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. Edmund’s research interests are in mathematical modelling of cellular processes and pathways underlying human disease. Current projects include modelling heart cells to understand the development of heart disease; computational approaches to study the network of genetic interactions underlying cancer; mathematical modelling in nano medicine and drug delivery; and development of modelling approaches, computational tools and standards for integrative systems biology.
More about Edmund

542413pictureProfessor Peter Gawthrop
Peter is a Professorial Fellow in the Department of Biomedical Engineering 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 developing intermittent control theory as a new paradigm for engineering and physiological control, and application of bond graphs in systems biology to model the network thermodynamics of biochemical systems.
Peter’s website

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

Research Fellows

Daniel HurleyDr Daniel Hurley (Senior Research Fellow)
Model reproducibility and reuse in computational biology
Daniel completed his BSc, MSc and PhD degrees at the University of Auckland. His research focuses on techniques for regulatory network inference from large-scale transcriptomic and proteomic data, and application of those techniques to drive the formulation and testing of experimental hypotheses. Before returning to research, his career was in commercial IT, software development, software consultancy and technical communication.

Dr Matthew Faria (Research Fellow)
Measuring and modelling bio-nano interactions
Matt completed his PhD at the Systems Biology Lab in 2018, jointly supervised by Professor Frank Caruso, Nanostructured Interfaces and Materials Science Group, on modelling of the interactions between nanoparticles and biological systems. His postdoctoral work will continue in this direction, in particular focusing on automation of nano-bio interaction measurement. He graduated with a BSc (Computer Science) from Carnegie Mellon University.

Stuart JohnstonDr Stuart Johnston (Research Fellow)
Mathematical modelling of bio-nano interactions
Stuart completed his PhD in Applied Mathematics at the Queensland University of Technology in 2017, during which he investigated models of collective cell behaviour and techniques for interfacing these models with experimental data. Stuart’s current focus is on developing methods for investigating the influence of nanoparticle polydispersity on nanoparticle-cell interactions and modelling cellular uptake pathways.

Agne TilunaiteDr Agne Tilunaite (Research Fellow)
Cardiac cell systems biology
Agne completed her PhD in Mathematics at the University of Nottingham, during which she used a range of mathematical techniques to explore how non-excitable cells react to time dependent stimulations of agonists. The aim of Agne’s current project is to develop biophysically realistic and structurally detailed mathematical models of calcium signalling in heart cells.

PhD Students

Michael Pan
A bond graph approach to integrative biophysical modelling
Supervised with Professor Peter Gawthrop and Dr Joe Cursons (Bioinformatics, WEHI)
Michael completed his Bachelor of Biomedicine and Master of Engineering (Biomedical) at the University of Melbourne. He is using bond graph theory to develop methods for coupling biophysical models, with a focus towards cardiac cell modelling.

Hilary HuntHilary Hunt
Calcium signalling in cardiac hypertrophy
Supervised with Dr Vijay Rajagopal (Department of Biomedical Engineering).
Following a Bachelor of Philosophy (Science) at the Australian National University, Hilary is now developing models of intracellular calcium signals involved in the development of heart disease.

Claire MillerClaire Miller
Multiscale modelling of the epidermis
Cosupervised with Dr James Osborne (School of Mathematics and Statistics)
Claire completed her undergraduate degree in Computational and Mechanical Engineering (Hons) at the University of Adelaide. She started her PhD in early 2016 and is interested in using multi-cellular and sub-cellular models to understand how the developed epidermis maintains structure in homeostasis.

Dharmesh Bhuva
Cancer systems biology
Cosupervised with Dr Melissa Davis (Bioinformatics, WEHI)

Recent Alumni

david-laddDr David Ladd (Research Fellow 2017-2019)
Computational cell modelling for bio-nano interactions
David completed his PhD in Bioengineering at the Auckland Bioengineering Institute, University of Auckland, working 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 a biotech startup company.

Peter CudmoreDr 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 GhoshShouryadipta 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 has now taken up a position at CSL Ltd.

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.

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 is currently a Research Fellow at the Walter and Eliza Hall Institute (WEHI) in Melbourne.

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.