iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences. - Zhen Chen 009; Pei Zhao; Fuyi Li; André Leier; Tatiana T. Marquez-Lago; Yanan Wang 003; Geoffrey I. Webb; Alexander Ian Smith; Roger J. Daly; Kuo-Chen Chou; Jiangning Song (Bioinform., 2018)

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. - Fuyi Li; Chen Li 021; Tatiana T. Marquez-Lago; André Leier; Tatsuya Akutsu; Anthony W. Purcell; Alexander Ian Smith; Trevor Lithgow; Roger J. Daly; Jiangning Song; Kuo-Chen Chou (Bioinform., 2018)

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. - Fuyi Li; Yanan Wang 003; Chen Li 021; Tatiana T. Marquez-Lago; André Leier; Neil D. Rawlings; Gholamreza Haffari; Jerico Nico De Leon Revote; Tatsuya Akutsu; Kuo-Chen Chou; Anthony W. Purcell; Robert N. Pike; et al. (Briefings Bioinform., 2019)

iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. - Zhen Chen 009; Pei Zhao; Fuyi Li; Tatiana T. Marquez-Lago; André Leier; Jerico Nico De Leon Revote; Yan Zhu 006; David R. Powell; Tatsuya Akutsu; Geoffrey I. Webb; Kuo-Chen Chou; Alexander Ian Smith; et al. (Briefings Bioinform., 2020)

HEAL: an automated deep learning framework for cancer histopathology image analysis. - Yanan Wang 003; Nicolas Coudray; Yun Zhao; Fuyi Li; Changyuan Hu; Yao-Zhong Zhang; Seiya Imoto; Aristotelis Tsirigos; Geoffrey I. Webb; Roger J. Daly; Jiangning Song (Bioinform., 2021)

DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images. - Yanan Wang 003; Changyuan Hu; Terry Kwok; Christopher A. Bain; Xiangyang Xue 001; Robin B. Gasser; Geoffrey I. Webb; Alex Boussioutas; Xian Shen; Roger J. Daly; Jiangning Song (Bioinform., 2022)

Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. - Zhikang Wang; Yue Bi; Tong Pan; Xiaoyu Wang 016; Chris Bain; Richard Bassed; Seiya Imoto; Jianhua Yao 001; Roger J. Daly; Jiangning Song (Bioinform., 2023)

Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images. - Zhikang Wang; Qian Gao; Xiaoping Yi; Xinyu Zhang 017; Yiwen Zhang; Daokun Zhang; Pietro Liò; Chris Bain; Richard Bassed; Shanshan Li; Yuming Guo 001; Seiya Imoto; et al. (Comput. Methods Programs Biomed., 2023)