Smart Card-Based Irregular Access Patterns Detection System. - António Leong; Simon Fong 001; Shirley W. I. Siu (EEE, 2004)

DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. - Iris Antes; Shirley W. I. Siu; Thomas Lengauer (ISMB (Supplement of Bioinformatics), 2006)

Comparison of Cutoff Strategies for Geometrical Features in Machine Learning-Based Scoring Functions. - Shirley W. I. Siu; Thomas K. F. Wong; Simon Fong 001 (ADMA (2), 2013)

Predicting favorable protein docking poses on a solid surface by particle swarm optimization. - Jimmy C. F. Ngai; Pui-In Mak; Shirley W. I. Siu (CEC, 2015)

PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking. - Marcus C. K. Ng; Simon Fong 001; Shirley W. I. Siu (J. Bioinform. Comput. Biol., 2015)

Improving the efficiency of PSOVina for protein-ligand docking by two-stage local search. - Hio Kuan Tai; Hang Lin; Shirley W. I. Siu (CEC, 2016)

ProtPOS: a python package for the prediction of protein preferred orientation on a surface. - Jimmy C. F. Ngai; Pui-In Mak; Shirley W. I. Siu (Bioinform., 2016)

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers. - Han Cao; Marcus C. K. Ng; Siti Azma Jusoh; Hio Kuan Tai; Shirley W. I. Siu (J. Comput. Aided Mol. Des., 2017)

Chaos-embedded particle swarm optimization approach for protein-ligand docking and virtual screening. - Hio Kuan Tai; Siti Azma Jusoh; Shirley W. I. Siu (J. Cheminformatics, 2018)

Adaptive Incremental Genetic Algorithm for Task Scheduling in Cloud Environments. - Kairong Duan; Simon Fong 001; Shirley W. I. Siu; Wei Song 004; Steven Sheng-Uei Guan (Symmetry, 2018)

BESTox: A Convolutional Neural Network Regression Model Based on Binary-Encoded SMILES for Acute Oral Toxicity Prediction of Chemical Compounds. - Jiarui Chen; Hong-Hin Cheong; Shirley Weng In Siu (AlCoB, 2020)

Evaluating Variants of Firefly Algorithm for Ligand Pose Prediction in Protein-ligand Docking Program. - Meng Chi Ao; Shirley W. I. Siu (ICBBT, 2020)

Study of Data Imbalanced Problem in Protein-peptide Binding Prediction. - Lu Gao; Shirley W. I. Siu (ICBBT, 2020)

White learning methodology: A case study of cancer-related disease factors analysis in real-time PACS environment. - Tengyue Li; Simon Fong 001; Shirley W. I. Siu; Xin-She Yang 001; Liansheng Liu; Sabah Mohammed (Comput. Methods Programs Biomed., 2020)

Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network. - Jiarui Chen; Yain-Whar Si; Chonwai Un; Shirley W. I. Siu (J. Cheminformatics, 2021)

LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds. - Faraz Shaikh; Hio Kuan Tai; Nirali Desai; Shirley W. I. Siu (J. Cheminformatics, 2021)

xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning. - Jiarui Chen; Hong-Hin Cheong; Shirley W. I. Siu (J. Chem. Inf. Model., 2021)

Multi-Branch-CNN: Classification of ion channel interacting peptides using multi-branch convolutional neural network. - Jielu Yan; Bob Zhang 001; Mingliang Zhou 001; Hang Fai Kwok; Shirley W. I. Siu (Comput. Biol. Medicine, 2022)

Instance-based deep transfer learning with attention for stock movement prediction. - Qi-Qiao He; Shirley Weng In Siu; Yain-Whar Si (Appl. Intell., 2023)

Attentive recurrent adversarial domain adaptation with Top-k pseudo-labeling for time series classification. - Qi-Qiao He; Shirley Weng In Siu; Yain-Whar Si (Appl. Intell., 2023)

Enhancing Diagnostic Precision in Gastric Bleeding through Automated Lesion Segmentation: A Deep DuS-KFCM Approach. - Xian-Xian Liu; Mingkun Xu; Yuanyuan Wei 008; Huafeng Qin; Qun Song 007; Simon Fong 001; Feng Tien; Wei Luo; Juntao Gao; Zhihua Zhang; Shirley W. I. Siu (CoRR, 2024)

Editorial: Machine learning approaches to antimicrobials: discovery and resistance. - Shira L. Broschat; Shirley W. I. Siu; Cesar de la Fuente-Nunez (Frontiers Bioinform., 2024)

Identification of Anticancer Peptides from the Genome of Candida albicans: in Silico Screening, in Vitro and in Vivo Validations. - Hong-Hin Cheong; Weimin Zuo; Jiarui Chen; Chonwai Un; Yain-Whar Si; Koon Ho Wong; Hang Fai Kwok; Shirley W. I. Siu (J. Chem. Inf. Model., 2024)

CALM-AcPEP: Predicting Anticancer Peptides Using Cross-Attention and Pre-Trained Language Model. - Xinke Zhan; Tiantao Liu; Pratiti Bhadra; Yu-An Huang; Zhuhong You; Shirley W. I. Siu (ICIC (26), 2025)

BERT-AmPEP60: A BERT-Based Transfer Learning Approach to Predict the Minimum Inhibitory Concentrations of Antimicrobial Peptides for Escherichia coli and Staphylococcus aureus. - Jianxiu Cai; Jielu Yan; Chonwai Un; Yapeng Wang; François-Xavier Campbell-Valois; Shirley W. I. Siu (J. Chem. Inf. Model., 2025)