| 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 |
| 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 Scopus2 |
| 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 Scopus2 Europe PMC1 |
| 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 |
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 Scopus3 |
| 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), 5649-5657.
DOI Scopus1 |
| 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 Scopus2 Europe PMC1 |
| 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 Scopus1 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 |
| 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 Scopus2 Europe PMC2 |
| 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), 2340-2348.
DOI |
| 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 Scopus10 Europe PMC2 |
| 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 Scopus7 |
| 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 Scopus8 Europe PMC6 |
| 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 Scopus7 Europe PMC3 |
| 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 |
| 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 Scopus5 WoS3 Europe PMC4 |
| 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 Scopus15 WoS4 Europe PMC9 |
| 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 Scopus15 WoS1 Europe PMC10 |
| 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 Scopus6 Europe PMC2 |
| 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 Scopus44 WoS2 Europe PMC25 |
| 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), 12 pages.
DOI Scopus6 Europe PMC3 |
| 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 WoS1 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 Europe PMC8 |
| 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 Scopus13 Europe PMC7 |
| 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 Scopus7 Europe PMC4 |
| 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 Scopus21 WoS11 Europe PMC11 |
| 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 Scopus19 WoS4 Europe PMC10 |
| 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 Scopus10 WoS2 Europe PMC5 |
| 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 Scopus31 WoS9 Europe PMC22 |
| 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 Scopus46 WoS12 Europe PMC30 |
| 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 Scopus9 WoS4 Europe PMC6 |
| 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 Scopus19 WoS2 Europe PMC8 |
| 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 Scopus5 WoS1 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 Scopus22 WoS8 Europe PMC15 |
| 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 WoS3 Europe PMC14 |
| 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 Scopus12 WoS3 Europe PMC7 |
| 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 Scopus2 |
| 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 Scopus46 WoS16 Europe PMC36 |
| 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 Scopus35 WoS17 Europe PMC32 |
| 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, 37(22), 4291-4295.
DOI Scopus24 WoS14 Europe PMC13 |
| 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 WoS9 Europe PMC9 |
| 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 Scopus24 WoS14 Europe PMC17 |
| 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 Scopus12 WoS7 Europe PMC7 |
| 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 Scopus41 WoS23 Europe PMC26 |
| 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 Scopus18 WoS16 Europe PMC4 |
| 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 Scopus50 WoS38 Europe PMC31 |
| 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 Scopus93 WoS32 Europe PMC62 |
| 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 Scopus47 WoS31 Europe PMC28 |
| 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 Scopus38 WoS20 Europe PMC11 |
| 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 WoS46 Europe PMC37 |
| 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 Scopus16 WoS7 Europe PMC7 |
| 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 Scopus183 WoS72 Europe PMC116 |
| 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 Scopus61 WoS32 Europe PMC28 |
| 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 Scopus44 WoS23 Europe PMC27 |
| 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 Scopus100 WoS66 Europe PMC48 |
| 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 Scopus34 WoS27 Europe PMC22 |
| 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 Scopus104 WoS81 Europe PMC55 |
| 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 Scopus51 WoS27 Europe PMC11 |
| 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 Scopus1 WoS1 |
| 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 Scopus75 WoS47 Europe PMC64 |
| 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 Scopus329 WoS228 Europe PMC171 |
| 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 Scopus106 WoS70 Europe PMC72 |
| 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 Scopus126 WoS74 Europe PMC51 |
| 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 Scopus74 WoS42 Europe PMC33 |
| 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 WoS13 Europe PMC16 |
| 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 Scopus69 WoS57 Europe PMC38 |
| 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 Scopus93 WoS68 Europe PMC53 |
| 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 Scopus13 WoS9 Europe PMC5 |
| 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 Scopus105 WoS85 Europe PMC57 |
| 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 WoS21 Europe PMC24 |
| 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 Scopus116 WoS76 Europe PMC84 |
| 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 Scopus25 WoS17 Europe PMC22 |
| 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 Scopus68 WoS58 Europe PMC30 |
| 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 Scopus167 WoS142 Europe PMC82 |
| 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 Scopus145 WoS117 Europe PMC75 |
| 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 Scopus529 WoS351 Europe PMC272 |
| 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 Scopus122 WoS106 Europe PMC70 |
| 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 Scopus122 WoS104 Europe PMC51 |
| 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 Scopus109 WoS87 Europe PMC48 |
| 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 Scopus82 WoS65 Europe PMC47 |
| 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 Scopus172 WoS133 Europe PMC105 |
