Alexander Ian Smith

13 papers Journal 12
YearRankTypeTitle / Venue / Authors
2021 J jnl
A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Menglu Li, Yanan Wang, Fuyi Li, Yun Zhao, Mengya Liu, Sijia Zhang, Yannan Bin, Alexander Ian Smith, Geoffrey I. Webb, Jian Li, Jiangning Song, Junfeng Xia
2020 J jnl
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction.
Briefings Bioinform.
Shutao Mei, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Kailin Giam, Nathan P. Croft, Tatsuya Akutsu, Alexander Ian Smith, Jian Li, Jamie Rossjohn, Anthony W. Purcell, Jiangning Song
2020 J jnl
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences.
Briefings Bioinform.
Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, Alexander Ian Smith, Geoffrey I. Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song
2020 J jnl
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites.
Bioinform.
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
2020 J jnl
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact.
Briefings Bioinform.
Fuyi Li, Cunshuo Fan, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Cangzhi Jia, Yan Zhu, Alexander Ian Smith, Geoffrey I. Webb, Quanzhong Liu, Leyi Wei, Jian Li, Jiangning Song
2020 J jnl
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.
Bioinform.
Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, Zongyuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song
2020 J jnl
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information.
Genom. Proteom. Bioinform.
Fuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, Alexander Ian Smith, Tatiana T. Marquez-Lago, Jian Li, Jiangning Song
2020 J jnl
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data.
Briefings Bioinform.
Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Yan Zhu, David R. Powell, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Alexander Ian Smith, Roger J. Daly, Jian Li, Jiangning Song
2019 J jnl
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.
Briefings Bioinform.
Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Dakang Xu, Alexander Ian Smith, Lei Li, Kuo-Chen Chou, Jiangning Song
2019 J jnl
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.
Briefings Bioinform.
Fuyi Li, Yanan Wang, Chen Li, 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, Geoffrey I. Webb, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, James C. Whisstock, Jiangning Song
2018 J jnl
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.
Bioinform.
Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Anthony W. Purcell, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, Jiangning Song, Kuo-Chen Chou
2018 J jnl
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences.
Bioinform.
Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Yanan Wang, Geoffrey I. Webb, Alexander Ian Smith, Roger J. Daly, Kuo-Chen Chou, Jiangning Song
2015 — —
On the design of finite-state type systems.
Alexander Ian Smith