Fuyi Li

Research Interests

Bioinformatics and computational biology Knowledge Representation and Machine Learning Machine learning Cancer Biology and Clinical Oncology Artificial Intelligence

Dr Fuyi Li

NHMRC Externally-Funded Research Fellow C

SAIGENCI

College of Health

Eligible to supervise Masters and PhD - email supervisor to discuss availability.

Dr Fuyi Li is the Group Leader of Artificial Intelligence for Biological Innovation (ABI Lab) in SAiGENCI. His lab focuses on developing Artificial Intelligence and Machine Learning approaches for cancer research. Dr Li finished his PhD in 2020 at Monash University under the supervision of Professor Jiangning Song and Professor Trevor Lithgow. He then joined the laboratory of Professor Lachlan Coin as a bioinformatics research fellow (Level B) at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne. With a strong background in machine learning and a profound understanding of bioinformatics, Dr Li has garnered recognition for his pioneering work in developing advanced data-driven bioinformatics algorithms and tools. His primary focus lies in tackling intricate biological challenges by harnessing the power of these innovative computational approaches. Dr Li's research interests are at the forefront of the rapidly evolving field of bioinformatics. His work centres on the development and application of cutting-edge machine-learning techniques to interpret vast and diverse biological datasets. These datasets encompass a wide spectrum of biological information, ranging from a wide range of biomolecules data, omics data and histopathology image data. He has developed over 40 bioinformatics software/webservers, and these tools have been used/downloaded in >80 countries, processing >1,200,000 calculation jobs.

I am motivated to investigate, develop, and deploy cutting-edge computational methodologies to better understand and address a range of open and challenging problems in bioinformatics. One of my key contributions is developing AI-driven approaches to study gene expression regulation. This program yielded 35 published bioinformatics approaches (1st-, co-1st, and corresponding author) that enhanced prediction and analysis of gene regulation across genomics, transcriptomics, and proteomics, covering genomic elements annotation to Biomacromolecular Covalent Modification prediction, including DNA modifications, RNA post- transcriptomic modifications, and protein post-translational modifications (PTMs). Among these, 12 papers were Clarivate Highly Cited and 2 were Hot Papers. The research cited and used my tools are from countries including the US, UK, Japan, China, etc., showing the global impacts.

My developed tools have enhanced both academic and industrial pursuits, particularly in refining biomarker identification. For instance:

- Procleave [PMID: 32413515] (1st author, FWCI 4.40, 88 citations, >60,000 job submissions) has impacted many fields including structural biology, microbiology, agriculture, and industry field. (i) Procleave identified cleavage sites for proteins linked to neurodegenerative diseases, such as TMEM106B, enhancing understanding of TMEM106B’s role in amyloid fibril formation and contributing to potential therapeutic targets exploration for these disorders [PMID: 35247328, Cell, research from the US]. (ii) In microbiology, Procleave predicted the Esp743 cleavage site on the Enterococcal surface protein, influencing biofilm formation and antimicrobial resistance studies [PMID: 36103556, PLOS Pathogens, research from the US]. (iii) In agricultural biotechnology, Procleave predicted the cleavage site for Mpf2Ba1 protein activation, crucial for forming pores in insect cells. This enhances Mpf2Ba1’s effectiveness against the western corn rootworm, improving pest control and crop protection [PMID: 37443175, Nat Commun., research from the UK]. (iv) Procleave also impacted neurological research by predicting caspase-3 cleavage sites in Collectin-12, informed studies on brain immunity and neurodegenerative diseases’ phagocytic activity [PMID: 36906641, Cell Death Dis., research from Sweden]. Moreover, (v) a US company was satisfied with Procleave’s capabilities and purchased a 1-year commercial license for two protease-specific models. This transaction underscores Procleave’s commercial viability and potential to impact novel therapeutic development.

- My other tools have also had broad impacts, i.e., DeepCleave [PMID: 31566664, Bioinformatics] (1st author, FWCI 8.47, ESI top 1%, 116 citations, > 48,000 job submissions) impacted proteomics, enhanced understanding of protein degradation linked to O-GlcNAc [PMID: 35705054, Cell Reports], and supported CD95L studies, a protein involved apoptosis signalling, aiding in identifying novel regulatory mechanisms [PMID: 36694998]. GlycoMine [PMID: 25568279, Bioinformatics] (1st author, FWCI 4.61, 189 citations, >76,000 job submissions) was used in the human surfaceome study to predict glycosylation sites, distinguishing surface from intracellular proteins, and aiding targeted drug development [PMID: 30373828, PNAS]. A Swiss company was satisfied with ProsperousPlus [PMID: 37874948] (1st author)'s capabilities and showed their great interest in purchasing the commercial license, currently negotiating.

Date Position Institution name
2023 - ongoing Group leader University of Adelaide
2020 - 2023 Bioinformatics Research Officer University of Melbourne

Language Competency
Chinese (Mandarin) Can read, write, speak, understand spoken and peer review
English Can read, write, speak, understand spoken and peer review

Year Citation
2026 Wang, X., Li, F., Gasser, R. B., & Song, J. (2026). A unified framework for multiomics deconvolution. Nature Methods, 23(3), 493-494.
DOI
2026 Gu, T., Ran, Z., Li, W., Guo, X., Li, B., Li, F., & Jia, C. (2026). Drug screening for α-synuclein aggregation inhibitors via multimodal graph neural network.. Brief Bioinform, 27(2), 11 pages.
DOI Scopus1 WoS1 Europe PMC1
2026 Xu, J., Li, C., Wang, X., Peleg, A. Y., Li, F., Song, J., & de la Fuente-Nunez, C. (2026). Artificial intelligence in antibiotic discovery: Applications, challenges, and future outlook. Cell Biomaterials, 2(8), 1-32.
DOI Scopus3
2026 Liu, Y., Zhang, Z., Qiu, M., Wang, S., Salim, F. D., Shen, J., . . . Bian, J. (2026). GatorSC: multi-scale cell and gene graphs with mixture-of-experts fusion for single-cell transcriptomics. Briefings in Bioinformatics, 27(3), bbag330-1-bbag330-14.
DOI
2026 Sun, Y., Wang, X., Jia, Y., Imoto, S., Li, F., Li, C., & Song, J. (2026). Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models. Briefings in Bioinformatics, 27(3), bbag329-1-bbag329-22.
DOI
2026 Hao, Y., Sun, H., Ran, Z., Guo, X., Liu, M., Bi, Y., . . . Li, F. (2026). Graph-based RNA structural representation reveals determinants of subcellular localization. Briefings in Bioinformatics, 27(3), bbag325-1-bbag325-15.
DOI
2026 Guo, X., Jia, R., Sun, H., Ran, Z., Liu, M., & Li, F. (2026). Language Model-Enhanced Geometric Learning for Metalloprotein Pathogenic Mutations. IEEE Journal of Biomedical and Health Informatics, PP, 1-14.
DOI
2026 Xu, L., Zhou, S., Ran, Z., Qin, X., Liu, T., Zou, Q., . . . Jia, C. (2026). PhaseOM: an integrated multi-task framework for phase separation analysis and key residue detection. Journal of Advanced Research, 1-44.
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 Scopus7 WoS4 Europe PMC5
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 Scopus7 WoS6 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 Scopus4 WoS4 Europe PMC4
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 Scopus13 WoS12 Europe PMC5
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), 1-12.
DOI Scopus2 WoS2 Europe PMC2
2025 Zhang, C., Pu, X., Teng, G., Li, F., Bai, H., Lin, K., . . . Tian, F. (2025). pH-Sensitive Metal–Organic Frameworks for the Improved Inhibition of HepG2 Cell via Folate Receptor-Mediated Targeting and Cascaded CDT Effect. Advanced Healthcare Materials, 15(11), e04093.
DOI Scopus11 WoS10 Europe PMC1
2025 Ran, Z., Guo, X., Pan, T., Bi, Y., Hao, Y., Sun, H., . . . Li, F. (2025). A scalable equivariant graph network framework for precise protein function prediction. Genome Biology, 26(1), 23 pages.
DOI Scopus4 WoS2 Europe PMC3
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 Scopus27 WoS12 Europe PMC9
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 Scopus34 WoS33
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 Scopus14 WoS11 Europe PMC12
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 Scopus24 WoS19 Europe PMC19
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 WoS2 Europe PMC1
2024 Sweeney, C. J., Bottoms, M., & Schulz, L. (2024). Soil-specific outcomes in the OECD 216 Nitrogen Transformation Test. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT, 25(6), 14 pages.
DOI Scopus17 WoS16 Europe PMC5
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 Scopus4 WoS4 Europe PMC3
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 Scopus15 WoS12 Europe PMC10
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 Scopus10 WoS10 Europe PMC5
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), bbae446.
DOI Scopus24 WoS17
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 Scopus1 WoS1 Europe PMC2
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 Scopus20 WoS15 Europe PMC13
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 Scopus7 WoS5 Europe PMC3
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 Scopus27 WoS27 Europe PMC17
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), bbae558.
DOI Europe PMC9
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 Scopus7 WoS6 Europe PMC3
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 Scopus11 WoS10 Europe PMC11
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 Scopus10 WoS7 Europe PMC5
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 Scopus108 WoS82 Europe PMC85
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 Scopus11 WoS10 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 Scopus22 WoS22 Europe PMC24
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 Scopus21 WoS21 Europe PMC20
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 Scopus16 WoS17 Europe PMC9
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 Scopus26 WoS21 Europe PMC16
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 Scopus35 WoS35 Europe PMC27
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 Scopus39 WoS36 Europe PMC38
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 Scopus31 WoS26 Europe PMC22
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 Scopus28 WoS25 Europe PMC26
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 Scopus17 WoS17 Europe PMC13
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 Scopus85 WoS79 Europe PMC83
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 Scopus18 WoS14 Europe PMC14
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 Scopus22 WoS20 Europe PMC17
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 Scopus8 WoS8 Europe PMC6
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 Scopus29 WoS27 Europe PMC19
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 Scopus23 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 Scopus20 WoS15 Europe PMC11
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 Scopus5 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 Scopus74 WoS61 Europe PMC49
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 Scopus43 WoS28 Europe PMC23
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 Scopus67 WoS66 Europe PMC55
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 Scopus24 WoS20 Europe PMC19
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 Scopus246 WoS218 Europe PMC206
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 Scopus77 WoS72 Europe PMC59
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 Scopus68 WoS61 Europe PMC56
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 Scopus113 WoS103 Europe PMC76
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 Scopus20 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 Scopus58 WoS59 Europe PMC45
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 Scopus57 WoS54 Europe PMC47
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 Scopus16 WoS22 Europe PMC11
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 Scopus140 WoS127 Europe PMC107
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 Scopus50 WoS52 Europe PMC44
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 Scopus22 WoS19 Europe PMC14
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 Scopus28 WoS28 Europe PMC26
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 Scopus28 WoS25 Europe PMC22
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 Scopus42 WoS40 Europe PMC41
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 Scopus164 WoS150 Europe PMC93
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 Scopus81 WoS78 Europe PMC61
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 Scopus122 WoS115 Europe PMC100
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 Scopus98 WoS39 Europe PMC97
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 Scopus372 WoS341 Europe PMC282
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 PMC32
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 Scopus123 WoS111 Europe PMC93
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 Scopus64 WoS48 Europe PMC27
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 Scopus4 WoS4 Europe PMC6
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 Scopus27 WoS26 Europe PMC22
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
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 Scopus74 WoS68 Europe PMC46
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 Scopus142 WoS130 Europe PMC129
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 Scopus29 WoS29 Europe PMC30
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 Scopus81 WoS77 Europe PMC63
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 Scopus106 WoS99 Europe PMC88
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 Scopus17 WoS13 Europe PMC11
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 Scopus114 WoS108 Europe PMC80
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 Scopus26 WoS26 Europe PMC29
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 Scopus177 WoS149 Europe PMC119
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 Scopus128 WoS117 Europe PMC81
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 Scopus154 WoS149 Europe PMC127
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 Scopus631 WoS571 Europe PMC465
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 Scopus134 WoS128 Europe PMC118
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 Scopus132 WoS122 Europe PMC99
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 Scopus86 WoS79 Europe PMC61
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 Scopus191 WoS170 Europe PMC154
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 WoS136 Europe PMC127
1998 Li, F. Y., & Zhang, Q. Z. (1998). Ordering contraction mapping principle and applications. ACTA MATHEMATICA SCIENTIA, 18(4), 457-460.
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- Sun, H., Guo, X., Hao, Y., Li, X., Li, W., Liu, M., & Li, F. (2024). PIONEER: A structure-informed graph neural network for PE/PPE protein identification. Computational Biomedicine.
DOI

Year Citation
2023 Chen, Z., Li, F., Wang, X., Wang, Y., Kurgan, L., & Song, J. (2023). Designing Effective Predictors of Protein Post-Translational Modifications Using iLearnPlus. In L. Kurgan (Ed.), Machine Learning in Bioinformatics of Protein Sequences: Algorithms, Databases and Resources for Modern Protein Bioinformatics (pp. 309-328). WORLD SCIENTIFIC.
DOI
2023 Guo, X., Li, F., & Song, J. (2023). Predicting Pseudouridine Sites with Porpoise. In Methods in Molecular Biology (Vol. 2624, pp. 139-151). Springer US.
DOI Scopus1 WoS1
2022 Chen, Z., Liu, X., Li, F., Li, C., Marquez-Lago, T., Leier, A., . . . Song, J. (2022). Systematic Characterization of Lysine Post-translational Modification Sites Using MUscADEL. In D. B. KC (Ed.), Computational Methods for Predicting Post-Translational
Modification Sites. Methods in Molecular Biology (Vol. 2499, pp. 205-219). Springer US.
DOI Scopus2 Europe PMC1

Year Citation
2025 Pan, J., Liu, Y., Zheng, X., Zheng, Y., Liew, A. W. C., Li, F., & Pan, S. (2025). A Label-Free Heterophily-Guided Approach for Unsupervised Graph Fraud Detection. In Proceedings of the 39th Annual AAAI Conference on Artificial Intelligence (AAAI-25) Vol. 39 (pp. 12443-12451). Philadelphia, Pennsylvania: Association for the Advancement of Artificial Intelligence (AAAI).
DOI Scopus38 WoS25
2024 Zhang, Z., Liu, Y., Bian, J., Yepes, A. J., Shen, J., Li, F., . . . Salim, F. D. (2024). Boosting Patient Representation Learning via Graph Contrastive Learning. In A. Bifet, T. Krilavicius, I. Miliou, & S. Nowaczyk (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) Vol. 14949 LNAI (pp. 335-350). LITHUANIA, Vilnius: SPRINGER INTERNATIONAL PUBLISHING AG.
DOI Scopus3 WoS2
2023 Liu, Y., Ding, K., Lu, Q., Li, F., Zhang, L. Y., & Pan, S. (2023). Towards Self-Interpretable Graph-Level Anomaly Detection. In Proceedings of the 37th Annual Conference on Neural Information Processing Systems (NeurIPS, 2023) ) as published in Advances in Neural Information Processing Systems Vol. 36 (pp. 1-13). Online: Neural information processing systems foundation.
Scopus93
2003 Cockburn, B., Li, F. Y., & Shu, C. W. (2003). Discontinuous Galerkin methods for equations with divergence-free solutions: preliminary results. In K. J. Bathe (Ed.), COMPUTATIONAL FLUID AND SOLID MECHANICS 2003, VOLS 1 AND 2, PROCEEDINGS (pp. 1900-1902). MA, MIT, CAMBRIDGE: ELSEVIER SCIENCE BV.

Year Citation
2026 Hao, Y., Sun, H., Ran, Z., Guo, X., Liu, M., Bi, Y., . . . Li, F. (2026). Graph-based RNA structural representation reveals determinants of subcellular localization.
DOI
2026 Liu, J., Pan, T., Guo, X., Ran, Z., Hao, Y., Yang, Y., . . . Li, F. (2026). MolX: A Geometric Foundation Model for Protein-Ligand Modelling.
DOI
2026 Xu, J., Torres, M. D. T., Li, C., Li, J., Li, F., Song, J., & de la Fuente-Nunez, C. (2026). Modification-aware AI enables terminal chemical modifications for peptide design and discovers potent antimicrobials..
DOI
2026 Shi, B., Liu, J., Pan, T., Hao, Y., Isbel, L., Roy, M., . . . Li, F. (2026). DesignMaster: A Multi-Conditional Diffusion Framework for Rational PROTAC Design.
DOI
2026 Li, F., He, X., Hao, Y., Guo, X., Wang, M., Shen, J., . . . Zhang, H. (2026). Measuring self-related behaviour in large language models.
DOI
2025 Liu, J., Roy, M., Isbel, L., & Li, F. (2025). Accurate PROTAC targeted degradation prediction with DegradeMaster.
DOI Europe PMC1
2025 Guo, X., Ran, Z., & Li, F. (2025). Kinase-Inhibitor Binding Affinity Prediction with Pretrained Graph Encoder and Language Model.
DOI
2025 Hao, Y., Guo, X., Ran, Z., Bi, Y., & Li, F. (2025). LncTracker: a unified multi-channel framework for multi-label lncRNA localization.
DOI
2025 Lv, B., Huang, X., Zhou, Q., Li, M., Xiao, X., & Li, F. (2025). Diet-Seg: Dynamic Hardness-Aware Learning for Enhanced Brain Tumor Segmentation.
DOI
2025 Jia, P., Liu, N., Ran, Z., Maiolo, S., Zhang, T., Mohenska, M., . . . Li, F. (2025). DOMINO: graph diffusion learning identifies spatial domain structures with enhanced accuracy and scalability.
DOI

Date Role Research Topic Program Degree Type Student Load Student Name
2026 Co-Supervisor Predicting drug resistance from chemical properties and gene/protein expression Doctor of Philosophy Doctorate Full Time Mr Rieley Peter Andrew West
2026 Principal Supervisor Comprehensively analysing molecular features of metabolic dysfunction-associated steatohepatitis-driven liver cancer Doctor of Philosophy Doctorate Full Time Miss Jingjing Gao
2025 Co-Supervisor To explore the possibility of using Artificial Intelligence models to answer questions about the immune system's fight against cancer Doctor of Philosophy Doctorate Full Time Mr Galen Raphael Pereira

Date Role Editorial Board Name Institution Country
2022 - ongoing Board Member BMC Bioinformatics Springer Nature United States
2020 - ongoing Board Member Frontiers in Bioinformatics Frontiers United States

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