Protein function prediction based on physiochemical properties and protein granularity. - Wanlu Wang; Xin Zhang; Jun Meng; Yushi Luan (GrC, 2013)

Gene selection using rough set based on neighborhood for the analysis of plant stress response. - Jun Meng; Jing Zhang; Rui Li 006; Yushi Luan (Appl. Soft Comput., 2014)

Prediction of plant pre-microRNAs and their microRNAs in genome-scale sequences using structure-sequence features and support vector machine. - Jun Meng; Dong Liu; Chao Sun; Yushi Luan (BMC Bioinform., 2014)

Inferring plant microRNA functional similarity using a weighted protein-protein interaction network. - Jun Meng; Dong Liu; Yushi Luan (BMC Bioinform., 2015)

Gene Selection Integrated with Biological Knowledge for Plant Stress Response Using Neighborhood System and Rough Set Theory. - Jun Meng; Jing Zhang; Yushi Luan (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Plant miRNA function prediction based on functional similarity network and transductive multi-label classification algorithm. - Jun Meng; Guan-Li Shi; Yushi Luan (Neurocomputing, 2016)

Classifier ensemble selection based on affinity propagation clustering. - Jun Meng; Han Hao; Yushi Luan (J. Biomed. Informatics, 2016)

Genome-Wide Analysis of Response Regulator Genes in Solanum lycopersicum. - Jun Cui 004; Ning Jiang; Jun Meng; Yushi Luan (ISBRA, 2017)

Parallel gene selection and dynamic ensemble pruning based on Affinity Propagation. - Jun Meng; Jing Zhang; Yushi Luan; Xinyu He 001; Li-Shuang Li; Yuan-Feng Zhu (Comput. Biol. Medicine, 2017)

Prediction of LncRNA by Using Muitiple Feature Information Fusion and Feature Selection Technique. - Jun Meng; Dingling Jiang; Zheng Chang; Yushi Luan (ICIC (2), 2018)

Ensemble classification for gene expression data based on parallel clustering. - Jun Meng; Dingling Jiang; Jing Zhang; Yushi Luan (Int. J. Data Min. Bioinform., 2018)

lncRNA-LSTM: Prediction of Plant Long Non-coding RNAs Using Long Short-Term Memory Based on p-nts Encoding. - Jun Meng; Zheng Chang; Peng Zhang; Wenhao Shi; Yushi Luan (ICIC (3), 2019)

Prediction of Plant lncRNA-Protein Interactions Using Sequence Information Based on Deep Learning. - Haoran Zhou; Yushi Luan; Jael Sanyanda Wekesa; Jun Meng (ICIC (3), 2019)

LPI-DL: A recurrent deep learning model for plant lncRNA-protein interaction and function prediction with feature optimization. - Jael Sanyanda Wekesa; Yushi Luan; Jun Meng (BIBM, 2020)

PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA-lncRNA interaction prediction. - Qiang Kang; Jun Meng; Jun Cui 004; Yushi Luan; Ming Chen 005 (Bioinform., 2020)

Optimized combination methods for exploring and verifying disease-resistant transcription factors in melon. - Zhicheng Wang; Yushi Luan; Xiaoxu Zhou; Jun Cui 004; Feishi Luan; Jun Meng (Briefings Bioinform., 2021)

PlncRNA-HDeep: plant long noncoding RNA prediction using hybrid deep learning based on two encoding styles. - Jun Meng; Qiang Kang; Zheng Chang; Yushi Luan (BMC Bioinform., 2021)

PRPI-SC: an ensemble deep learning model for predicting plant lncRNA-protein interactions. - Haoran Zhou; Jael Sanyanda Wekesa; Yushi Luan; Jun Meng (BMC Bioinform., 2021)

Predicting Protein Functions Based on Differential Co-expression and Neighborhood Analysis. - Jael Sanyanda Wekesa; Yushi Luan; Jun Meng (J. Comput. Biol., 2021)

Predicting the interactions between plant lncRNA-encoded peptide and protein using domain knowledge-based prototypical network. - Siyuan Zhao; Jun Meng; Yushi Luan (BIBM, 2022)

RNAI-FRID: novel feature representation method with information enhancement and dimension reduction for RNA-RNA interaction. - Qiang Kang; Jun Meng; Yushi Luan (Briefings Bioinform., 2022)

Mining plant endogenous target mimics from miRNA-lncRNA interactions based on dual-path parallel ensemble pruning method. - Qiang Kang; Jun Meng; Chenglin Su; Yushi Luan (Briefings Bioinform., 2022)

Identifying LncRNA-Encoded Short Peptides Using Optimized Hybrid Features and Ensemble Learning. - Siyuan Zhao; Jun Meng; Qiang Kang; Yushi Luan (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

TGAAL: Combining Transformer-based GAN and active learning to identify the coding potential of sORFs in plant lncRNAs. - Yu Wang; Jun Meng; Shihao Xia; Haibin Li; Zhaowei Wang 005; Yushi Luan (BIBM, 2023)

A multi-granularity information-enhanced pre-training method for predicting the coding potential of sORFs in plant lncRNAs. - Shihao Xia; Jun Meng; Zhaowei Wang 005; Yu Wang; Haibin Li; Zhaojing Qin; Yushi Luan (BIBM, 2023)

Identification of small open reading frames in plant lncRNA using class-imbalance learning. - Siyuan Zhao; Jun Meng; Jael Sanyanda Wekesa; Yushi Luan (Comput. Biol. Medicine, 2023)

PAMPred: A hierarchical evolutionary ensemble framework for identifying plant antimicrobial peptides. - Zhaowei Wang 005; Jun Meng; Haibin Li; Shihao Xia; Yu Wang; Yushi Luan (Comput. Biol. Medicine, 2023)

A Prompt and Contrastive Learning-Based Model for Plant Antimicrobial Peptide Prediction. - Zhaojing Qin; Jun Meng; Haibin Li; Youwei Tang; Yushi Luan (ICAI (1), 2024)

DeepPepPI: A deep cross-dependent framework with information sharing mechanism for predicting plant peptide-protein interactions. - Zhaowei Wang 005; Jun Meng; Qiguo Dai; Haibin Li; Shihao Xia; Ruirui Yang; Yushi Luan (Expert Syst. Appl., 2024)

miPEPPred-FRL: A Novel Method for Predicting Plant MiRNA-Encoded Peptides Using Adaptive Feature Representation Learning. - Haibin Li; Jun Meng; Zhaowei Wang 005; Youwei Tang; Shihao Xia; Yu Wang; Zhaojing Qin; Yushi Luan (J. Chem. Inf. Model., 2024)

Attention-augmented multi-domain cooperative graph representation learning for molecular interaction prediction. - Zhaowei Wang 005; Jun Meng; Haibin Li; Qiguo Dai; Xiaohui Lin 002; Yushi Luan (Neural Networks, 2025)