People

Faculty

Professor Edmund Crampin
Edmund is Rowden White Chair of Systems Biology, Chair of the Computational Biology Research Initiative, and Director of the Systems Biology Lab at the University of Melbourne. He studied physics at Imperial College London and gained a DPhil in mathematical biology at the University of Oxford, where he also held a Junior Research Fellowship. Edmund was previously Associate Professor and Group Leader at the Auckland Bioengineering Institute.
More about Edmund

Professor Peter Gawthrop
Peter is a Professorial Fellow at the University of Melbourne, and Emeritus Professor of Control Engineering at the University of Glasgow. Peter obtained his BA (Hons), DPhil and MA degrees in Engineering Science from the University of Oxford, and previously held the Wylie Chair of Control Engineering at Glasgow University. He is a Fellow of the Institution of Engineering and Technology, and the Institution of Mechanical Engineers. Peter’s current research interests include application of bond graphs in systems biology to model the network thermodynamics of biochemical systems.
Peter’s website

Dr Vijay Rajagopal
Vijay is a Senior Lecturer in the Department of Biomedical Engineering, and leads the Cell Structure and Mechanobiology Group. He completed his PhD at the Auckland Bioengineering Institute in 2007, focusing on the development of computational models of breast tissue mechanics to aid breast cancer diagnostic procedures. He gained expertise in experimental and computational cellular mechanics at the Singapore-MIT Alliance for Research and Technology, prior to moving to the University of Melbourne.
Vijay’s website

Research Fellows

Dr Matthew Faria (PhD 2018)
Rejane Langlois Fellow, Department of Biomedical Engineering
Matt completed his PhD at the Systems Biology Lab in 2018, supervised jointly with Professor Frank Caruso, on modelling the interactions between nanoparticles and biological systems. His postdoctoral work as a CBNS Research Fellow focused on standardising nano-bio interaction measurements. For his Rejane Langlois Fellowship Matt will focus on combining nanomaterials and synthetic biology for improved therapeutic delivery systems.

Dr Stuart Johnston
ARC DECRA Fellow, School of Mathematics and Statistics
Stuart completed his PhD in Applied Mathematics at the Queensland University of Technology in 2017 on models of collective cell behaviour, with Prof Mat Simpson. Stuart joined the Systems Biology Lab as a CBNS Research Fellow, investigating the influence of nanoparticle polydispersity on nanoparticle-cell interactions and cellular uptake pathways, and since March 2020 has been an ARC DECRA Fellow in the School of Mathematics and Statistics.

Dr Michael Pan (PhD 2019)
CBNS Research Fellow: Energy-based whole cell modelling
Michael completed his PhD at the Systems Biology Lab in 2019, jointly supervised with Professor Peter Gawthrop and Dr Joe Cursons (WEHI). His PhD focused on bond graph modelling of biophysical systems, and his postdoctoral work explores the use of bond graph theory to develop integrated, modular whole cell models.

PhD Students

Mr Dharmesh Bhuva

Dharmesh Bhuva
Cancer systems biology
Cosupervised with Dr Melissa Davis (Bioinformatics, WEHI). Dharmesh’s thesis is focused on computational approaches for identification of molecular phenotypes and their regulation in cancer, in particular developing context-specific regulatory network inference algorithms.

Domenic Germano
3D modelling of the colonic crypt
Cosupervised with Dr James Osborne. 
Domenic is developing a multi-scale cell-based deformable tissue mechanics model to understand the mechanics of the colonic crypt epithelium.

Joshua Forrest
Whole cell modelling
Cosupervised with Prof Michael Stumpf (Biosciences and Melbourne Integrative Genomics).
Joshua is developing models of cell processes using energy-based modelling approaches, focusing initially on bacterial sensing.

Niloofar Shahidi
Bond Graph Semantics for Modular Physiological Modelling
University of Auckland, cosupervised with Dr David Nickerson and Dr Kenneth Tran.
The focus of Niloofar’s project is to develop methodology (standards, tools and databases) for automating the composition of mathematical models of physiological processes.

Recent Alumni

Hilary Hunt (PhD 2020)
Calcium signalling in cardiac hypertrophy
Hilary’s thesis on modelling crosstalk between RyRs and IP3Rs in the heart, was cosupervised by Dr Vijay Rajagopal, Professor Christian Soeller (Exeter) and Professor Llew Roderick (Leuven). Hilary was awarded the Australian Mathematical Society Lift-off Fellowship. She is currently a postdoctoral fellow working with Lee Sweetlove at the University of Oxford Department of Plant Sciences, working on plant metabolism.

Claire Miller (PhD 2020)
Multiscale modelling of the epidermis
Cosupervised with Dr James Osborne, Claire built a multi-cellular computational model of the epidermis — the outer-most layer of the skin — to understand how epidermal thickness is regulated. Claire moved to a postdoctoral position at the University of Amsterdam (UvA), working with Prof Alfons Hoekstra’s Computational Science Lab as a part of the INSIST ‘in silico stroke trials’ project.

Agne Tilunaite

Agne Tilūnaitė (Research Fellow 2017-2019)
Cardiac cell systems biology
Agne completed her PhD in Mathematics at the University of Nottingham on modelling cell signalling. Agne’s project was to develop biophysically realistic and structurally detailed mathematical models of calcium signalling in heart cells. Agne is currently working at Swiss biotech company InterAx Biotech, on  computational systems biology for intelligent drug design.

Daniel Hurley

Daniel Hurley (Senior Research Fellow 2017-2019)
Model reproducibility and reuse in computational biology
Daniel completed his BSc, MSc and PhD degrees at the University of Auckland, and worked in commercial IT, software development, software consultancy and technical communication prior to returning to research. His work focused on techniques for regulatory network inference from large-scale transcriptomic data, and on methodologies for reproducibility of computational results.

david-ladd

David Ladd (Research Fellow 2017-2019)
Computational cell modelling for bio-nano interactions
David completed his PhD at the Auckland Bioengineering Institute on multiscale modelling methods for arterial fluid mechanics. David’s project focused on computational approaches for 3D cell modelling, in particular using imaging data, and applying these approaches to develop frameworks that link computational models and related experimental data. David is currently working at oNKo-innate, a Melbourne-based discovery-stage biotechnology company dedicated to immuno-oncology target identification and therapeutic development.

Peter Cudmore

Peter Cudmore (Research Fellow 2017-2019)
Modelling and design for synthetic biology
Pete completed his PhD in Mathematics at the University of Queensland where he studied emergent phenomena in systems of nonlinearly coupled oscillators. Pete’s project involved developing software to implement bond graph methodology to advance modelling, design and control of synthetic biological systems. Pete is currently a research fellow in the Applied Optimisation and Control group in the Melbourne School of Engineering.

Shourya Ghosh

Shouryadipta Ghosh (PhD 2019)
The role of ultrastructural alterations in diabetic cardiomyopathy
Cosupervised with Dr Vijay Rajagopal, Shourya used a combination of electron microscopy and finite element modelling to study the spatial distribution of mitochondria in cardiac myocytes and how this distribution changes in disorders such as diabetes. Shourya is currently a research fellow in the Department of Biomedical Engineering.

Greg Bass (PhD 2018)
Decoding calcium signalling crosstalk in cardiac hypertrophy
Supervised with Dr Vijay Rajagopal, Greg investigated calcium signalling in heart muscle cells using imaging data and mathematical models. He showed that two distinct messages can be conveyed simultaneously by modifying the shape of the calcium curve, providing clues for how calcium signals may be encoded and decoded in many cell types. Greg is currently Research Scientist – Image Analytics & Systems Biology at CSL Innovation.

David Budden (PhD 2017)
The Systems Biology of Eukaryotic Transcription
Supervised with Dr Melissa Davis (Bioinformatics, WEHI), David’s research involved modeling the regulation of gene expression using machine learning and information-theoretic approaches, with particular focus on the interactions and feedback mechanisms between transcription factors, histone modifications and microRNAs in cancer. Following a Postdoctoral Fellowship at MIT, David took took up a role as Research Engineer at DeepMind in London.

Joe Cursons (Research Fellow 2012-2016)
Joe completed his PhD and a postdoctoral fellowship in the Systems Biology Lab. Joe’s PhD work considered ERK-MAPK signalling in situ in the epidermis (skin) from both experimental and modelling perspectives, while his postdoctoral work focused on analysis of transcriptional datasets in cancer. Joe was then a Senior Research Officer at the Walter and Eliza Hall Institute, and is currently head of Computational Biology & Bioinformatics at oNKo-innate, a Melbourne-based discovery-stage biotechnology company dedicated to immuno-oncology target identification and therapeutic development.

Ivo Siekmann (Research Fellow 2009-2015)
Ivo’s research focused on mathematical analysis and modelling of ion channel data, specifically the IP3-Receptor. Ivo’s work uncovered a new ‘modal’ model to explain the dynamical behaviour of the channel. Ivo is currently Lecturer in Applied Mathematics at Liverpool John Moores University.
Ivo’s website

Melissa Davis (Senior Research Fellow 2013-2015)
Melissa is currently laboratory head and group leader in the Bioinformatics division at WEHI. She holds a BSc (Genetics) and a PhD from the University of Queensland. Melissa’s research is focused on the systems biology of epithelial-mesenchymal plasticity in breast cancer. Melissa specialises in the integration of genomic, transcriptomic, and proteomic data with knowledge-based network models to identify sub-networks and pathways disrupted in cancer. Melissa’s website

Jerry Gao (Research Fellow 2014-2015)
Following a postdoctoral position at the Walter and Eliza Hall Institute (WEHI) in Melbourne, Jerry took up a role as a Quantitative Analyst at the Future Fund Management Agency.