| 2025 |
Zhao, Z., Shi, G., Wu, X., Ren, R., Gao, X., & Li, F. (2025). DIG-Mol: A Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction. IEEE Journal of Biomedical and Health Informatics, 29(3), 1735-1746.
DOI Scopus4 WoS2 Europe PMC3 |
| 2025 |
Guo, X., Ran, Z., & Li, F. (2025). Kinase-inhibitor binding affinity prediction with pretrained graph encoder and language model.. Briefings in bioinformatics, 26(4), bbaf338.
DOI |
| 2025 |
Liu, J., Roy, M. J., Isbel, L., & Li, F. (2025). Accurate PROTAC-targeted degradation prediction with DegradeMaster. Bioinformatics, 41(Supplement_1), i342-i351.
DOI Scopus2 WoS1 Europe PMC2 |
| 2025 |
Hao, Y., Guo, X., Ran, Z., Bi, Y., & Li, F. (2025). LncTracker: a unified multi-channel framework for multi-label lncRNA localization. IEEE Journal of Biomedical and Health Informatics, PP, 1-12.
DOI |
| 2025 |
Wu, C., Zhang, N., Li, H., Wang, H., Han, L., Wang, Y., . . . Tian, F. (2025). Preparation of immobilized xanthine oxidase with magnetic metal–organic framework and its application in screening of active ingredients in traditional Chinese medicine. Microchimica Acta, 192(5), 12 pages.
DOI Scopus3 WoS3 Europe PMC2 |
| 2024 |
Lappan, R., Chown, S. L., French, M., Perlaza-Jiménez, L., Macesic, N., Davis, M., . . . Greening, C. (2024). Towards integrated cross-sectoral surveillance of pathogens and antimicrobial resistance: Needs, approaches, and considerations for linking surveillance to action. Environment International, 192, 109046-1-109046-19.
DOI Scopus9 WoS9 Europe PMC5 |
| 2024 |
Zhang, Z., Liu, Y., Xiao, M., Wang, K., Huang, Y., Bian, J., . . . Li, F. (2024). Graph contrastive learning as a versatile foundation for advanced scRNA-seq data analysis. Briefings in Bioinformatics, 25(6).
DOI |
| 2024 |
Song, R., J Sutton, G., Li, F., Liu, Q., & Wong, J. J. -L. (2024). Variable calling of m6A and associated features in databases: a guide for end-users. Briefings in Bioinformatics, 25(5), bbae434-1-bbae434-13.
DOI |
| 2024 |
Liu, T., Jia, C., Bi, Y., Guo, X., Zou, Q., & Li, F. (2024). scDFN: enhancing single-cell RNA-seq clustering with deep fusion networks.. Brief Bioinform, 25(6), 12 pages.
DOI Scopus11 WoS7 Europe PMC9 |
| 2024 |
Jia, R., He, Z., Wang, C., Guo, X., & Li, F. (2024). MetalPrognosis: A Biological Language Model-Based Approach for Disease-Associated Mutations in Metal-Binding Site Prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 21(6), 1-10.
DOI Scopus4 WoS3 Europe PMC2 |
| 2024 |
Zhang, Z., Liu, Y., Xiao, M., Wang, K., Huang, Y., Bian, J., . . . Li, F. (2024). Graph contrastive learning as a versatile foundation for advanced scRNA-seq data analysis. Briefings in Bioinformatics, 25(6), 15 pages.
DOI Scopus6 WoS8 Europe PMC2 |
| 2024 |
Ran, Z., Wang, C., Sun, H., Pan, S., & Li, F. (2024). Characterizing Secretion System Effector Proteins With Structure-Aware Graph Neural Networks and Pre-Trained Language Models. IEEE Journal of Biomedical and Health Informatics, 28(9), 1-9.
DOI Scopus2 WoS2 Europe PMC2 |
| 2024 |
Li, F., Bi, Y., Guo, X., Tan, X., Wang, C., & Pan, S. (2024). Advancing mRNA subcellular localization prediction with graph neural network and RNA structure.. Bioinformatics (Oxford, England), 40(8), btae504.
DOI Scopus8 WoS6 Europe PMC5 |
| 2024 |
Bi, Y., Li, F., Wang, C., Pan, T., Davidovich, C., Webb, G. I., & Song, J. (2024). Advancing microRNA target site prediction with transformer and base-pairing patterns.. Nucleic acids research, 52(19), gkae782.
DOI Scopus2 WoS3 Europe PMC1 |
| 2024 |
Wang, X., Li, F., Zhang, Y., Imoto, S., Shen, H. H., Li, S., . . . Song, J. (2024). Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects. Briefings in Bioinformatics, 25(5), 15 pages.
DOI Scopus9 WoS7 |
| 2024 |
Wang, X., Patil, N., Li, F., Wang, Z., Zhan, H., Schmidt, D., . . . Song, J. (2024). PmxPred: A data-driven approach for the identification of active polymyxin analogues against gram-negative bacteria. Computers in Biology and Medicine, 168, 107681-1-107681-10.
DOI Scopus15 WoS4 Europe PMC3 |
| 2024 |
Wang, L., Zheng, Y., Jin, D., Li, F., Qiao, Y., & Pan, S. (2024). Contrastive Graph Similarity Networks. ACM Transactions on the Web, 18(2), 17-1-17-20.
DOI Scopus21 WoS17 |
| 2024 |
Wang, C., He, Z., Jia, R., Pan, S., Coin, L. J. M., Song, J., & Li, F. (2024). PLANNER: a multi-scale deep language model for the origins of replication site prediction. IEEE Journal of Biomedical and Health Informatics, 28(4), 2445-2454.
DOI Scopus9 WoS8 Europe PMC9 |
| 2024 |
Yan, Z., Ge, F., Liu, Y., Zhang, Y., Li, F., Song, J., & Yu, D. J. (2024). TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. Journal of Chemical Information and Modeling, 64(4), 1407-1418.
DOI Scopus17 WoS15 Europe PMC14 |
| 2024 |
He, Z., Wang, C., Guo, X., Sun, H., Bi, Y., Pitt, M. E., . . . Li, F. (2024). MERITS: a web-based integrated <i>mycobacterial</i> PE/PPE protein database. Bioinformatics Advances, 4(1), 8 pages.
DOI Europe PMC1 |
| 2023 |
Chen, J., Wang, M., Zhao, D., Li, F., Wu, H., Liu, Q., & Li, S. (2023). MSINGB: A Novel Computational Method Based on NGBoost for Identifying Microsatellite Instability Status from Tumor Mutation Annotation Data. Interdisciplinary Sciences – Computational Life Sciences, 15(1), 100-110.
DOI Scopus9 WoS10 Europe PMC6 |
| 2023 |
Zhang, Y., Ge, F., Li, F., Yang, X., Song, J., & Yu, D. -J. (2023). Prediction of Multiple Types of RNA Modifications via Biological Language Model. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(5), 3205-3214.
DOI Scopus19 WoS14 Europe PMC13 |
| 2023 |
Li, F., Wang, C., Guo, X., Akutsu, T., Webb, G. I., Coin, L. J. M., . . . Song, J. (2023). ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction.. Briefings in Bioinformatics, 24(6), 14 pages.
DOI Scopus17 WoS16 Europe PMC13 |
| 2023 |
Ge, F., Li, C., Iqbal, S., Muhammad, A., Li, F., Thafar, M. A., . . . Yu, D. J. (2023). VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings in Bioinformatics, 24(1), 1-16.
DOI Scopus17 WoS17 Europe PMC17 |
| 2023 |
Chen, R., Li, F., Guo, X., Bi, Y., Li, C., Pan, S., . . . Song, J. (2023). ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. Briefings in Bioinformatics, 24(3), 15 pages.
DOI Scopus18 WoS17 Europe PMC17 |
| 2023 |
Jia, X., Zhao, P., Li, F., Qin, Z., Ren, H., Li, J., . . . Song, J. (2023). ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning. Briefings in Bioinformatics, 24(2), 13 pages.
DOI Scopus7 WoS4 Europe PMC3 |
| 2023 |
Xu, J., Li, F., Li, C., Guo, X., Landersdorfer, C., Shen, H. H., . . . Song, J. (2023). iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. Briefings in Bioinformatics, 24(4), 1-20.
DOI Scopus65 WoS49 Europe PMC48 |
| 2023 |
Zhu, Y., Li, F., Guo, X., Wang, X., Coin, L. J. M., Webb, G. I., . . . Jia, C. (2023). TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters.. Briefings in bioinformatics, 24(4), bbad209.
DOI Scopus8 WoS7 Europe PMC6 |
| 2023 |
Bu, Y., Jia, C., Guo, X., Li, F., & Song, J. (2023). COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants.. Briefings in functional genomics, 22(3), 274-280.
DOI Scopus4 WoS4 Europe PMC2 |
| 2023 |
Li, F., Guo, X., Bi, Y., Jia, R., Pitt, M. E., Pan, S., . . . Song, J. (2023). Digerati - A multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins.. Computers in biology and medicine, 163, 107155.
DOI Scopus10 WoS9 Europe PMC10 |
| 2022 |
Li, F., Guo, X., Xiang, D., Pitt, M. E., Bainomugisa, A., & Coin, L. J. M. (2022). Computational analysis and prediction of PE_PGRS proteins using machine learning.. Computational and structural biotechnology journal, 20, 662-674.
DOI Scopus26 WoS23 Europe PMC19 |
| 2022 |
Bi, Y., Li, F., Guo, X., Wang, Z., Pan, T., Guo, Y., . . . Song, J. (2022). Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations. Briefings in Bioinformatics, 23(6), bbac467-1-bbac467-12.
DOI Scopus22 WoS19 Europe PMC17 |
| 2022 |
Liu, Q., Fang, H., Wang, X., Wang, M., Li, S., Coin, L. J. M., . . . Song, J. (2022). DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions.. Bioinformatics (Oxford, England), 38(17), 4053-4061.
DOI Scopus13 WoS13 Europe PMC11 |
| 2022 |
Iqbal, S., Ge, F., Li, F., Akutsu, T., Zheng, Y., Gasser, R. B., . . . Song, J. (2022). PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations.. Journal of chemical information and modeling, 62(17), 4270-4282.
DOI Scopus35 WoS33 Europe PMC29 |
| 2022 |
Chen, Z., Liu, X., Zhao, P., Li, C., Wang, Y., Li, F., . . . Song, J. (2022). iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. Nucleic Acids Research, 50(W1), W434-W447.
DOI Scopus62 WoS61 Europe PMC57 |
| 2022 |
Lin, Y., Huo, P., Li, F., Chen, X., Jiang, Y., Zhang, Y., . . . Yang, L. (2022). A critical review on cathode modification methods for efficient Electro-Fenton degradation of persistent organic pollutants. CHEMICAL ENGINEERING JOURNAL, 450, 13 pages.
DOI WoS77 |
| 2022 |
Zhu, L., Wang, X., Li, F., & Song, J. (2022). PreAcrs: a machine learning framework for identifying anti-CRISPR proteins. BMC Bioinformatics, 23(1), 444-1-444-21.
DOI Scopus12 WoS10 Europe PMC11 |
| 2022 |
Peng, X., Wang, X., Guo, Y., Ge, Z., Li, F., Gao, X., & Song, J. (2022). RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins. Briefings in Bioinformatics, 23(4), 1-15.
DOI Scopus20 WoS16 Europe PMC12 |
| 2022 |
Wang, M., Li, F., Wu, H., Liu, Q., & Li, S. (2022). PredPromoter-MF(2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest. Interdisciplinary Sciences – Computational Life Sciences, 14(3), 697-711.
DOI Scopus6 WoS6 Europe PMC3 |
| 2022 |
Zhang, M., Jia, C., Li, F., Li, C., Zhu, Y., Akutsu, T., . . . Song, J. (2022). Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. Briefings in Bioinformatics, 23(2), 1-25.
DOI Scopus25 WoS23 Europe PMC16 |
| 2022 |
Wang, X., Li, F., Xu, J., Rong, J., Webb, G. I., Ge, Z., . . . Song, J. (2022). ASPIRER: A new computational approach for identifying non-classical secreted proteins based on deep learning. Briefings in Bioinformatics, 23(2), 1-12.
DOI Scopus21 WoS15 Europe PMC19 |
| 2022 |
Packiam, K. A. R., Ooi, C. W., Li, F., Mei, S., Tey, B. T., Ong, H. F., . . . Ramanan, R. N. (2022). PERISCOPE-Opt: Machine learning-based prediction of optimal fermentation conditions and yields of recombinant periplasmic protein expressed in Escherichia coli. Computational and Structural Biotechnology Journal, 20, 2909-2920.
DOI Scopus14 WoS13 Europe PMC9 |
| 2022 |
Chen, J., Li, F., Wang, M., Li, J., Marquez-Lago, T. T., Leier, A., . . . Song, J. (2022). BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data. Frontiers in Big Data, 4, 16 pages.
DOI Scopus4 WoS1 Europe PMC1 |
| 2022 |
Li, F., Dong, S., Leier, A., Han, M., Guo, X., Xu, J., . . . Song, J. (2022). Positive-unlabeled learning in bioinformatics and computational biology: A brief review. Briefings in Bioinformatics, 23(1), bbab461-1-bbab461-13.
DOI Scopus60 WoS52 Europe PMC45 |
| 2021 |
Iqbal, S., Li, F., Akutsu, T., Ascher, D. B., Webb, G. I., & Song, J. (2021). Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. Briefings in Bioinformatics, 22(6), 1-23.
DOI Scopus37 WoS37 Europe PMC35 |
| 2021 |
Wang, Y., Coudray, N., Zhao, Y., Li, F., Hu, C., Zhang, Y. -Z., . . . Song, J. (2021). HEAL: an automated deep learning framework for cancer histopathology image analysis.. Bioinformatics (Oxford, England), 37(22), 4291-4295.
DOI Scopus26 WoS21 Europe PMC18 |
| 2021 |
Zhu, Y. -H., Hu, J., Ge, F., Li, F., Song, J., Zhang, Y., & Yu, D. -J. (2021). Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings in Bioinformatics, 22(3), 1-14.
DOI Scopus19 WoS15 Europe PMC13 |
| 2021 |
Chai, D., Jia, C., Zheng, J., Zou, Q., & Li, F. (2021). Staem5: A novel computational approachfor accurate prediction of m5C site.. Molecular therapy. Nucleic acids, 26, 1027-1034.
DOI Scopus25 WoS25 Europe PMC20 |
| 2021 |
Wang, Y., Li, F., Bharathwaj, M., Rosas, N. C., Leier, A., Akutsu, T., . . . Song, J. (2021). DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases. Briefings in Bioinformatics, 22(4), 1-12.
DOI Scopus15 WoS19 Europe PMC9 |
| 2021 |
Mei, S., Li, F., Xiang, D., Ayala, R., Faridi, P., Webb, G. I., . . . Song, J. (2021). Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules. Briefings in Bioinformatics, 22(5), 1-16.
DOI Scopus47 WoS44 Europe PMC42 |
| 2021 |
Jia, C., Zhang, M., Fan, C., Li, F., & Song, J. (2021). Formator: Predicting Lysine Formylation Sites Based on the Most Distant Undersampling and Safe-Level Synthetic Minority Oversampling. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(5), 1937-1945.
DOI Scopus19 WoS19 Europe PMC7 |
| 2021 |
Zhu, Y., Li, F., Xiang, D., Akutsu, T., Song, J., & Jia, C. (2021). Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks. Briefings in Bioinformatics, 22(4), 1-11.
DOI Scopus53 WoS56 Europe PMC35 |
| 2021 |
Xu, J., Li, F., Leier, A., Xiang, D., Shen, H. -H., Marquez Lago, T. T., . . . Song, J. (2021). Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides.. Briefings in Bioinformatics, 22(5), 1-22.
DOI Scopus112 WoS98 Europe PMC82 |
| 2021 |
Li, F., Guo, X., Jin, P., Chen, J., Xiang, D., Song, J., & Coin, L. J. M. (2021). Porpoise: a new approach for accurate prediction of RNA pseudouridine sites. Briefings in Bioinformatics, 22(6), 1-12.
DOI Scopus48 WoS46 Europe PMC37 |
| 2021 |
Chen, H., Li, F., Wang, L., Jin, Y., Chi, C. -H., Kurgan, L., . . . Shen, J. (2021). Systematic evaluation of machine learning methods for identifying human–pathogen protein–protein interactions. Briefings in Bioinformatics, 22(3), 1-21.
DOI Scopus39 WoS27 Europe PMC17 |
| 2021 |
Li, F., Chen, J., Ge, Z., Wen, Y., Yue, Y., Hayashida, M., . . . Song, J. (2021). Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework. Briefings in Bioinformatics, 22(2), 2126-2140.
DOI Scopus60 WoS61 Europe PMC49 |
| 2021 |
Ozols, M., Eckersley, A., Platt, C. I., Stewart-Mcguinness, C., Hibbert, S. A., Revote, J., . . . Sherratt, M. J. (2021). Predicting proteolysis in complex proteomes using deep learning. International Journal of Molecular Sciences, 22(6), 1-20.
DOI Scopus17 WoS14 Europe PMC11 |
| 2021 |
Chen, Z., Zhao, P., Li, C., Li, F., Xiang, D., Chen, Y. -Z., . . . Song, J. (2021). iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization. Nucleic Acids Research, 49(10), 1-19.
DOI Scopus207 WoS173 Europe PMC154 |
| 2021 |
Liang, X., Li, F., Chen, J., Li, J., Wu, H., Li, S., . . . Liu, Q. (2021). Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification. Briefings in bioinformatics, 22(4), 1-17.
DOI Scopus66 WoS61 Europe PMC44 |
| 2021 |
Li, M., Wang, Y., Li, F., Zhao, Y., Liu, M., Zhang, S., . . . Xia, J. (2021). A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction. IEEE/ACM transactions on computational biology and bioinformatics, 18(5), 1801-1810.
DOI Scopus51 WoS46 Europe PMC39 |
| 2021 |
Liu, Q., Chen, J., Wang, Y., Li, S., Jia, C., Song, J., & Li, F. (2021). DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites. Briefings in Bioinformatics, 22(3), 1-14.
DOI Scopus104 WoS95 Europe PMC67 |
| 2020 |
Li, F., Fan, C., Marquez-Lago, T. T., Leier, A., Revote, J., Jia, C., . . . Song, J. (2020). PRISMOID: A comprehensive 3D structure database for post-translational modifications and mutations with functional impact. Briefings in Bioinformatics, 21(3), 1069-1079.
DOI Scopus36 WoS34 Europe PMC28 |
| 2020 |
Li, F., Chen, J., Leier, A., Marquez-Lago, T., Liu, Q., Wang, Y., . . . Song, J. (2020). DeepCleave: A deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. Bioinformatics, 36(4), 1057-1065.
DOI Scopus107 WoS99 Europe PMC77 |
| 2020 |
Zhu, Y., Jia, C., Li, F., & Song, J. (2020). Inspector: a lysine succinylation predictor based on edited nearest-neighbor undersampling and adaptive synthetic oversampling. Analytical Biochemistry, 593, 1-10.
DOI Scopus59 WoS43 Europe PMC20 |
| 2020 |
Li, P., Zhang, H., Zhao, X., Jia, C., Li, F., & Song, J. (2020). Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins. Journal of Bioinformatics and Computational Biology, 18(2), 2050008.
DOI Scopus3 WoS3 Europe PMC3 |
| 2020 |
Li, F., Leier, A., Liu, Q., Wang, Y., Xiang, D., Akutsu, T., . . . Song, J. (2020). Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. Genomics, Proteomics and Bioinformatics, 18(1), 52-64.
DOI Scopus83 WoS71 Europe PMC80 |
| 2020 |
Chen, Z., Zhao, P., Li, F., Marquez-Lago, T. T., Leier, A., Revote, J., . . . Song, J. (2020). iLearn: An integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. Briefings in Bioinformatics, 21(3), 1047-1057.
DOI Scopus344 WoS319 Europe PMC238 |
| 2020 |
Chen, Z., Zhao, P., Li, F., Wang, Y., Smith, A. I., Webb, G. I., . . . Song, J. (2020). Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. Briefings in Bioinformatics, 21(5), 1676-1696.
DOI Scopus113 WoS106 Europe PMC87 |
| 2020 |
Bi, Y., Xiang, D., Ge, Z., Li, F., Jia, C., & Song, J. (2020). An Interpretable Prediction Model for Identifying N⁷-Methylguanosine Sites Based on XGBoost and SHAP. Molecular Therapy : Nucleic Acids, 22, 362-372.
DOI Scopus135 WoS125 Europe PMC67 |
| 2020 |
Jia, C., Bi, Y., Chen, J., Leier, A., Li, F., & Song, J. (2020). PASSION: An ensemble neural network approach for identifying the binding sites of RBPs on circRNAs. Bioinformatics, 36(15), 4276-4282.
DOI Scopus78 WoS75 Europe PMC50 |
| 2020 |
Ozols, M., Eckersley, A., Platt, C., McGuinness, C., Hibbert, S., Revote, J., . . . Sherratt, M. (2020). Predicting and validating protein degradation in proteomes using deep learning.
DOI |
| 2020 |
Chen, Z., Zhao, P., Li, F., Leier, A., Marquez-Lago, T. T., Webb, G. I., . . . Song, J. (2020). PROSPECT: A web server for predicting protein histidine phosphorylation sites. Journal of Bioinformatics and Computational Biology, 18(4), 2050018.
DOI Scopus26 WoS25 Europe PMC20 |
| 2019 |
Li, F., Wang, Y., Li, C., Marquez-Lago, T. T., Leier, A., Rawlings, N. D., . . . Song, J. (2019). Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: A comprehensive revisit and benchmarking of existing methods. Briefings in Bioinformatics, 20(6), 2150-2166.
DOI Scopus76 WoS73 Europe PMC52 |
| 2019 |
Chen, Z., Liu, X., Li, F., Li, C., Marquez-Lago, T., Leier, A., . . . Song, J. (2019). Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. Briefings in Bioinformatics, 20(6), 2267-2290.
DOI Scopus102 WoS96 Europe PMC78 |
| 2019 |
Wang, X., Li, C., Li, F., Sharma, V. S., Song, J., & Webb, G. I. (2019). SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models. BMC Bioinformatics, 20(1), 12 pages.
DOI Scopus14 WoS10 Europe PMC7 |
| 2019 |
Zhang, M., Li, F., Marquez-Lago, T. T., Leier, A., Fan, C., Kwoh, C. K., . . . Jia, C. (2019). MULTiPly: A novel multi-layer predictor for discovering general and specific types of promoters. Bioinformatics, 35(17), 2957-2965.
DOI Scopus110 WoS105 Europe PMC71 |
| 2019 |
Ma, X., Zhang, L., Song, J., Nguyen, E., Lee, R. S., Rodgers, S. J., . . . Daly, R. J. (2019). Characterization of the Src-regulated kinome identifies SGK1 as a key mediator of Src-induced transformation. Nature Communications, 10(1), 16 pages.
DOI Scopus24 WoS25 Europe PMC26 |
| 2019 |
Mei, S., Li, F., Leier, A., Marquez-Lago, T. T., Giam, K., Croft, N. P., . . . Song, J. (2019). A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. Briefings in Bioinformatics, 21(4), 1119-1135.
DOI Scopus131 WoS118 Europe PMC111 |
| 2019 |
Dunstan, R. A., Pickard, D., Dougan, S., Goulding, D., Cormie, C., Hardy, J., . . . Lithgow, T. (2019). The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre. Molecular Microbiology, 112(6), 1831-1846.
DOI Scopus26 WoS27 Europe PMC27 |
| 2019 |
Li, F., Zhang, Y., Purcell, A. W., Webb, G. I., Chou, K. C., Lithgow, T., . . . Song, J. (2019). Positive-unlabelled learning of glycosylation sites in the human proteome. BMC Bioinformatics, 20(1), 1-17.
DOI Scopus71 WoS66 Europe PMC37 |
| 2019 |
Song, J., Wang, Y., Li, F., Akutsu, T., Rawlings, N. D., Webb, G. I., & Chou, K. C. (2019). iProt-Sub: A comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. Briefings in Bioinformatics, 20(2), 638-658.
DOI Scopus174 WoS146 Europe PMC103 |
| 2018 |
Li, F., Li, C., Marquez-Lago, T. T., Leier, A., Akutsu, T., Purcell, A. W., . . . Chou, K. C. (2018). Quokka: A comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. Bioinformatics, 34(24), 4223-4231.
DOI Scopus150 WoS147 Europe PMC108 |
| 2018 |
Chen, Z., Zhao, P., Li, F., Leier, A., Marquez-Lago, T. T., Wang, Y., . . . Song, J. (2018). iFeature: A Python package and web server for features extraction and selection from protein and peptide sequences. Bioinformatics, 34(14), 2499-2502.
DOI Scopus567 WoS517 Europe PMC382 |
| 2018 |
Song, J., Li, F., Leier, A., Marquez-Lago, T. T., Akutsu, T., Haffari, G., . . . Pike, R. N. (2018). PROSPERous: High-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. Bioinformatics, 34(4), 684-687.
DOI Scopus128 WoS121 Europe PMC96 |
| 2018 |
Song, J., Li, F., Takemoto, K., Haffari, G., Akutsu, T., Chou, K. C., & Webb, G. I. (2018). PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework. Journal of Theoretical Biology, 443, 125-137.
DOI Scopus129 WoS120 Europe PMC79 |
| 2018 |
Wei, L., Hu, J., Li, F., Song, J., Su, R., & Zou, Q. (2018). Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms. Briefings in Bioinformatics, 21(1), 106-119.
DOI Scopus115 WoS106 Europe PMC65 |
| 2017 |
Li, F., Song, J., Li, C., Akutsu, T., & Zhang, Y. (2017). PAnDE: Averaged n-dependence estimators for positive unlabeled learning. ICIC Express Letters, Part B: Applications, 8(9), 1287-1297.
Scopus7 |
| 2016 |
Li, F., Li, C., Revote, J., Zhang, Y., Webb, G. I., Li, J., . . . Lithgow, T. (2016). GlycoMinestruct : A new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features. Scientific Reports, 6(1), 1-16.
DOI Scopus84 WoS78 Europe PMC54 |
| 2015 |
Li, F., Li, C., Wang, M., Webb, G. I., Zhang, Y., Whisstock, J. C., & Song, J. (2015). GlycoMine: A machine learning-based approach for predicting N-, C-and O-linked glycosylation in the human proteome. Bioinformatics, 31(9), 1411-1419.
DOI Scopus178 WoS160 Europe PMC130 |
| 2006 |
Chang, P. C., Chi, C. W., Chau, G. Y., Li, F. Y., Tsai, Y. H., Wu, J. C., & Lee, Y. H. W. (2006). DDX3, a DEAD box RNA helicase, is deregulated in hepatitis virus-associated hepatocellular carcinoma and is involved in cell growth control. ONCOGENE, 25(14), 1991-2003.
DOI WoS134 Europe PMC116 |
