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2020 – today
- 2024
[c13]Jianing Wang, Jin A, Hanjun Pan, Ruiqing Zheng, Chaojin Wu, Min Li:
CellCom: A web server for prediction, visualization, and evaluation of cell-cell communication mediated by ligand-receptor pairs. BCB 2024: 3:1-3:7- [c12]Ju Xiang, Shengkai Chen, Xiangmao Meng, Ruiqing Zheng, Ying Zheng, Min Li:
MSMK: Multiscale Module Kernel for Identifying Disease-Related Genes. ISBRA (1) 2024: 13-24 - [c11]Yongxin He, Jin Liu, Min Li, Ruiqing Zheng:
scCoRR: A Data-Driven Self-correction Framework for Labeled scRNA-Seq Data. ISBRA (2) 2024: 47-58 - [c10]Wei Lan, Weihao Zhou, Qingfeng Chen, Ruiqing Zheng, Yi Pan, Yi-Ping Phoebe Chen
:
Modeling Single-Cell ATAC-Seq Data Based on Contrastive Learning. ISBRA (1) 2024: 473-482 - 2023
- [j22]Siqi Chen, Xuhua Yan, Ruiqing Zheng, Min Li:
Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data. Briefings Bioinform. 24(1) (2023) - [j21]Yanping Zeng, Yongxin He, Ruiqing Zheng, Min Li:
Inferring single-cell gene regulatory network by non-redundant mutual information. Briefings Bioinform. 24(5) (2023) - [j20]Xuhua Yan, Ruiqing Zheng, Fang-Xiang Wu, Min Li:
CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity. Bioinform. 39(3) (2023) - [j19]Xuhua Yan, Ruiqing Zheng, Jinmiao Chen, Min Li:
scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization. Bioinform. 39(8) (2023) - [j18]Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang:
CellBRF: a feature selection method for single-cell clustering using cell balance and random forest. Bioinform. 39(Supplement-1): 368-376 (2023) - [j17]Xiaolin Wang, Hongli Gao, Ren Qi, Ruiqing Zheng, Xin Gao, Bin Yu:
scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means. IEEE ACM Trans. Comput. Biol. Bioinform. 20(3): 2007-2015 (2023) - [c9]Ruiqing Zheng, Yanping Zeng, Weixing Zeng, Min Li:
A flexible gene regulatory network reconstruction method based on autoencoder and graph attention network. BIBM 2023: 215-221 - 2022
- [j16]Wei Lan, Yi Dong, Qingfeng Chen, Ruiqing Zheng, Jin Liu, Yi Pan, Yi-Ping Phoebe Chen:
KGANCDA: predicting circRNA-disease associations based on knowledge graph attention network. Briefings Bioinform. 23(1) (2022) - [j15]Xuhua Yan, Ruiqing Zheng, Min Li:
GLOBE: a contrastive learning-based framework for integrating single-cell transcriptome datasets. Briefings Bioinform. 23(5) (2022) - [j14]Haonan Feng, Ruiqing Zheng, Jianxin Wang, Fang-Xiang Wu, Min Li:
NIMCE: A Gene Regulatory Network Inference Approach Based on Multi Time Delays Causal Entropy. IEEE ACM Trans. Comput. Biol. Bioinform. 19(2): 1042-1049 (2022) - [j13]Xiangmao Meng, Ju Xiang, Ruiqing Zheng, Fang-Xiang Wu, Min Li:
DPCMNE: Detecting Protein Complexes From Protein-Protein Interaction Networks Via Multi-Level Network Embedding. IEEE ACM Trans. Comput. Biol. Bioinform. 19(3): 1592-1602 (2022) - [c8]Siqi Chen, Ruiqing Zheng, Luyi Tian, Fang-Xiang Wu, Min Li:
BayesImpute: a Bayesian imputation method for single-cell RNA-seq data. BIBM 2022: 194-199 - [c7]Ziwei Xu, Ruiqing Zheng, Yuxuan Chen, Edwin Wang, Min Li:
A single cell potency inference method based on the local cell-specific network entropy. BIBM 2022: 247-252 - 2021
- [j12]Senbiao Fang, Ruoqian Zheng, Chuqi Lei, Jianxin Wang, Ruiqing Zheng, Min Li:
Key residues influencing binding affinities of 2019-nCoV with ACE2 in different species. Briefings Bioinform. 22(2): 963-975 (2021) - [j11]Ju Xiang, Jiashuai Zhang, Ruiqing Zheng, Xingyi Li, Min Li:
NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction. Briefings Bioinform. 22(5) (2021) - [j10]Zhenlan Liang, Min Li, Ruiqing Zheng, Yu Tian, Xuhua Yan, Jin Chen, Fang-Xiang Wu, Jianxin Wang:
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement. Genom. Proteom. Bioinform. 19(2): 282-291 (2021) - [j9]Ruiqing Zheng, Min Li, Xiang Chen, Siyu Zhao, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
An Ensemble Method to Reconstruct Gene Regulatory Networks Based on Multivariate Adaptive Regression Splines. IEEE ACM Trans. Comput. Biol. Bioinform. 18(1): 347-354 (2021) - [j8]Min Li, Yake Wang, Ruiqing Zheng, Xinghua Shi, Yaohang Li, Fang-Xiang Wu, Jianxin Wang:
DeepDSC: A Deep Learning Method to Predict Drug Sensitivity of Cancer Cell Lines. IEEE ACM Trans. Comput. Biol. Bioinform. 18(2): 575-582 (2021) - [c6]Yanping Zeng, Xuhua Yan, Zhenlan Liang, Ruiqing Zheng, Min Li:
MKG: a mutual information based method to infer single cell gene regulatory network. BIBM 2021: 223-228 - [c5]Zhenlan Liang, Ruiqing Zheng, Siqi Chen, Xuhua Yan, Min Li:
DeepCI: a deep learning based clustering method for single cell RNA-seq data. BIBM 2021: 302-307 - 2020
- [j7]Xingyi Li, Wenkai Li, Min Zeng, Ruiqing Zheng, Min Li:
Network-based methods for predicting essential genes or proteins: a survey. Briefings Bioinform. 21(2): 566-583 (2020) - [j6]Min Li, Xiangmao Meng, Ruiqing Zheng, Fang-Xiang Wu, Yaohang Li, Yi Pan, Jianxin Wang:
Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network. IEEE ACM Trans. Comput. Biol. Bioinform. 17(3): 817-827 (2020) - [c4]Ruiqing Zheng, Zhenlan Liang, Xiangmao Meng, Yu Tian, Min Li:
A robust single cell clustering method based on subspace learning and partial imputation. BIBM 2020: 140-145
2010 – 2019
- 2019
- [j5]Ruiqing Zheng, Min Li, Xiang Chen, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks. Bioinform. 35(11): 1893-1900 (2019) - [j4]Ruiqing Zheng, Min Li, Zhenlan Liang, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation. Bioinform. 35(19): 3642-3650 (2019) - [j3]Qingfeng Chen, Canshang Deng, Wei Lan, Zhixian Liu, Ruiqing Zheng, Jin Liu, Jianxin Wang:
Identifying Interactions Between Kinases and Substrates Based on Protein-Protein Interaction Network. J. Comput. Biol. 26(8): 836-845 (2019) - [j2]Min Li, Ruiqing Zheng, Yaohang Li, Fang-Xiang Wu, Jianxin Wang:
MGT-SM: A Method for Constructing Cellular Signal Transduction Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 16(2): 417-424 (2019) - 2018
- [c3]Yake Wang, Min Li, Ruiqing Zheng, Xinghua Shi, Yaohang Li, Fang-Xiang Wu, Jianxin Wang:
Using Deep Neural Network to Predict Drug Sensitivity of Cancer Cell Lines. ICIC (2) 2018: 223-226 - [c2]Siyu Zhao, Ruiqing Zheng, Xiang Chen, Yaohang Li, Fang-Xiang Wu, Min Li:
PBMarsNet: A Multivariate Adaptive Regression Splines Based Method to Reconstruct Gene Regulatory Networks. ISBRA 2018: 38-48 - [c1]Canshang Deng, Qingfeng Chen, Zhixian Liu, Ruiqing Zheng, Jin Liu, Jianxin Wang, Wei Lan:
KSIBW: Predicting Kinase-Substrate Interactions Based on Bi-random Walk. ISBRA 2018: 151-162 - 2017
- [j1]Jin Liu, Min Li, Yi Pan, Wei Lan, Ruiqing Zheng, Fang-Xiang Wu, Jianxin Wang:
Complex Brain Network Analysis and Its Applications to Brain Disorders: A Survey. Complex. 2017: 8362741:1-8362741:27 (2017)
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