Application of learning to rank to protein remote homology detection. - Bin Liu 014; Junjie Chen 004; Xiaolong Wang 001 (Bioinform., 2015)

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences. - Bin Liu 014; Fule Liu; Xiaolong Wang 001; Junjie Chen 004; Longyun Fang; Kuo-Chen Chou (Nucleic Acids Res., 2015)

SOFM-Top: Protein Remote Homology Detection and Fold Recognition Based on Sequence-Order Frequency Matrix. - Junjie Chen 004; Mingyue Guo; Xiaolong Wang 001; Bin Liu 014 (ICIC (2), 2017)

ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank. - Junjie Chen 004; Mingyue Guo; Shumin Li; Bin Liu 014 (Bioinform., 2017)

Protein remote homology detection based on bidirectional long short-term memory. - Shumin Li; Junjie Chen 004; Bin Liu 014 (BMC Bioinform., 2017)

A comprehensive review and comparison of different computational methods for protein remote homology detection. - Junjie Chen 004; Mingyue Guo; Xiaolong Wang 001; Bin Liu 014 (Briefings Bioinform., 2018)

A Sparse Convolutional Predictor with Denoising Autoencoders for Phenotype Prediction. - Junjie Chen 004; Xinghua Shi (BCB, 2019)

Protein Remote Homology Detection and Fold Recognition Based on Sequence-Order Frequency Matrix. - Bin Liu 014; Junjie Chen 004; Mingyue Guo; Xiaolong Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Population-scale Genomic Data Augmentation Based on Conditional Generative Adversarial Networks. - Junjie Chen 004; Mohammad Erfan Mowlaei; Xinghua Shi (BCB, 2020)

PAR-GAN: Improving the Generalization of Generative Adversarial Networks Against Membership Inference Attacks. - Junjie Chen 004; Wendy Hui Wang; Hongchang Gao; Xinghua Shi (KDD, 2021)

Differential Privacy Protection Against Membership Inference Attack on Machine Learning for Genomic Data. - Junjie Chen 004; Wendy Hui Wang; Xinghua Shi (PSB, 2021)

iEnhancer-ELM: Improve Enhancer Identification by Extracting Multi-scale Contextual Information based on Enhancer Language Models. - Jiahao Li; Zhourun Wu; Wenhao Lin; Jiawei Luo; Jun Zhang 078; Qingcai Chen; Junjie Chen 004 (CoRR, 2022)

ProtRe-CN: Protein Remote Homology Detection by Combining Classification Methods and Network Methods via Learning to Rank. - Jiangyi Shao; Junjie Chen 004; Bin Liu 014 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction. - Zhourun Wu; Mingyue Guo; Xiaopeng Jin; Junjie Chen 004; Bin Liu 014 (Bioinform., 2023)

Discriminative Forests Improve Generative Diversity for Generative Adversarial Networks. - Junjie Chen 004; Jiahao Li; Chen Song; Bin Li; Qingcai Chen; Hongchang Gao; Wendy Hui Wang; Zenglin Xu; Xinghua Shi (AAAI, 2024)

Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization. - Xianliang Liu; Jiawei Luo; Xinyan Wang; Yang Zhang 057; Junjie Chen 004 (Briefings Bioinform., 2024)

iMFP-LG: Identify Novel Multi-functional Peptides Using Protein Language Models and Graph-based Deep Learning. - Jiawei Luo; Kejuan Zhao; Junjie Chen 004; Caihua Yang; Fuchuan Qu; Yumeng Liu; Xiaopeng Jin; Ke Yan 003; Yang Zhang 057; Bin Liu 014 (Genom. Proteom. Bioinform., 2025)

ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction. - Jiangyi Shao; Junjie Chen 004; Bin Liu 014 (IEEE Trans. Neural Networks Learn. Syst., 2025)