Personal profile


Jiangning is a Senior Research Fellow and Group Leader in the Cancer and Infection and Immunity Programs in the Biomedicine Discovery Institute (BDI) and Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University. He was recruited from Kyoto University Japan to undertake a four-year NHMRC Peter Doherty Biomedical Training Fellowship with his supervisor ARC Federation Fellow Prof James Whisstock in 2008 and since then has been working at Monash University for ten years.


He is an Associate Investigator (AI) of the ARC Centre of Excellence in Advanced Molecular Imaging at Monash University. He is also a member of the Monash Centre for Data Science and the Monash Bioinformatics Platform. His main research interests are bioinformatics, heterogeneous data modelling, machine learning, and data analytics in the areas of infection and immunity, and cancer biology. Jiangning is currently an Academic Editor of BMC Bioinformatics (one of the three top-tier journals in Bioinformatics), an Advisory Board Member of Current Protein & Peptide Science, and a Guest Editor of Current Bioinformatics and BioMed Res International.


Jiangning is a recipient of the prestigious NHMRC Peter Doherty Fellowship (undertaken at Monash University), both Long-term and Short-term JSPS Postdoctoral Fellowships (undertaken at Kyoto University, Japan), Hundred Talents Professorship of the Chinese Academy of Sciences (CAS), the Nomination Award of the National Excellent Doctoral Dissertation in China, the Excellent Doctoral Dissertation Award of Jiangsu Province, and the Postgraduate Research Innovation Award of Jiangsu Province, China. He is a Program Committee (PC) member for more than 20 international conferences on Bioinformatics, Computational Biology, and Systems Biology, including BIBM, IEEE e-Science, InCoB, ISB, ICPB, ICIC, IIBM, and GIW. He is an invited reviewer for >50 journals (on average 50 reviews per year) in bioinformatics, computational biology, systems biology, and chemoinformatics, including top-tier journals Briefings in BioinformaticsBioinformaticsNucleic Acids ResPLoS Comput Biol, J Theor Biol, Pattern Recog, Mol Cell ProteomicsBMC Bioinformatics, J Comput Chem, and BMC Syst Biol.


He has published a career total of 150+ scientific articles, 7 reviews, 4 editorials, and 4 book chapters in the field of bioinformatics and computational biology. Remarkably, he is one of the very few Australian bioinformaticians that have published more than 20 research papers to date in both top-tier journals Briefings in Bioinformatics and Bioinformatics (10+ papers in each journal). According to Google Scholar, his publications have received a total of ~2000 citations with an H-index of 24 and i10-index of 50.  Since 2007, he has been awarded 28 grants ($10.8M, 19 as CIA/CIB) by the US NIH, Australian NHMRC/ARC, and other granting bodies (e.g. the Japan Society for the Promotion of Science [JSPS], the Ministry of Science and Technology of  China [MOST], the Chinese Academy of Sciences [CAS] and the National Natural Science Foundation of China [NSFC], Monash University, and Kyoto University). In particular, in 2014, he secured a major five-year NIH R01 project (CIB, AI111965, US$4.56 million) with the program lead Professor Jian Li at Monash and other US collaborators to develop cutting-edge systems pharmacology approaches for predicting and validating antibiotic/small-molecule non-antibiotic combinations for new targeted therapies for treating life-threatening infections caused by antibiotic-resistant bacterial 'superbugs'. His recent work with Prof. Tatsuya Akutsu at Kyoto University on developing novel bioinformatic algorithms for identifying substrates of apoptotic caspases has been recognised and awarded a Collaborative Research grant by Kyoto University Japan.


Jiangning is motivated to investigate, develop and deploy cutting-edge bioinformatics methodologies to better understand and address a range of open and challenging problems in genomics, molecular biology and systems biology. To date, he and his team members have developed 60+ bioinformatics toolkits/webservers/software to serve the wider research community, including CISPEP, Disulfide, Cascleave, Cascleave 2.0, APIS, PRORATE, Pred-PFR, Prodepth, PROSPER, SSPKA, hCKSAAP_UbSite, PredPPCrys, Crysalis, Crysf, DephosSite, Periscope, GlycoMine, GlycoMinestruct, SecretEPDB, ProtVecDMPROSPERous, Bastion4, Bastion6, Bastion3, PhosphoPredict, PhosContext2Vec, POSSUM, iFeature, iProt-SubQuokka, SIMLIN, Muscadel, RNATargetsite, iFeature-in-One, Deep-S2D, and DeepCleave. Many of these tools have been highlighted as useful bioinformatic tools and have been widely used by the international research community.


For instance, PROSPER (, a bioinformatic tool for predicting target substrates and their specific cleavage sites for 23 proteases, delivered as a representative outcome of the support of the NHMRC Program Grant on Protease Systems Biology headed by Prof. James Whisstock at Monash University), has attracted more than 30,000 unique users worldwide and processed >80,000 job submissions since its inception in the end of 2012. The PROSPER paper has been highlighted as among the top 10% most cited PLoS ONE articles in 2017 (being cited ~100 times to date). This tool, together with Cascleave (, a bioinformatic tool for predicting substrates of cell apoptosis caspases, enzymes that play essential roles in programmed cell death and inflammation), has been highlighted as two powerful bioinformatic tools by the International Proteolysis Society (IPS). An ultrafast and high-throughput tool PROSPERous has been recently published in Bioinformatics for predicting the target substrates and cleavage sites for 90 different proteases and can be freely accessible at The high impact of these tools signifies how biomedical knowledge discovery can indeed be alternatively catalysed by data-driven computational techniques.


A career is a journey.  Some of the challenges encountered are part of his fast-paced, continuous learning curve, as a function of an incomplete knowledge in the 'biomedical big data' era.  Jiangning is always on the road to search for new knowledge, just like Monash University's motto says - "Ancora Imparo" ("I am still learning").  He is seen as a 'rare bird' as he holds both Doctor of Engineering degree in bioengineering and Doctor of Philosophy degree in computer science, and has been extremely fortunate to work with and have three ARC Australian Federation/Laureate Fellows Prof Kevin Burrage (University of Queensland & University of Oxford, now at Queensland University of Technology), Prof James Whisstock (Monash) and Prof Trevor Lithgow (FAA, Monash), Prof Tatsuya Akutsu (Kyoto University, Japan) and ARC DORA & IEEE Fellow Prof Geoff Webb (Monash) as his supervisors and mentors throughout his academic career. Down the track along the journey, he has received substantial training in fermentation engineering, applied microbiology, protein engineering, applied mathematics, high-performance computing, computer science, statistics, bioinformatics, algorithms, structural biology, machine learning, data mining and integrative systems biology. Such a rare but critical 'blend' of calibre, expertise and skill sets places him in a privileged position to tackle and address inter-disciplinary research projects involving large-scale heterogeneous biomedical data analysis and modelling.


In his spare time, Jiangning enjoys his family time with his two adorable daughters Evelyn and Eleanor, watching movies, listening to music, and indulging himself in meandering the villages and discovering the heart of the beautiful Dandenong Ranges and Mornington Peninsula.


If you are interested in his research, you might want to read this most-recent Monash BDI featured story that reports on his team's bioinformatics research:


If you would like to find out more about his research or inquire about potential collaboration opportunities, please contact  Prospective postgraduate students in Australia or overseas who wish to pursue a PhD career path with Jiangning at Monash University are also welcome to contact.


  • Bioinformatics
  • Computational biology
  • Computer science
  • Machine learning
  • Pattern Recognition
  • Multi-variable data modeling
  • Data analytics
  • Cancer genome
  • From Genotype to Phenotype
  • Functional genomics
  • Infection and Immunity
  • Host-pathogen interaction
  • Sequence analysis
  • Feature engineering
  • Structural biology
  • Protein post-translational modification
  • Heterogeneous data analysis
  • High-throughput screening
  • Network biology
  • Data-driven knowledge discovery
  • Knowledge base
  • Bioinformatics software

Network Recent external collaboration on country level. Dive into details by clicking on the dots.

Projects 2007 2023

Research Output 2004 2018

ACPred-FL: A sequence-based predictor based on effective feature representation to improve the prediction of anti-cancer peptides

Wei, L., Zhou, C., Chen, H., Song, J. & Su, R. 1 Jun 2018 (Accepted/In press) In : Bioinformatics. 9 p.

Research output: Contribution to journalArticle

Open Access

Bastion6: A bioinformatics approach for accurate prediction of type VI secreted effectors

Wang, J., Yang, B., Leier, A., Marquez-Lago, T., Hayashida, M., Rocker, A., Zhang, Y., Akutsu, T., Chou, K-C., Strugnell, R. A., Song, J. & Lithgow, T. 2018 (Accepted/In press) In : Bioinformatics. 8 p.

Research output: Contribution to journalArticle

Characteristic and mechanism of immobilization effect of Staphylococcus aureus on human spermatozoa

Li, J., Li, B., Song, J., Liu, H., Bi, W., Dong, G. & Zhou, T. 1 Jun 2018 In : Microbial Pathogenesis. 119, p. 28-34 7 p.

Research output: Contribution to journalArticle

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI

An, Y., Wang, J., Li, C., Leier, A., Marquez-Lago, T., Wilksch, J., Zhang, Y., Webb, G. I., Song, J. & Lithgow, T. 1 Jan 2018 In : Briefings in Bioinformatics. 19, 1, p. 148-161 14 p., bbw100

Research output: Contribution to journalArticle


Award of Excellent Doctoral Dissertation of Jiangsu Province, China

Jiangning Song (Recipient), 6 Jul 2006

Prize: National/international honour

Hundred Talents Program of the Chinese Academy of Sciences

Jiangning Song (Recipient), 10 Jan 2009

Prize: Competitive Fellowships

JSPS Long-term Postdoctoral Fellowship for Foreign Researchers

Jiangning Song (Recipient), 1 Oct 2007

Prize: Competitive Fellowships

JSPS Short-term Invitation Fellowship

Jiangning Song (Recipient), 1 Dec 2011

Prize: Competitive Fellowships

NHMRC Peter Doherty Biomedical Fellowship

Jiangning Song (Recipient), 1 Jul 2008

Prize: Competitive Fellowships