Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses. - Fransiskus Xaverius Ivan; Xinrui Zhou; Akhila Deshpande; Rui Yin 002; Jie Zheng 002; Chee Keong Kwoh 001 (BCB, 2017)

Identification of Potential Critical Virulent Sites Based on Hemagglutinin of Influenza a Virus in Past Pandemic Strains. - Rui Yin 002; Xinrui Zhou; Fransiskus Xaverius Ivan; Jie Zheng 002; Vincent T. K. Chow; Chee Keong Kwoh 001 (ICBBS, 2017)

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses. - Xinrui Zhou; Jie Zheng 002; Fransiskus Xaverius Ivan; Rui Yin 002; Shoba Ranganathan; Vincent T. K. Chow; Chee-Keong Kwoh 001 (BMC Genom., 2018)

Computational identification of physicochemical signatures for host tropism of influenza A virus. - Rui Yin 002; Xinrui Zhou; Jie Zheng 002; Chee Keong Kwoh 001 (J. Bioinform. Comput. Biol., 2018)

An Encoding Scheme Capturing Generic Priors and Properties of Amino Acids Improves Protein Classification. - Xinrui Zhou; Rui Yin 002; Jie Zheng 002; Chee Keong Kwoh 001 (IEEE Access, 2019)

Ensemble Prediction of Synergistic Drug Combinations Incorporating Biological, Chemical, Pharmacological, and Network Knowledge. - Pingjian Ding; Rui Yin 002; Jiawei Luo 001; Chee Keong Kwoh 001 (IEEE J. Biomed. Health Informatics, 2019)

Whole Genome Sequencing Analysis. - Rui Yin 002; Chee Keong Kwoh 001; Jie Zheng 002 (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

DL-CRISPR: A Deep Learning Method for Off-Target Activity Prediction in CRISPR/Cas9 With Data Augmentation. - Yu Zhang 084; Yahui Long; Rui Yin 002; Chee Keong Kwoh 001 (IEEE Access, 2020)

Tempel: time-series mutation prediction of influenza A viruses via attention-based recurrent neural networks. - Rui Yin 002; Emil Luusua; Jan Dabrowski; Yu Zhang 084; Chee Keong Kwoh 001 (Bioinform., 2020)

COMET: Convolutional Dimension Interaction for Deep Matrix Factorization. - Zhuoyi Lin; Lei Feng 006; Xingzhi Guo; Rui Yin 002; Chee Keong Kwoh 001; Chi Xu (CoRR, 2020)

Time series computational prediction of vaccines for influenza A H3N2 with recurrent neural networks. - Rui Yin 002; Yu Zhang 084; Xinrui Zhou; Chee Keong Kwoh 001 (J. Bioinform. Comput. Biol., 2020)

Meta-analysis on the lethality of influenza A viruses using machine learning approaches - Rui Yin 002 (2020)

VirPreNet: a weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all eight segments. - Rui Yin 002; Zihan Luo 001; Pei Zhuang; Zhuoyi Lin; Chee Keong Kwoh 001 (Bioinform., 2021)

GLIMG: Global and local item graphs for top-N recommender systems. - Zhuoyi Lin; Lei Feng 006; Rui Yin 002; Chi Xu; Chee Keong Kwoh 001 (Inf. Sci., 2021)

A framework for predicting variable-length epitopes of human-adapted viruses using machine learning methods. - Rui Yin 002; Xianghe Zhu; Min Zeng; Pengfei Wu; Min Li 007; Chee Keong Kwoh 001 (Briefings Bioinform., 2022)

IAV-CNN: A 2D Convolutional Neural Network Model to Predict Antigenic Variants of Influenza A Virus. - Rui Yin 002; Nyi Nyi Thwin; Pei Zhuang; Zhuoyi Lin; Chee Keong Kwoh 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

PESI: Paratope-Epitope Set Interaction for SARS-CoV-2 Neutralization Prediction. - Zhang Wan; Zhuoyi Lin; Shamima Rashid; Shaun Yue-Hao Ng; Rui Yin 002; J. Senthilnath 001; Chee Keong Kwoh 001 (BIBM, 2023)

GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation. - Min Li 007; Baoying Zhao; Rui Yin 002; Chengqian Lu; Fei Guo 001; Min Zeng (Briefings Bioinform., 2023)

A review of enzyme design in catalytic stability by artificial intelligence. - Yongfan Ming; Wenkang Wang; Rui Yin 002; Min Zeng; Li Tang; Shizhe Tang; Min Li 007 (Briefings Bioinform., 2023)

ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences. - Rui Yin 002; Zihan Luo 001; Pei Zhuang; Min Zeng; Min Li 007; Zhuoyi Lin; Chee Keong Kwoh 001 (J. Biomed. Informatics, 2023)

COMET: Convolutional Dimension Interaction for Collaborative Filtering. - Zhuoyi Lin; Lei Feng 006; Xingzhi Guo; Yu Zhang 084; Rui Yin 002; Chee Keong Kwoh 001; Chi Xu (ACM Trans. Intell. Syst. Technol., 2023)

LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism. - Min Zeng; Yifan Wu 008; Yiming Li; Rui Yin 002; Chengqian Lu; Junwen Duan; Min Li 007 (Bioinform., 2023)

SGCL-LncLoc: An Interpretable Deep Learning Model for Improving IncRNA Subcellular Localization Prediction with Supervised Graph Contrastive Learning. - Min Li 007; Baoying Zhao; Yiming Li; Pingjian Ding; Rui Yin 002; Shichao Kan; Min Zeng (Big Data Min. Anal., 2024)

GenoM7GNet: An Efficient N7-Methylguanosine Site Prediction Approach Based on a Nucleotide Language Model. - Chuang Li 004; Heshi Wang; Yanhua Wen; Rui Yin 002; Xiangxiang Zeng; Keqin Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

EF-Net: Mental State Recognition by Analyzing Multimodal EEG-fNIRS via CNN. - Aniqa Arif; Yihe Wang; Rui Yin 002; Xiang Zhang 012; Ahmed Helmy (Sensors, 2024)