| 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 PMC2 |
| 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 |
| 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 Scopus6 WoS7 Europe PMC4 |
| 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 Scopus10 WoS6 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 Scopus7 WoS4 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 Scopus8 WoS5 |
| 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 Scopus14 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 Scopus18 WoS15 |
| 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 WoS14 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 Scopus18 WoS12 Europe PMC11 |
| 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 Scopus13 WoS14 Europe PMC12 |
| 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 Scopus16 WoS17 Europe PMC16 |
| 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 PMC16 |
| 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 Scopus59 WoS44 Europe PMC44 |
| 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 Scopus7 WoS6 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 Scopus25 WoS22 Europe PMC18 |
| 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 WoS18 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 WoS12 Europe PMC10 |
| 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 WoS31 Europe PMC28 |
| 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 Scopus57 WoS52 Europe PMC47 |
| 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 WoS76 |
| 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 WoS15 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 Scopus24 WoS22 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 WoS14 Europe PMC18 |
| 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 Scopus59 WoS52 Europe PMC44 |
| 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 Scopus36 WoS36 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 PMC19 |
| 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 Scopus46 WoS43 Europe PMC41 |
| 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 WoS55 Europe PMC34 |
| 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 Scopus108 WoS94 Europe PMC80 |
| 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 PMC36 |
| 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 PMC48 |
| 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 WoS13 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 Scopus199 WoS168 Europe PMC150 |
| 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 Scopus64 WoS60 Europe PMC42 |
| 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 Scopus48 WoS44 Europe PMC36 |
| 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 Scopus103 WoS94 Europe PMC66 |
| 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 Scopus35 WoS33 Europe PMC25 |
| 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 WoS98 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 Scopus58 WoS42 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 Scopus2 WoS2 Europe PMC2 |
| 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 Scopus79 WoS69 Europe PMC78 |
| 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 Scopus341 WoS317 Europe PMC230 |
| 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 PMC83 |
| 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 PMC66 |
| 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 WoS74 Europe PMC46 |
| 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 Scopus25 WoS24 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 Scopus75 WoS71 Europe PMC50 |
| 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 Scopus101 WoS95 Europe PMC76 |
| 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 Scopus107 WoS103 Europe PMC67 |
| 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 PMC25 |
| 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 PMC107 |
| 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 Scopus70 WoS65 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 Scopus170 WoS144 Europe PMC102 |
| 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 WoS144 Europe PMC105 |
| 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 Scopus562 WoS508 Europe PMC371 |
| 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 Scopus126 WoS119 Europe PMC95 |
| 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 Scopus127 WoS119 Europe PMC77 |
| 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.
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| 2017 |
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