Systems Biology: The Next Frontier for Bioinformatics. - Vladimir A. Likic; Malcolm J. McConville; Trevor Lithgow; Antony Bacic (Adv. Bioinformatics, 2010)

POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles. - Jiawei Wang 002; Bingjiao Yang; Jerico Nico De Leon Revote; André Leier; Tatiana T. Marquez-Lago; Geoffrey I. Webb; Jiangning Song; Kuo-Chen Chou; Trevor Lithgow (Bioinform., 2017)

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI. - Yi An; Jiawei Wang 002; Chen Li 021; André Leier; Tatiana T. Marquez-Lago; Jonathan Wilksch; Yang Zhang 010; Geoffrey I. Webb; Jiangning Song; Trevor Lithgow (Briefings 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)

Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. - Jiawei Wang 002; Bingjiao Yang; André Leier; Tatiana T. Marquez-Lago; Morihiro Hayashida; Andrea Rocker; Yanju Zhang; Tatsuya Akutsu; Kuo-Chen Chou; Richard A. Strugnell; Jiangning Song; Trevor Lithgow (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)

Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. - Jiawei Wang 002; Bingjiao Yang; Yi An; Tatiana T. Marquez-Lago; André Leier; Jonathan Wilksch; Qingyang Hong; Yang Zhang 010; Morihiro Hayashida; Tatsuya Akutsu; Geoffrey I. Webb; Richard A. Strugnell; et al. (Briefings Bioinform., 2019)

Bastion3: a two-layer ensemble predictor of type III secreted effectors. - Jiawei Wang 002; Jiahui Li 007; Bingjiao Yang; Ruopeng Xie; Tatiana T. Marquez-Lago; André Leier; Morihiro Hayashida; Tatsuya Akutsu; Yanju Zhang; Kuo-Chen Chou; Joel Selkrig; Tieli Zhou; et al. (Bioinform., 2019)

Positive-unlabelled learning of glycosylation sites in the human proteome. - Fuyi Li; Yang Zhang 010; Anthony W. Purcell; Geoffrey I. Webb; Kuo-Chen Chou; Trevor Lithgow; Chen Li 021; Jiangning Song (BMC Bioinform., 2019)

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)

PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins. - Jiawei Wang 002; Wei Dai; Jiahui Li 007; Ruopeng Xie; Rhys A. Dunstan; Christopher Stubenrauch; Yanju Zhang; Trevor Lithgow (Nucleic Acids Res., 2020)

DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy. - Ruopeng Xie; Jiahui Li 007; Jiawei Wang 002; Wei Dai; André Leier; Tatiana T. Marquez-Lago; Tatsuya Akutsu; Trevor Lithgow; Jiangning Song; Yanju Zhang (Briefings Bioinform., 2021)

AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses. - Le Huang; Bowen Yang; Haidong Yi; Amina Asif; Jiawei Wang 002; Trevor Lithgow; Han Zhang 017; Fayyaz ul Amir Afsar Minhas; Yanbin Yin (Nucleic Acids Res., 2021)

AcrHub: an integrative hub for investigating, predicting and mapping anti-CRISPR proteins. - Jiawei Wang 002; Wei Dai; Jiahui Li 007; Qi Li; Ruopeng Xie; Yanju Zhang; Christopher Stubenrauch; Trevor Lithgow (Nucleic Acids Res., 2021)

BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. - Jiawei Wang 002; Jiahui Li 007; Yi Hou; Wei Dai; Ruopeng Xie; Tatiana T. Marquez-Lago; André Leier; Tieli Zhou; Von Torres; Iain Hay; Christopher Stubenrauch; Yanju Zhang; et al. (Nucleic Acids Res., 2021)