion Based on Ecosystem Service Value and Public Willingness: A Case Study of Beijing

Ruiqing Zheng, M. Ding, Zhu Peng, 2021, Sustainability.

Integrate multiscale module kernel for disease-gene discovery in biological networks

Ruiqing Zheng, Ju Xiang, Xiangmao Meng, 2022, bioRxiv.

A deep matrix factorization based approach for single-cell RNA-seq data clustering.

Ruiqing Zheng, Min Li, Xuhua Yan, 2022, Methods.

DPCMNE: Detecting Protein Complexes From Protein-Protein Interaction Networks Via Multi-Level Network Embedding

Fangxiang Wu, Ruiqing Zheng, Ju Xiang, 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

GLOBE: a contrastive learning-based framework for integrating single-cell transcriptome datasets

Ruiqing Zheng, Min Li, Xuhua Yan, 2022, Briefings Bioinform..

DeepDSC: A Deep Learning Method to Predict Drug Sensitivity of Cancer Cell Lines

Min Li, Xinghua Shi, Jianxin Wang, 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Using Deep Neural Network to Predict Drug Sensitivity of Cancer Cell Lines

Yaohang Li, Fang-Xiang Wu, Min Li, 2018, ICIC.

SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation

Yi Pan, Fang-Xiang Wu, Jianxin Wang, 2019, Bioinform..

BayesImpute: a Bayesian imputation method for single-cell RNA-seq data

Fangxiang Wu, Ruiqing Zheng, Siqi Chen, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

A data-driven clustering recommendation method for single-cell RNA-sequencing data

Fang-Xiang Wu, Ruiqing Zheng, Zhenlan Liang, 2021 .

A robust single cell clustering method based on subspace learning and partial imputation

Yu Tian, Xiangmao Meng, Min Li, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement

Yu Tian, Fang-Xiang Wu, Min Li, 2020, bioRxiv.

scGMAI: a Gaussian mixture model for clustering single-cell RNA-Seq data based on deep autoencoder.

Xiaolin Wang, Bin Yu, Chen Chen, 2020, Briefings in bioinformatics.

An Adaptive Sparse Subspace Clustering for Cell Type Identification

Xiang Chen, Min Li, Chen Cao, 2020, Frontiers in Genetics.

PBMarsNet: A Multivariate Adaptive Regression Splines Based Method to Reconstruct Gene Regulatory Networks

Xiang Chen, Yaohang Li, Fang-Xiang Wu, 2018, ISBRA.

A novel method of gene regulatory network structure inference from gene knock-out expression data

Yaohang Li, Min Li, Fang-Xiang Wu, 2019, Tsinghua Science and Technology.

Key residues influencing binding affinities of 2019-nCoV with ACE2 in different species

Jianxin Wang, Min Li, Ruiqing Zheng, 2020, Briefings Bioinform..

Identifying Interactions Between Kinases and Substrates Based on Protein-Protein Interaction Network

Jin Liu, Jianxin Wang, Wei Lan, 2019, J. Comput. Biol..

KSIBW: Predicting Kinase-Substrate Interactions Based on Bi-random Walk

Jin Liu, Wei Lan, Qingfeng Chen, 2018, ISBRA.

A single cell potency inference method based on the local cell-specific network entropy

E. Wang, Ruiqing Zheng, Min Li, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

MGT-SM: A Method for Constructing Cellular Signal Transduction Networks

Yaohang Li, Fang-Xiang Wu, Jianxin Wang, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction

Ruiqing Zheng, Jiashuai Zhang, Ju Xiang, 2021, Briefings Bioinform..

Complex Brain Network Analysis and Its Applications to Brain Disorders: A Survey

Yi Pan, Jianxin Wang, Fang-Xiang Wu, 2017, Complex..

Network-based methods for predicting essential genes or proteins: a survey

Wenkai Li, Xingyi Li, Min Li, 2019, Briefings Bioinform..

An Ensemble Method to Reconstruct Gene Regulatory Networks Based on Multivariate Adaptive Regression Splines

Yi Pan, Xiang Chen, Min Li, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Effective identification of essential proteins based on priori knowledge, network topology and gene expressions.

Jianxin Wang, Min Li, Yi Pan, 2014, Methods.

Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network

Yi Pan, Yaohang Li, Min Li, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

KGANCDA: predicting circRNA-disease associations based on knowledge graph attention network

Y. Chen, Wei Lan, Qingfeng Chen, 2021, Briefings Bioinform..

scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means

Ruiqing Zheng, Xiaolin Wang, Bin Yu, 2022, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

A posterior probability based Bayesian method for single-cell RNA-seq data imputation.

Fang-Xiang Wu, Ruiqing Zheng, Siqi Chen, 2023, Methods.

DeepCI: a deep learning based clustering method for single cell RNA-seq data

Min Li, Zhenlan Liang, Ruiqing Zheng, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data

Ruiqing Zheng, Siqi Chen, Xuhua Yan, 2022, Briefings Bioinform..

CellBRF: a feature selection method for single-cell clustering using cell balance and random forest

Hongdong Li, Yaohang Li, Ruiqing Zheng, 2023, Bioinform..

BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks

Yi Pan, Xiang Chen, Fang-Xiang Wu, 2018, Bioinform..

scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization

Jinmiao Chen, Ruiqing Zheng, Xuhua Yan, 2023, Bioinformatics.

CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity

Fangxiang Wu, Ruiqing Zheng, Xuhua Yan, 2023, Bioinformatics.

NIMCE: A Gene Regulatory Network Inference Approach Based on Multi Time Delays Causal Entropy

Jianxin Wang, Min Li, Fangxiang Wu, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

JLONMFSC: Clustering scRNA-seq data based on joint learning of non-negative matrix factorization and subspace clustering.

Ruiqing Zheng, Jianwei Chen, Jin Ye, 2023, Methods.

scMAE: a masked autoencoder for single-cell RNA-seq clustering

Ruiqing Zheng, Zhao-Yu Fang, Min Li, 2024, Bioinformatics.

CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification

Ruiqing Zheng, Min Li, Jin Liu, 2023, Briefings in bioinformatics.

stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics

Ruiqing Zheng, Teng Liu, Zhao-Yu Fang, 2023, Briefings in bioinformatics.

SPIDE: A single cell potency inference method based on the local cell-specific network entropy.

Ruiqing Zheng, Ziwei Xu, Min Li, 2023, Methods.

A flexible gene regulatory network reconstruction method based on autoencoder and graph attention network

Ruiqing Zheng, Min Li, Weixing Zeng, 2023, 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).