On the design of finite-state type systems. - Alexander Ian Smith (2015)

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)

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. - Zhen Chen 009; Xuhan Liu; Fuyi Li; Chen Li 021; Tatiana T. Marquez-Lago; André Leier; Tatsuya Akutsu; Geoffrey I. Webb; Dakang Xu; Alexander Ian Smith; Lei Li 013; Kuo-Chen Chou; et al. (Briefings Bioinform., 2019)

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)

Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. - Zhen Chen 009; Pei Zhao; Fuyi Li; Yanan Wang 003; Alexander Ian Smith; Geoffrey I. Webb; Tatsuya Akutsu; Abdelkader Baggag; Halima Bensmail; Jiangning Song (Briefings Bioinform., 2020)

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. - Fuyi Li; Cunshuo Fan; Tatiana T. Marquez-Lago; André Leier; Jerico Nico De Leon Revote; Cangzhi Jia; Yan Zhu 006; Alexander Ian Smith; Geoffrey I. Webb; Quanzhong Liu; Leyi Wei; Jian Li 052; et al. (Briefings Bioinform., 2020)

A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. - Shutao Mei; Fuyi Li; André Leier; Tatiana T. Marquez-Lago; Kailin Giam; Nathan P. Croft; Tatsuya Akutsu; Alexander Ian Smith; Jian Li 052; Jamie Rossjohn; Anthony W. Purcell; Jiangning Song (Briefings Bioinform., 2020)

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. - Fuyi Li; Jinxiang Chen; André Leier; Tatiana T. Marquez-Lago; Quanzhong Liu; Yanze Wang; Jerico Nico De Leon Revote; Alexander Ian Smith; Tatsuya Akutsu; Geoffrey I. Webb; Lukasz A. Kurgan; Jiangning Song (Bioinform., 2020)

PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. - Yanju Zhang; Sha Yu; Ruopeng Xie; Jiahui Li 007; André Leier; Tatiana T. Marquez-Lago; Tatsuya Akutsu; Alexander Ian Smith; Zongyuan Ge; Jiawei Wang 002; Trevor Lithgow; Jiangning Song (Bioinform., 2020)

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. - Fuyi Li; André Leier; Quanzhong Liu; Yanan Wang 003; Dongxu Xiang; Tatsuya Akutsu; Geoffrey I. Webb; Alexander Ian Smith; Tatiana T. Marquez-Lago; Jian Li 052; Jiangning Song (Genom. Proteom. Bioinform., 2020)

A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction. - Menglu Li; Yanan Wang 003; Fuyi Li; Yun Zhao; Mengya Liu; Sijia Zhang; Yannan Bin; Alexander Ian Smith; Geoffrey I. Webb; Jian Li 052; Jiangning Song; Junfeng Xia (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)