Fuyi Li

Dr Fuyi Li

Group Leader, Computational Systems Oncology

South Australian Immunogenomics Cancer Institute

Faculty of Health and Medical Sciences

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

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 most important contributions to the field is that I have developed versatile bioinformatics techniques and tools to further our understanding of the sequence-structure-function relationship of Biomacromolecular Covalent Modifications (BCMs), which include post-translational modifications (PTMs) and nucleic acid (DNA/RNA) modifications. To date, I have developed 20+ bioinformatics toolkits, web servers, and databases to serve the wider research community for BCMs (the first, co-first, and corresponding author papers), including GlycoMine (PMID: 25568279), GlycoMineStruct (PMID: 27708373), Quokka (PMID: 29947803), PROSPERous (PMID: 29069280), PRISMOID (PMID: 31161204), GlycoMine-PU (PMID: 30841845), DeepCleave (PMID: 31566664), Formator (PMID: 31804942), Inspector (PMID: 31968210), Procleave (PMID: 32413515), DeepTorrent (PMID: 32608476), XG-m7G (PMID: 33230441), and Porpoise (PMID: 34226915). These developed bioinformatics algorithms, approaches and resources span multiple BCMs: kinase-specific phosphorylation, protein glycosylation, protease-specific substrate cleavage, DNA N4-methylcytosine sites, and RNA pseudouridine sites. Many of these tools have been highlighted as useful bioinformatic tools and have been widely used by the international research community. Particularly, Quokka (PMID: 29947803) and DeepCleave (PMID: 31566664) (both are published on Bioinformatics) have been selected as Clarivate Highly cited papers. In addition, I have also developed bioinformatics algorithms and tools for other bioinformatics sequence analysis problems (the first, co-first and corresponding author papers), such as MULTiPly (PMID: 30649179), SELECTOR (PMID: 32363397), and Depicter (PMID: 33227813) for promoter identification, Anthem (PMID: 33454737) for peptides and HLA class I molecules binding prediction, ACPredStackL (PMID: 33316035) for anti-cancer peptide identification, and PASSION (PMID: 32426818) for protein-circular RNA binding sites prediction. Altogether, these research outputs are published in top-tier bioinformatics journals such as Bioinformatics and Briefings in Bioinformatics, and these bioinformatics resources have attracted more than 260,000 job submissions and data enquires (more than 25,000+ users) from >80 countries worldwide and more than 2300 citations. Unique users (identified using job submissions based on their email address and IP address) include academic staff, research fellows, and graduate students from world-class universities. I have a keen interest in developing bioinformatic resources that can help biologists understand the functional mechanisms of biological problems and generate biological hypotheses for biological validation. For example, my developed tool GlycoMine has recently helped scientists to predict the novel potential C-, N-, and O-linked glycosylation sites and help human surfaceome analysis (PMID: 30373828).

  • Editorial Boards

    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
  • Position: Group Leader, Computational Systems Oncology
  • Phone: 83133424
  • Email: fuyi.li@adelaide.edu.au
  • Campus: West End Health Precinct
  • Building: AHMS - Adelaide Health and Medical Sciences, floor Ninth Floor
  • Room: 9055
  • Org Unit: South Australian Immunogenomics Cancer Institute

Connect With Me
External Profiles