phd biomedical science monash

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Jiangning Song

• Professor (Research) , Biochemistry & Molecular Biology
• Monash Biomedicine Discovery Institute
• Centre to Impact Antimicrobial Resistance
• Monash Data Futures Institute

Accepting PhD Students

PhD projects

Artificial Intelligence, Bioinformatics, Biomedical Big Data Analytics, Digital Health, Medical Imaging, Computational Biomedicine, Computational Oncology, Computer Vision, Deep Learning, Pattern Recognition

Research activity per year

Personal profile

Jiangning is a Professor and Group Leader in the Cancer and Infection and Immunity Programs in the  Monash Biomedicine Discovery Institute (BDI) , and Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia. Trained as a bioinformatician and data-savvy scientist, he has a very strong specialty in Artificial Intelligence, Bioinformatics, Comparative Genomics, Cancer Genomics, Bacterial Genomics, Computational Biomedicine, Data Mining, Infection and Immunity, Machine Learning, Proteomics, and Biomedical Big Data Analytics, which are highly sought-after expertise and skill sets in data-driven, paradigm-shifting biomedical research.

He is Head of the AI-driven Bioinformatics and Biomedicine Laboratory in the Monash BDI  and an Associate Investigator of the  ARC Centre of Excellence in Advanced Molecular Imaging . He is also a member of the Monash Data Futures Institute (MDFI), Alliance for Digital Health at Monash (ADAM) and Center to Impact Antimicrobial Resistance (AMR). His main research interests are bioinformatics, digital health, heterogeneous data modeling, machine learning, and data analytics in the fields of infection and immunity, cancer biology/pathology and pharmaco-informatics. He is currently an Associate Editor of five top-tier bioinformatics and computational medicine journals  IEEE Journal of Biomedical and Health Informatics,  BMC Bioinformatics,   Genomics, Proteomics & Bioinformatics , Frontiers in Bioinformatics, and  BMC Genomic Data . He has been recently invited to join the editorial team of Heliyon Bioinformatics and Computational Biology , a section in Heliyon , as an Associate Editor with a focus on Pharmaceutical Bioinformatics. He also serves as an Editorial Board member of Computers in Biology and Medicine ,  Biomolecules, Protein & Peptide Letters,  and The Innovation Life , and Advisory Board Member of  Current Protein & Peptide Science , Guest Editor of IEEE/ACM Transactions on Computational Biology and Bioinformatics,  Current Bioinformatics, Frontiers in Genetics, Frontiers in Developmental and Cell Biology,   BMC Genomics  and BMC Medical Genomics . He is the Program Committee (PC) member for more than 20 international conferences in the fields of bioinformatics, computational biology, and e-Science. He is the PC Co-Chair of the 30th International Conference on Genome Informatics (GIW) & Australian Bioinformatics and Computational Biology Society (ABACBS) Annual Conference, held in Sydney on 9-11 December 2019. He is also the PC Co-Chair of the 10th International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB) 2020, held in Kyoto, Japan during January 19-22, 2020. He is the Publicity Co-Chair of The IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2021 Houston, USA. He is a session chair and member of the Technical Committe of the 1st Asia & Pacific Bioinformatics Joint Conference  2024 (APBJC) in Okinawa, Japan.  He has an honorary position as Associate Professor at the Bioinformatics Center, Institute for Chemical Research and is an International Expert Committee member on Bioinformatics, the International Joint Usage/Research Center (iJURC), Kyoto University, Japan. He is also an Honorary Principal Fellow of the University of Melbourne. He joined Monash University's Centre to Impact AMR as a founding member in 2020 and chairs the bioinformatics and computational biomedicine group. He is developing the Centre’s AMR Big Data and AI-driven research capacity.

Jiangning is a PC member for more than 20 international conferences on bioinformatics, computational biology, health informatics, and e-Science, including BIBM, IEEE e-Science, InCoB, ISB, ICPB, ICIC, IIBM, and GIW. He is an invited reviewer for >60 journals (on average 50-80 reviews per year) in bioinformatics, computational biology, machine learning, data mining, systems biology, and chemoinformatics, including top-tier journals Nature Machine Intelligence , Nature Chemical Biology ,  Nature Communications , Nucleic Acids Res ,  Genome Biology ,  Briefings in Bioinformatics ,  Bioinformatics , iScience , Cell Reports Medicine, IEEE Journal of Biomedical and Health Informatics,  PLoS Comput Biol , Neurocomuting,   Pattern Recog, Neurocomputing, Mol Cell Proteomics ,  BMC Bioinformatics, IEEE/ACM Trans Comput Biol and Bioinform, and  J Chem Info Model .

As Chief Investigator, he has been awarded 35 grants (~$20.0M, 25 as CIA/CIB) by the US NIH, Australian MRFF/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, Kyoto University and The University of Tokyo). Remarkably, he secured a major five-year NIH R01 project (CIB, AI111965, US$4.56 million) with the program lead  Professor Jian Li  FAA FAHMS at Monash University 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 novel substrates of apoptotic caspases and limited proteolysis has been recognised and awarded three consecutive Collaborative Research grants by Kyoto University, Japan. More recently, he has been awarded an International Joint Research grant in collaboration with Prof Seiya Imoto by the Institute of Medical Science of the University of Tokyo (IMSUT) to conduct collaborative research in the frontier of interdisciplinary research in human genomic data analytics.

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 PROSPERous, iFeature, iFeatureOmega, iProt-Sub, Quokka, Muscadel, iLearn, iLearnPlus, Procleave, and DeepCleave. Many of these tools have been highlighted as useful bioinformatic tools and have been widely used by the international research community. The high impact of these tools signifies how biomedical knowledge discovery can indeed be alternatively catalysed by data-driven machine-learning techniques.

A career is a journey. Jiangning has received substantial training in the cutting-edge, cross-disciplinary bioinformatics, computational biomedicine, high-performance computing, mathematical modelling, machine learning, and biomedical big data analytics. Some of the challenges encountered are part of his fast-paced, continuous learning curve, as a function of incomplete knowledge in the new Era of ' Data Science and Analytics '.  Jiangning is always on the road to searching for new knowledge, just like  Monash University's motto  quotes - "Ancora Imparo" ("I am still learning").  He is seen as a 'rare bird' as he has been extremely fortunate to work with and have three ARC Australian Federation/Laureate Fellows  Prof Kevin Burrage  (The University of Queensland & University of Oxford),  Prof James Whisstock  (Monash), Prof Trevor Lithgow  (FAA, Monash), and Prof Geoff Webb (IEEE Fellow, Monash) as his collaborators and supervisors 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 caliber, expertise, and skillsets places him in a privileged position to tackle and address interdisciplinary research projects in the context of large-scale heterogeneous biomedical data analysis and modeling in the new era of Data Science and Analytics .

In his spare time, Jiangning enjoys his family time, 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 the following Monash featured stories that report on his team and collaborators' most-recent interdisciplinary research:

https://www.monash.edu/discovery-institute/news-and-events/news/2023-articles/developing-ai-to-help-identify-at-risk-bowel-cancer-patients

https://www.monash.edu/it/news/2023/boost-for-a-digital-health-revolution

https://www.monash.edu/data-futures-institute/news/mdfi-seed-grants-to-foster-international-partnerships-in-ai-for-good

https://www.monash.edu/data-futures-institute/research/mdfi-flagship-projects/ai-and-smart-drug-design-against-superbugs

https://www.monash.edu/impact-amr/case-studies-and-stories/antimicrobial-resistance-evolves-quickly,-and-we-need-to-be-prepared

https://www.monash.edu/medicine/news/latest/2020-articles/funding-for-fight-against-superbugs

https://www.monash.edu/discovery-institute/news-and-events/news/2019-articles/combating-superbugs-with-ai-and-big-data

https://www.monash.edu/medicine/discovery-institute/news-and-events/news/new-tool-to-speed-up-translation-of-genome-sequences

https://research.monash.edu/en/clippings/bioinformatics-tool-to-unearth-new-pointers-to-disease

University ranking: Monash University is one of Australia’s group of eight - the most research-intensive universities in the country - and consistently ranks among the world's top 50 universities ( US News  Best Global Universities Rankings: 35th;  QS World University Rankings: 37th; Times Higher Education World University Rankings: 44th; CWTS Leiden World: 49th; Academic Ranking of World Universities, i.e. ShanghaiRanking: 75th); Top 1 QS World University Rankings of Pharmacy & Pharmacology, Top 32th QS World University Rankings of Medicine. Monash has an international reputation for interdisciplinary research with an emphasis on global issues.

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

Supervision interests

Jiangning is a Monash University Ph.D. mentor/supervisor and examiner. He currently supervises 12 PhD students (6 as primary supervisor) in the areas of bioinformatics, computational biomedicine, medical imaging, machine learning, and multi-omics data analysis, as well as multimodal data modelling. He has supervised 8 PhD and 3 master students to successful completion to date at Monash University. He currently chairs the PhD review committee or sits on the panel for 6 Monash PhD students. Among his Ph.D. graduates, some received NHMRC CJ Martin Overseas Fellowships and others work as research leaders and staff members elsewhere. Approximately 70% of his graduate students work in the industry whereas 30% work in the academia.

Monash teaching commitment

BMS5022 Advanced Bioinformatics - teaching Bioinformatics and Aligning genomes and modelling

Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

External positions

MRFF – Genomics Health Futures Mission – Genomics Health Futures Grant Assessment Committee Member, National Health and Medical Research Council (NHMRC) (Australia)

9 Jan 2024 → 30 Jun 2024

Visiting Professor, University of Tokyo

Honorary Principal Fellow, University of Melbourne

20 Oct 2021 → 20 Jan 2025

Machine Learning Advisor and Scientific Advisory Board Member, GenieUs Genomics Pty Limited

1 Oct 2021 → …

International Expert Committee Member on Bioinformatics, the international Joint Usage/Research Center (iJURC), Kyoto University

1 Jan 2021 → 31 Mar 2026

Honorary Professor, Kyoto University

1 Jan 2021 → 31 Dec 2025

Research area keywords

• Artificial intelligence
• Bioinformatics
• Computer science
• Computational medicine
• Digital oncology
• Computer vision, image and signal processing
• Machine learning
• Big Data Analytics
• From Genotype to Phenotype
• Health Informatics
• Functional genomics
• Sequence analysis
• Infectious diseases
• Multimodal data
• Chemoinformatics
• Single-cell data analysis
• Structural biology
• Antimicrobial resistance
• Bioinformatics software
• Software engineering
• Feature engineering
• Multi-variable data modeling
• Heterogeneous data analysis
• Computational pipeline
• Data-driven knowledge discovery
• Host-pathogen interaction
• High-throughput screening
• Protein post-translational modification
• Pattern recognition

Collaborations and top research areas from the last five years

Dive into details.

Select a country/territory to view shared publications and projects

• 1 Not started
• 19 Finished

Projects per year

Artificial intelligence to explore and combat eukaryotic pathogens

Gasser, R. B., Song, J. & Chang, B. C. H.

Australian Research Council (ARC)

1/07/23 → …

Project : Research

Development of a precision oncology program focused on a novel therapeutic target in triple negative breast cancer

Daly, R. , Chueh, A. , Abud, H. , Jarde, T. , Loi, S., Tiganis, T. , Swarbrick, A., Rosenbluh, S. , Nguyen, L. , Song, J. & Nekkalapudi, N.

National Breast Cancer Foundation

1/01/23 → 31/12/25

Improvement of school indoor air quality and children's health

Guo, Y. , Li, S. , Abramson, M. , Dharmage, S. C., Carroll, M. , Berger, E. , Gao, C. , Song, J. , Chang, V. & Zhou, J.

1/08/22 → 31/07/25

AIpathology: Artificial intelligence-enabled cancer diagnosis, type classification and mutation prediction

Song, J. , Liò, P., Imoto, S., Zhang, D. & Boussioutas, A.

1/07/22 → 30/06/25

Genomics, Digital Health and Machine Learning: the SuperbugAi Flagship

Peleg, A. , Holt, K. , Song, J. , Macesic, N. , Ananda-Rajah, M., Webb, G. , Korman, T. , Stuart, R. , Cheng, A. , Peel, T. , Stewardson, A. , Ayton, D. & Bain, C.

2/01/21 → 7/12/24

Research output

• 262 Article
• 17 Conference Paper
• 12 Review Article
• 7 Chapter (Book)
• 4 Editorial
• 3 Comment / Debate
• 1 Other contribution

Research output per year

Ambient fine particulate matter and daily mortality: A comparative analysis of observed and estimated exposure in 347 cities

Research output : Contribution to journal › Article › Research › peer-review

AutoCancer as an automated multimodal framework for early cancer detection

'bingo'-a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data: bingo, blam6a-merge: leveraging attention mechanisms and feature fusion strategies to improve the identification of rna n6-methyladenosine sites, complete spatially resolved gene expression is not necessary for identifying spatial domains, biomedicine discovery fellowship (monash university).

Song, Jiangning (Recipient), 2018

Prize : Prize (including medals and awards)

Exceptional Achievement Award, Faculty of Medicine, Nursing and Health Sciences (Monash University)

Song, Jiangning (Recipient), 4 Mar 2022

Frontier and Interdisciplinary Research Award, the International Joint Usage/Research Center (iJURC, Kyoto University)

Song, Jiangning (Recipient), 2021

IMSUT International Joint Research Award (The University of Tokyo)

Song, Jiangning (Recipient), 2022

Japan Society for the Promotion of Science Invitational Fellowship

Prize : Competitive Fellowships

Press/Media

Mdfi seed grants to foster international partnerships in ai for good.

1 Media contribution

Press/Media : Public Engagement Activities

Combating superbugs with AI and big data

Press/Media : Article/Feature

AI tool to boost genomic data analysis

Jiangning Song , Roger Daly & Jian Li

Press/Media : Research

Bioinformatics tool to unearth new pointers to disease

Jiangning Song , Roger John Daly & Fuyi Li

New computational tool to defend against the molecular weapons of ‘superbugs’

Jiawei Wang, Jiangning Song & Trevor James Lithgow

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Area of Study: Biomedical science - 2018

Undergraduate specialisation

• Biomedical science - Medicine, Nursing and Health Sciences

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Postgraduate specialisation

• Health Care
• Medical Studies

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1 PhD Degrees in Health Care Medical Studies Medicine in Novosibirsk, Russia for 2024/2025

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M3702 - Bachelor of Biomedical Science (Honours)