| iFeature: a python package and web server for features extraction and selection from protein and peptide sequences Z Chen, P Zhao, F Li, A Leier, TT Marquez-Lago, Y Wang, GI Webb, ... Bioinformatics 31 (14), 2499–2502, 2018 | 180 | 2018 |
| iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites J Song, Y Wang, F Li, T Akutsu, ND Rawlings, GI Webb, KC Chou Briefings in bioinformatics, 2019 | 144 | 2019 |
| GlycoMine: a machine learning-based approach for predicting N-, C-and O-linked glycosylation in the human proteome F Li, C Li, M Wang, GI Webb, Y Zhang, JC Whisstock, J Song Bioinformatics 31 (9), 1411-1419, 2015 | 113 | 2015 |
| PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy J Song*, F Li*, A Leier, TT Marquez-Lago, T Akutsu, G Haffari, KC Chou, ... Bioinformatics 34 (4), 684-687, 2018 | 103 | 2018 |
| PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework J Song, F Li, K Takemoto, G Haffari, T Akutsu, KC Chou, GI Webb Journal of theoretical biology 443, 125-137, 2018 | 101 | 2018 |
| Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. F Li, C Li, TT Marquez-Lago, A Leier, T Akutsu, AW Purcell, AI Smith, ... Bioinformatics (Oxford, England), 2018 | 98 | 2018 |
| iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data Z Chen, P Zhao, F Li, TT Marquez-Lago, A Leier, J Revote, Y Zhu, ... Briefings in Bioinformatics, 2020 | 84 | 2020 |
| MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters M Zhang*, F Li*, TT Marquez-Lago, A Leier, C Fan, KC Chou, J Song, ... Bioinformatics, 2019 | 58 | 2019 |
| Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods F Li, Y Wang, C Li, TT Marquez-Lago, A Leier, ND Rawlings, G Haffari, ... Briefings in Bioinformatics, 2019 | 54 | 2019 |
| Large-scale comparative assessment of computational predictors for lysine post-translational modification sites Z Chen, X Liu, F Li, C Li, T Marquez-Lago, A Leier, T Akutsu, GI Webb, ... Briefings in bioinformatics, 2019 | 52 | 2019 |
| GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features F Li, C Li, J Revote, Y Zhang, GI Webb, J Li, J Song, T Lithgow Scientific reports 6, 34595, 2016 | 47 | 2016 |
| Positive-unlabelled learning of glycosylation sites in the human proteome F Li, Y Zhang, AW Purcell, GI Webb, KC Chou, T Lithgow, C Li, J Song BMC Bioinformatics 20 (1), 112, 2019 | 42 | 2019 |
| A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction S Mei, F Li, A Leier, TT Marquez-Lago, K Giam, NP Croft, T Akutsu, ... Briefings in Bioinformatics, 2020 | 38 | 2020 |
| Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms L Wei, J Hu, F Li, J Song, R Su, Q Zou Briefings in Bioinformatics, 2020 | 36 | 2020 |
| DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites F Li, J Chen, A Leier, T Marquez-Lago, Q Liu, Y Wang, J Revote, AI Smith, ... Bioinformatics, 2020 | 29 | 2020 |
| Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences Z Chen, P Zhao, F Li, Y Wang, AI Smith, GI Webb, T Akutsu, A Baggag, ... Briefings in bioinformatics, 2019 | 25 | 2019 |
| PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact F Li, C Fan, TT Marquez-Lago, A Leier, J Revote, C Jia, Y Zhu, AI Smith, ... Briefings in Bioinformatics, 2020 | 13 | 2020 |
| PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs C Jia, Y Bi, J Chen, A Leier, F Li*, J Song* Bioinformatics, 2020 | 10 | 2020 |
| Characterization of the Src-regulated kinome identifies SGK1 as a key mediator of Src-induced transformation X Ma, L Zhang, J Song, E Nguyen, RS Lee, SJ Rodgers, F Li, C Huang, ... Nature communications 10 (1), 296, 2019 | 9 | 2019 |
| Formator: predicting lysine formylation sites based on the most distant undersampling and safe-level synthetic minority oversampling C Jia, M Zhang, C Fan, F Li*, J Song* IEEE/ACM transactions on computational biology and bioinformatics, 2019 | 8 | 2019 |
Jiangning SongAssociate Professor, Biomedicine Discovery Institute and Data Futures Institute, Monash UniversityVerified email at monash.edu
