Complex Brain Network Analysis and Its Applications to Brain Disorders: A Survey. - Jin Liu 012; Min Li 007; Yi Pan 001; Wei Lan; Ruiqing Zheng; Fang-Xiang Wu; Jianxin Wang 001 (Complex., 2017)

Using Deep Neural Network to Predict Drug Sensitivity of Cancer Cell Lines. - Yake Wang; Min Li 007; Ruiqing Zheng; Xinghua Shi; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (ICIC (2), 2018)

KSIBW: Predicting Kinase-Substrate Interactions Based on Bi-random Walk. - Canshang Deng; Qingfeng Chen; Zhixian Liu; Ruiqing Zheng; Jin Liu 012; Jianxin Wang 001; Wei Lan (ISBRA, 2018)

PBMarsNet: A Multivariate Adaptive Regression Splines Based Method to Reconstruct Gene Regulatory Networks. - Siyu Zhao; Ruiqing Zheng; Xiang Chen; Yaohang Li; Fang-Xiang Wu; Min Li 007 (ISBRA, 2018)

BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks. - Ruiqing Zheng; Min Li 007; Xiang Chen; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2019)

SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation. - Ruiqing Zheng; Min Li 007; Zhenlan Liang; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2019)

Identifying Interactions Between Kinases and Substrates Based on Protein-Protein Interaction Network. - Qingfeng Chen; Canshang Deng; Wei Lan; Zhixian Liu; Ruiqing Zheng; Jin Liu 012; Jianxin Wang 001 (J. Comput. Biol., 2019)

MGT-SM: A Method for Constructing Cellular Signal Transduction Networks. - Min Li 007; Ruiqing Zheng; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

A robust single cell clustering method based on subspace learning and partial imputation. - Ruiqing Zheng; Zhenlan Liang; Xiangmao Meng; Yu Tian; Min Li 007 (BIBM, 2020)

Network-based methods for predicting essential genes or proteins: a survey. - Xingyi Li; Wenkai Li; Min Zeng; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2020)

Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network. - Min Li 007; Xiangmao Meng; Ruiqing Zheng; Fang-Xiang Wu; Yaohang Li; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

DeepCI: a deep learning based clustering method for single cell RNA-seq data. - Zhenlan Liang; Ruiqing Zheng; Siqi Chen; Xuhua Yan; Min Li 007 (BIBM, 2021)

MKG: a mutual information based method to infer single cell gene regulatory network. - Yanping Zeng; Xuhua Yan; Zhenlan Liang; Ruiqing Zheng; Min Li 007 (BIBM, 2021)

Key residues influencing binding affinities of 2019-nCoV with ACE2 in different species. - Senbiao Fang; Ruoqian Zheng; Chuqi Lei; Jianxin Wang 001; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2021)

NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction. - Ju Xiang; Jiashuai Zhang; Ruiqing Zheng; Xingyi Li; Min Li 007 (Briefings Bioinform., 2021)

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement. - Zhenlan Liang; Min Li 007; Ruiqing Zheng; Yu Tian; Xuhua Yan; Jin Chen 004; Fang-Xiang Wu; Jianxin Wang 001 (Genom. Proteom. Bioinform., 2021)

DeepDSC: A Deep Learning Method to Predict Drug Sensitivity of Cancer Cell Lines. - Min Li 007; Yake Wang; Ruiqing Zheng; Xinghua Shi; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

An Ensemble Method to Reconstruct Gene Regulatory Networks Based on Multivariate Adaptive Regression Splines. - Ruiqing Zheng; Min Li 007; Xiang Chen; Siyu Zhao; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

BayesImpute: a Bayesian imputation method for single-cell RNA-seq data. - Siqi Chen; Ruiqing Zheng; Luyi Tian; Fang-Xiang Wu; Min Li 007 (BIBM, 2022)

A single cell potency inference method based on the local cell-specific network entropy. - Ziwei Xu; Ruiqing Zheng; Yuxuan Chen; Edwin Wang; Min Li 007 (BIBM, 2022)

KGANCDA: predicting circRNA-disease associations based on knowledge graph attention network. - Wei Lan; Yi Dong; Qingfeng Chen; Ruiqing Zheng; Jin Liu 012; Yi Pan 001; Yi-Ping Phoebe Chen (Briefings Bioinform., 2022)

GLOBE: a contrastive learning-based framework for integrating single-cell transcriptome datasets. - Xuhua Yan; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2022)

NIMCE: A Gene Regulatory Network Inference Approach Based on Multi Time Delays Causal Entropy. - Haonan Feng; Ruiqing Zheng; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

DPCMNE: Detecting Protein Complexes From Protein-Protein Interaction Networks Via Multi-Level Network Embedding. - Xiangmao Meng; Ju Xiang; Ruiqing Zheng; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

A flexible gene regulatory network reconstruction method based on autoencoder and graph attention network. - Ruiqing Zheng; Yanping Zeng; Weixing Zeng; Min Li 007 (BIBM, 2023)

CellBRF: a feature selection method for single-cell clustering using cell balance and random forest. - Yunpei Xu; Hong-Dong Li; Cui-Xiang Lin; Ruiqing Zheng; Yaohang Li; Jinhui Xu 001; Jianxin Wang 001 (Bioinform., 2023)

scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means. - Xiaolin Wang; Hongli Gao; Ren Qi; Ruiqing Zheng; Xin Gao 001; Bin Yu 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data. - Siqi Chen; Xuhua Yan; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2023)

CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity. - Xuhua Yan; Ruiqing Zheng; Fang-Xiang Wu; Min Li 007 (Bioinform., 2023)

scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization. - Xuhua Yan; Ruiqing Zheng; Jinmiao Chen; Min Li 007 (Bioinform., 2023)

Inferring single-cell gene regulatory network by non-redundant mutual information. - Yanping Zeng; Yongxin He; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2023)

CellCom: A web server for prediction, visualization, and evaluation of cell-cell communication mediated by ligand-receptor pairs. - Jianing Wang; Jin A; Hanjun Pan; Ruiqing Zheng; Chaojin Wu; Min Li 007 (BCB, 2024)

DP-BERT: a pre-trained deep language model for depression prediction using microarray data. - Junyu Gao 004; Min Zeng; Yiming Li; Fang Wang; Ruiqing Zheng; Jin Liu; Fei Guo; Min Li (BIBM, 2024)

ComLMEss: Combining multiple protein language models enables accurate essential protein prediction. - Xu Liu; Yiming Li; Fuhao Zhang; Ruiqing Zheng; Fei Guo; Min Li; Min Zeng (BIBM, 2024)

scGDCC: Graph-based Dual Contrastive Calibration for Single Cell MultiOmics Clustering. - Huayu Tao; Xinliang Sun; Yuxuan Chen; Min Li; Ruiqing Zheng (BIBM, 2024)

Aligning Multimodal Biomedical Images and Language via One Large Vision-Language Model. - Haojie Zhang; Min Zeng; Jinfeng Ding; Yixiong Liang; Ruiqing Zheng; Zhe Qu; Min Li 007; Shichao Kan (BIBM, 2024)

An Effective Tool for Differential Interaction Analysis in Single-Cell Hi-C Data. - Yichao Zhao; Ruiqing Zheng; Li Tang; Pengzhen Jia; Min Li 007 (BIBM, 2024)

scCoRR: A Data-Driven Self-correction Framework for Labeled scRNA-Seq Data. - Yongxin He; Jin Liu 012; Min Li 007; Ruiqing Zheng (ISBRA (2), 2024)

Modeling Single-Cell ATAC-Seq Data Based on Contrastive Learning. - Wei Lan; Weihao Zhou; Qingfeng Chen; Ruiqing Zheng; Yi Pan 001; Yi-Ping Phoebe Chen (ISBRA (1), 2024)

MSMK: Multiscale Module Kernel for Identifying Disease-Related Genes. - Ju Xiang; Shengkai Chen; Xiangmao Meng; Ruiqing Zheng; Ying Zheng; Min Li 007 (ISBRA (1), 2024)

scMLC: an accurate and robust multiplex community detection method for single-cell multi-omics data. - Yuxuan Chen; Ruiqing Zheng; Jin Liu 012; Min Li 007 (Briefings Bioinform., 2024)

stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics. - Zhaoyu Fang; Teng Liu; Ruiqing Zheng; Jin A; Mingzhu Yin; Min Li 007 (Briefings Bioinform., 2024)

CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification. - Jin Liu 012; Weixing Zeng; Shichao Kan; Min Li 007; Ruiqing Zheng (Briefings Bioinform., 2024)

scMoMtF: An interpretable multitask learning framework for single-cell multi-omics data analysis. - Wei Lan; Tongsheng Ling; Qingfeng Chen; Ruiqing Zheng; Min Li 007; Yi Pan 001 (PLoS Comput. Biol., 2024)

Contrastive Learning-Based Method for Single-Cell Multi-omics Data Clustering. - Zhenlan Liang; Ruiqing Zheng; Huayu Tao; Yuxuan Chen; Min Li (ISBRA (1), 2025)