Researcher

Associate Professor Fatemeh Vafaee

Keywords

Fields of Research (FoR)

Artificial intelligence, Systems biology, Bioinformatics and computational biology, Genomics and transcriptomics, Machine learning, Deep learning

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Biography

Professional Experience:

  • 2023 - Present: Associate Professor, School of Biotechnology and Biomolecular Sciences (BABS), UNSW Sydney
  • 2021 - Present: Deputy Director, UNSW Data Science Hub (uDASH), UNSW 
  • 2020 - Present: Theme Leader, Health Data Science, uDASH, UNSW
  • 2017 - 2022: Senior Lecturer, School of Biotechnology and Biomolecular Sciences (BABS), UNSW Sydney
  • 2013 - 2017: Research Fellow, Charles Perkins Centre, School of Mathematics and...view more

Professional Experience:

  • 2023 - Present: Associate Professor, School of Biotechnology and Biomolecular Sciences (BABS), UNSW Sydney
  • 2021 - Present: Deputy Director, UNSW Data Science Hub (uDASH), UNSW 
  • 2020 - Present: Theme Leader, Health Data Science, uDASH, UNSW
  • 2017 - 2022: Senior Lecturer, School of Biotechnology and Biomolecular Sciences (BABS), UNSW Sydney
  • 2013 - 2017: Research Fellow, Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney
  • 2011 - 2013: Postdoctoral Research Associate, University of Toronto, University Health Network and Ontario Cancer Institute
  • 2007 - 2011: PhD Computer Science, Artificial Intelligence (AI), the University of Illinois in Chicago

Brief Bio and Research Contribution:

Dr Vafaee is the Deputy Director of UNSW Data Science Hub (uDASH) since 2021 and an A/Professor in Computational Biomedicine and Bioinformatics at the School of BABS. She received her PhD in Artificial Intelligence from the School of Computer Science at the University of Illinois at Chicago, USA (2011) followed by 2 multidisciplinary postdoctoral fellowships on computational biomedicine at the University of Toronto, University Health Network (2011 – 2012), and at the University of Sydney, Charles Perkins Centre (2013 – 2017).

Dr Vafaee has launched (2017) and leads AI-enhanced Biomedicine Laboratory at UNSW (www.VafaeeLab.com), collaboratively working on deploying advanced AI techniques to address various pressing biomedical problems. Relying on multidisciplinary expertise and cross-faculty collaborations, Dr Vafaee and her team are developing advanced machine-learning methods and deep-learning models that leverage large omics data to find hidden structures within them, account for complex interactions among the measurements, integrate heterogeneous data and make accurate predictions in different biomedical applications ranging from multi-omics biomarker discovery to single-cell multi-omics and drug repositioning.

Dr Vafaee has a strong track record of multidisciplinary research leadership and industrial engagement. Her research has attracted >$12.3M for over 12 research projects and industrial partnership grants, including prestigious schemes of Cooperative Research Centre Project (CRC-P, 2019), Medical Research Future Fund (MRFF, 2020, 2021), ARC Discovery (2021), and NHMRC Development (2021), and Next-Generation Graduate Program, CSIRO/Data61 (2022). She has co-authored over 50 publications (68% first/corresponding author) in prestigious venues—e.g., Nucleic Acids Research (IF:19.160)*, Briefing in Bioinformatics x3 (IF:13.994)*, IEEE Trans on Cybernetics (IF:19.118)*, Bioinformatics (IF:6.931)*, Artificial Intelligence Review x2 (IF:9.588)*, IEEE Journal of Biomedical and Health Informatics (IF:7.021), Precision Oncology (IF:10.123), Cell & Bioscience (IF:9.597)*, Cancer Science (IF:6.716)*, Nature Methods (IF:47.990), Nature Communications (IF:17.694), Alzheimer’s & Dementia (IF:16.655); * indicates the corresponding authorship—demonstrating her research leadership and substantive contribution in methodological changes.


Governance and Executive memberships:


Editorial Activities:

  • Associate Editor of Artificial Intelligence Review, 2017 – Now (IF: 9.588, top 5% in AI), handled 180+ manuscripts.
  • Editorial Board of Journal of Cancers, 2021 – Now (IF: 6.639),
  • Advisory Board of Journal of Patterns, by Cell Press, 2021 – Now
  • Reviewer of multiple top-tier journals and grant agencies – e.g., Briefing in Bioinformatics (IF: 13:994), Bioinformatics (IF: 6.937), Cancers (IF: 6.639), Therapeutic Advances in Medical Oncology (IF: 8.168), Artificial Intelligence Review (IF: 9.588), IEEE Trans on Neural Networks & Learning Systems (IF: 14.26). I also review funding agencies, e.g., ARC (DP and DECRA).

Areas of Research Projects:

1) Minimally invasive biomarker discovery for personalised medicine and precision therapy: Recent advances in high-throughput technologies have provided a wealth of genomics, transcriptomics, and proteomics data to decipher disease mechanisms in a holistic and integrative manner. Such a plethora of -omics data has opened new avenues for translational medical research and has particularly facilitated the discovery of novel biomarkers for complex diseases such as cancers. My research lab – in close collaboration with experimentalists, clinicians, and oncologists – is adopting an innovative multi-disciplinary approach to tackle one of the biggest challenges of personalised cancer medicine, which is to identify robust and reproducible biomarkers in a minimally invasive way.  We are integrating multiple data sources, network and temporal information using advanced machine learning approaches to better understand the molecular complexity underpinning pathogenesis and to identify novel, precise and reproducible blood-based biomarkers for disease early detection, diagnosis, prognosis and drug responses, paving the way for personalised medicine.

Examples of publications: (Ebrahimkhani et al., Molecular Neurobiology, 2020), (Colvin et al. Cancer Science, 2020), (Vafaee et al., Systems Biology and Applications, 2018),  (Ebrahimkhani et al., Precision Oncology, 2018)

2) Single-cell sequencing data analysis and integration: Cellular heterogeneity is one of the main clinical drivers of the current inefficiency in treating cancer and other complex diseases as molecular-based prescriptions or personalised medicine have often relied on bulk pro/filing of cell populations, masking intercellular variations that are functionally and clinically important. In recent years, however, there has been an increasing effort to shift the focus from bulk to single-cell profiling. Single-cell sequencing will have a major global impact on precision medicine by detecting rare disease-associated cells and identifying cell-type-specific biomarkers and therapeutic targets. Single cells, however, make ‘big data’, provoking substantial analytical challenges to decipher underlying biological and clinical insights. Hence, there is an emerging demand for scalable yet accurate analysis pipelines for rapidly increasing single-cell sequencing data. 

Examples of publications: (Koch et al., Briefings in Bioinformatics, 2021), (Zandavi et al., NAR, doi.org/10.1093/nar/gkac436), (Zandavi et al., Artificial intelligence Review, doi: 10.1007/s10462-022-10357-4)

3) Computational drug repositioning and network pharmacology: Repositioning existing drugs for new indications is an innovative drug development strategy offering the possibility of reduced cost, time and risk as several phases of de-novo drug discovery can be bypassed for repositioning candidates. Biopharmaceutical companies have recognised the advantages of repositioning, and investment in the area is dramatically increasing. With the rapid advancement of high-throughput technologies and the explosion of various biological and medical data, computational drug repositioning has become an increasingly powerful approach to systematically identify potential repositioning candidates. My lab is the only group at UNSW, and one of the few across Australia, advancing the field of computational drug repositioning. We are developing computational tools and databases which integrate massive amounts of biological, pharmacological and biomedical information related to compounds into advanced machine learning or network-based models to predict accurate repositioning candidates.

Examples of publications: (Azad et al, Briefings in Bioinformatics, 2020), (Azad et al, Patterns, 2021)


My Grants

My research has attracted a total value of $12.3M (unapportioned) in research and industry-based competitive funding schemes as Chief Investigator and $1.1M as Associate Investigator (NHMRC Ideas, APP2012848). These include Category 1 grants in which I play major leadership roles (listed below). I have also led or contributed to securing > $400K from 8 UNSW seed funding schemes (2019 – 2022), not detailed here.

  • ARC Discovery (by Jai & Vafaee), DP220101938 (2022 – 2024, $575K, CIB), Role: Chief Investigator, Machine Learning and Bioinformatics Lead. Determining how small RNA sequences and structure defines function in bacteria. I lead the machine learning and system biology analyses of the study.
  • Next-Generation Graduate Program, CSIRO/Data61 (2023 – 2026, $1.7M, CIA), Role: Lead CI; leading a multidisciplinary team of 19 Investigators across 3 universities (UNSW, UTS, MQU) and 6 Industries (Metasense GenieUs, 23Strands, Trajan, Evidentli, Surround) to train a cohort of HDRs in AI-integrated BioMed technologies.
  • MRFF EPCDR Improving Diagnosis in Cancers with Low Survival Rates, APP2008996 (2021 – 2024, $4M, CIC), Role: Chief Investigator, Artificial Intelligence and Bioinformatics Lead; I am the main contributor to this multi-state, multi-institute interdisciplinary project and receive support for a postdoc and RA salary for four years. Title: Microbial-based biomarkers powered by AI for early detection of liver cancer in Australia.
  • MRFF Mental Health Pharmacogenomics, APP1200000 (2020 – 2023, $2.95M, CIJ). Role: Chief Investigator, Artificial Intelligence Lead; I lead the development of an AI model integrating clinical, pharmacogenomics, and neuroimaging data. Title: An Australian Multicentre Double-Blinded Randomised Controlled Trial of Genotype-guided versus Standard Psychotropic Therapy in Moderately-to-Severely Depressed Patients.
  • NHMRC Development Grant, APP2014538 (2020 – 2024, $564K, CIE). Role: Chief Investigator, Bioinformatics Lead; Title: Developing a novel blood test that accurately predicts response to checkpoint therapy.
  • Cooperative Research Centres Project, CRCPSIX000222 (2019 – 2022, $2.15M). Role: Chief Investigator, Artificial Intelligence Lead. Title: Smart Sensor and Deep Learning Behavioural Engine for Personalised Health Monitoring. This CRC-P project is in collaboration with Nutromics Pty Ltd and has a major AI component that I lead, i.e., developing models to predict an individual’s next dietary-relevant action and postprandial glucose level.
  • Mark Hughes Foundation Brain Cancer Innovation Project Grant, HMRI1151 (2019 – 2021, $150K; CIA), Role: Lead Investigator. Title: Combining artificial intelligence and genomics to non-invasively monitor glioblastoma patients and predict tumour recurrence. This project was in collaboration with UToronto, Canada.  
  • Vertex Innovation Fund (2018 – 2020, 157K Euro, equivalent to $250 AUD), Role: Key Investigator and Bioinformatics Lead. Title: Exosomal Biomarkers for Early Prediction of Cystic Fibrosis Related Diabetes

My Awards

  • 2021. Women in AI Australia and New Zealand Award Finalist: WAI recognises the most innovative women across the Australian and New Zealand AI communities. I was selected as one of the 3 women in the AI in Health category.
  • 2021. UNSW Academic Women in Leadership Program in recognition of strong leadership contributions.
  • 2020. Georgina Sweet Award for Women in Quantitative Biomedical Science Finalist. I ranked among the top 8% in this nationally competitive award primarily targeted at mid-career women in quantitative biomedicine who made substantial research impact and leadership contributions.
  • 2019. UNSW Science Visiting Research Fellowship ($6K)
  • 2019. Featured by the UNSW Faculty of Science Capability Statement in Health Science and UNSW Capability Statement in Biomedical Research for outstanding research in biomedical data science.
  • 2009. Grace Hopper Celebration of Women in Computing Award ($1K), National Science Foundation, USA

My Research Supervision


Supervision keywords


Areas of supervision

  • Bioinformatics and systems biology
  • AI and machine learning in disease diagnosis and precision medicine
  • Network pharmacology and computational drug repositioning
  • Single-cell sequencing data analysis

Currently supervising

  • Abir Kazaal (Primary Supervisor) co-supervision with Dr Emily Oates at the School of BABS, UNSW
  • Daniel Al Mouiee (Primary Supervisor) co-supervision with A/Prof Lois Holloway at Ingham Institute for Applied Medical Research
  • Fatemeh Safari (Primary Supervisor, Prospective) co-supervision with Dr Shafagh Waters at UNSW School of Biomedical Sciences
  • Mona Abedini  (Primary Supervisor, Prospective) co-supervision with Dr Hamid Rokny at UNSW School of Biomedical Engineering 
  • Daniel Martinez Formoso (Joint Supervisor) co-supervision with Dr Lindsay Wu at the School of Medical Science, UNSW
  • Jack Clarke (Secondary Supervisor) co-supervision with Dr Emily Wong at the School of BABS, UNSW

 

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Location

School of Biotechnology and Biomolecular Sciences
Room 2106
Level 2 West
Bioscience South E26

Contact

+61-2-9065 2699