Dr Vijini Mallawaarachchi
Research Fellow in Bioinformatics
College of Science and Engineering
Vijini is a Research Fellow in Bioinformatics at the Flinders Accelerator for Microbiome Exploration (FAME), where she works at the intersection of computer science and microbial genomics. Her research spans data science, algorithms, artificial intelligence, machine learning, software engineering, genomics, metagenomics and bacteriophages, with a focus on developing innovative computational approaches to tackle some of the most challenging problems in microbial omics.
Vijini completed her PhD in Computer Science at the Australian National University in 2022, where her thesis focused on developing models and algorithms for improved binning of complex environmental sequencing (metagenomic) data. She is experienced in algorithm design, graph theory, graph machine learning, representation learning, combinatorial optimisation, large-scale data analysis and software development. She has developed several metagenomic analysis tools that leverage sequence assembly graphs to recover and characterise microbial genomes from metagenomes. Currently, her research at FAME focuses on developing algorithmic and machine/deep learning methods to recover and characterise viral genomes from metagenomes, enabling the discovery of novel viruses that infect bacteria called bacteriophages, and the study of their properties.
Research Interests
- Bioinformatics / Computational Biology
- Metagenomics and Microbial Genome Reconstruction
- Graph Algorithms and Network Analysis
- Machine Learning on Graphs and Sequence Data
- Scientific Data Visualization and Web-Based Analytics
- Scientific Software Engineering
Doctor of Philosophy (Computer Science)
The Australian National University, Canberra, Australia
2018 - 2022
Bachelor of Science in Computer Science and Engineering (Honours)
University of Moratuwa, Sri Lanka
2014 - 2018
Grants (Total competitive funding: > A$ 2.5M)
National Computational Merit Allocation Scheme 2026 Supercomputing Grant; "Combining metagenomics and AI to discover and understand novel bacteriophages and viruses"; 15.9 million service units (worth A$636,000); Co-CI; Jan - Dec 2026.
South Australian Genomic Centre and Bioplatforms Australia; "The Genome and Transcriptome analysis of Karenia species from the SA HAB 2025"; A$90,000; Co-CI; 2026 - 2027.
Flinders Foundation Health Seed Grant 2025, Flinders Foundation, Flinders University, Australia; A$25,000; Co-CI; Mar 2025 - Feb 2027.
ARC Discovery Projects 2025 Grant, Australian Research Council, Australia; "Discovering new ways to generate targeted mutations"; A$685,781; CIB; 2025 - 2027.
National Computational Merit Allocation Scheme 2025 Supercomputing Grant "Phage Bioinformatics"; 10,300,000 service units (worth A$412,000); Co-CI; Jan - Dec 2025.
National Computational Merit Allocation Scheme 2024 Supercomputing Grant; "Large-scale mining and characterisation of phage genomes from metagenomes"; 3,085,000 service units (worth A$123,400); Co-CI; Jan - Dec 2024.
NCI Adapter Allocation Scheme Q3 2023 Grant, National Computational Infrastructure, Australia; "Large Graph Models and Variation Analysis in Viral Metagenomes"; 250,000 service units (worth A$10,000); Lead CI; Jul - Sep 2023.
CZI Essential Open Source Software for Science (Cycle 5) Grant, The Chan Zuckerberg Initiative, United States; "cogent3 Python APIs for IQ-TREE and GraphBin via a Plug-In Architecture"; US$325,000 (A$550,000); Co-PI; 2023 - 2024.
Awards
2024 - Outstanding PhD Thesis Award - Australian Bioinformatics and Computational Biology Society (ABACBS), Australia
2023 - President's Award for Scientific Research - The National Research Council of Sri Lanka
2023 - ASM SA/NT Branch Early Career Researcher Award - The Australian Society for Microbiology, Australia
2022 - Oracle for Research Cloud Starter Award - Oracle Corporation, United States
2022 - Best Lightning Talk at ABACBS 2022 - Australian Bioinformatics And Computational Biology Society, Australia
2022 - Outstanding Science Prize to a scientific poster at Genomes of Microbiomes 2022, Birmingham, UK
2018 - ANU PhD Scholarship (International) and HDR Merit Scholarship - The Australian National University, Australia
2018 - Excellent Oral Presentation Award - 7th ACM International Conference on Software and Computer Applications, Kuantan, Malaysia
2018 - ACM-W Scholarship 2018 - Association for Computing Machinery's Council on Women in Computing, USA
2015 - University Award - University of Moratuwa, Sri Lanka
2015 - Best Innovation award - Google I/O Hackathon, Sri Lanka
Undertake bioinformatics research, develop bioinformatics software and analyse novel ‘omics data aligned with the funded research projects.
Research student supervision (HDR and Honours students).
Association for Computing Machinery (ACM)
Institute of Electrical and Electronics Engineers (IEEE)
International Society for Computational Biology (ISMB)
International Society for Viruses of Microorganisms (ISVM)
International Society for Microbial Ecology (ISME)
Research Software Engineering Association of Australia and New Zealand (RSE AU/NZ)
Australian Bioinformatics And Computational Biology Society (ABACBS)
Australian Society for Microbiology (ASM)
Institute of Engineers Sri Lanka (IESL)
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South Australia 5042
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