The BioMimetic Systems Engineering (BMSE) Laboratory

At the BMSE Lab, we observe, simulate, and engineer tissue behaviour.

The BioMimetic Systems Engineering (BMSE) Laboratory at the University of Queensland (UQ) combines Tissue EngineeringBiomedical Image Analysis, and Computational Biology to study and solve biological and medical problems using biomimetic systems. 

Our work aligns with chemical engineering fundamentals, cell therapy or medical device manufacturing, and clinical collaborators in haematology, vascular surgery, neurosurgery, and radiology.

Our systems engineering approaches allow us to examine, model, engineer, optimise, control, scale, and automate dynamic systems of several entities such as multi-cellular tissues or cell-material and cell-fluid systems.

Recent work has focussed on systems of bloodblood vessels, and vascularised tissue, as these are essential building blocks for human and mammalian function.

Open Positions at the BMSE Lab (please contact Mark for details)

We are advertising four 2023 thesis projects for UQ student researchers:

We are always interested in recruiting strong postdoc candidates through joint grant or fellowship applications and PhD candidates through UQ's Annual PhD Scholarship Round

Contact us

Dr Mark C Allenby
Group Leader, Senior Lecturer

UQ Researchers@MCAllenby


Dr Mark C Allenby, Senior Lecturer in Biomedical Engineering

Mark leads the BioMimetic Systems Engineering (BMSE) Lab and is a Senior Lecturer of Biomedical Engineering in UQ's School of Chemical Engineering. Mark is an ARC DECRA Fellow (2022-2025), an Advance Queensland Fellow (2019-2022) and an Adjunct Senior Lecturer at QUT. Mark has principally supervised 5 PhDs and 2 MPhil/RAs, co-supervised 7 PhDs and has been awarded more than $2.5M of funding as chief investigator across 17 competitive funding rounds in 3 years. Mark received a PhD and MSc in chemical engineering from Imperial College London, UK and has undergraduate degrees in mathematics and chemistry from Pepperdine University, USA. Mark's background includes the engineering of dynamic stem cell bioreactors for tissue biomanufacturing, automated signal and image processing for tissue diagnostics, and model-based optimisation and control of 4D cell systems.


Dr Ashley Murphy, Postdoctoral Research Fellow

Ash has recently commenced as Postdoctoral Research Fellow at the University of Queensland, BioMimetic Systems Engineering Lab (BMSE), under the primary supervision of Dr Mark Allenby. His research will primarily focus on the development of dynamically controlled human angiogenic in vitro models for optimised tissue growth. Ash has previously worked as Postdoctoral Research Fellow at the CSIRO, where his research focussed on the development of engineered in vitro retinal models for the study and treatment of retinal disorders. In 2019, Ash received his PhD from the Department of Materials Science and Engineering, Monash University, which explored the development of stem cell-derived 3D neural tissue models. Ash's research interests lie at the intersection of materials science, stem cell biology and device engineering which are highly aligned with a strong desire for real work impact in the medical field.


Ms Sabrina Schoenborn, 3rd Year PhD Student

Sabrina is a third-year PhD Student at the UQ BioMimetic Systems Engineering (BMSE) Lab and focuses her research on the numerical and experimental characterisation of lower peripheral arteries and vascular graft anastomoses. During her work, Sabrina utilises numerical simulations (FEA, CFD, FSI), computer-aided design (CAD), additive manufacturing (3D printing), medical image segmentation, and plastics and silicone processing to create and validate patient-specific vascular models. She received her Bachelor of Science (Mechanical Engineering) and Master of Science (Plastics and Textile Technology) from RWTH Aachen University in Aachen, Germany and has made the biomedical application of mechanical, textile, and plastics engineering methods the main focus of her work and studies. Her passion is creating real-world impact with medical engineering to improve patient outcomes via science communication and translational research.


Ms Chloe De Nys, 1st Year PhD Student

Chloe is a first-year PhD stduent, focussing her research on developing a bioengineered cerebrovascular model that can simulate the physiological mechanobiology of an intracranial aneurysm, to aid surgical decision making. She recently graduated in 2021 from a Chemical and Biological Engineering degree at University of Queensland, with a dual Biomedical Sciences degree. Chloe also has a background in pharmaceutical chemistry, previously working as a student chemist at Viatris where she became skilled in High Preformance Liquid Chromatography. She is interested in combining chemical engineering, stem cell biology, computational modelling, and artificial intelligence to advance tissue engineering research and development. 


Mr Ryan McKinnon, 1st Year PhD Student

In 2022, Mr Ryan McKinnon began a PhD under the supervision of Dr. Mark Allenby with the goal of manufacturing lab-grown patient-specific grafts with inbuilt vascular conduits optimally designed for defect-specific regeneration. Mr McKinnon has a Bachelor of Biomedical Science and a Master’s in Medical Research (MMR). Previously under the mentorship of Associate Professor Andrew Bulmer (Griffith University, AUS), his research was centred around developing a pre-clinical biocompatibility assessment of medical devices, in humans. Since graduating from an MMR Ryan has worked in industry, most notably, a stage IIb/IIIa clinical trial and in an industry sponsored group at Griffith University. The methods utilised in his previous projects included flow cytometry, scanning electron microscopy, biochemical analysis, and functional medical device assessments (e.g., flow set-ups), sonography, microscopy and thromboelastometry. 


Ms Astrid Nausa Galeano, 1st Year PhD Student

Astrid is a first-year PhD student at the UQ BioMimetic Systems Engineering (BMSE) Lab. Her project, under the supervision of Dr. Mark Allenby, seeks to understand how tridimensional tissue formation can be controlled by manipulating its environment, such as microscale structure and macroscale nutrient transport. To do so, she is studying the effect of 3D microscaffolds and culture designs on cell morphology, growth, maturation, and tissue organisation. She has a Bachelor and a Master's degree in Chemical Engineering, both at the Universidad Nacional de Colombia. Previously she has worked in the production of therapeutic recombinant proteins employing mammalian cell culture and bioreactor optimization. Her motiviation is to develop high-impact biomedical engineering applications to facilitate patients' access to state-of-the-art technologies. 


Mr Mingyang (Aaron) Yuan, Summer Research Student

Mingyang (Aaron) is a Master of Engineering Science student and a summer research student at the BioMimetic Systems Engineering (BMSE) Lab. His project is focussing on developing biomechanics simulations for mechanically-active culture platforms by computational modelling under the supervision of Dr Mark Allenby and Ms Sabrina Schoenborn. Aaron recieved his Bachelor of Mechanical Engineering and Bachelor of Commerce from Monash University in 2021 and worked as an Associate Scientist at Health and Grooming Devices at Proctor & Gamble after graduation. 


Ms Amé Badenhorst, Summer Research Student 

Amé is in the first year of her Bachelor of Chemical and Biomedical Engineering, with a dual Master of Engineering degree. She is also a 2022/2023 summer research student at the BioMimetic Systems Engineering (BMSE) Lab. Under the supervision of Dr Mark Allenby and Dr Ashley Murphy, her project is focussing on spatiotemporal modelling of implant osseointegration and mechanotransduction. Amé also has a backrgound in phase 1 clinical research, currently working as a clinical unit assistant for Nucleus Network



Ms. Brenna Devlin (PhD 2021-2024): Development of geometric melt electrowritten polycaprolactone scaffolds to optimise cellular growth and mechanobiology. Principally supervised by Prof Maria Woodruff and Dr Naomi Paxton (QUT).


Mr. Trent Brooks-Richards (2018-2022): 3D printed composite biomaterials for personalised vascular implants. Principally supervised by Prof Maria Woodruff and Dr Naomi Paxton (QUT).

Mr. Mitchell Johnson (2020-2021) - Principal Supervisor - Medical image analysis of intracranial aneurysms.

Mr. Cody Fell (MPhil 2019-2020) - Principal Supervisor - Soft robotic devices for emulating vascular mechanobiology.

Ms. Victoria Nguyen (MSci, 2019) - Principal Supervisor - Histological imaging techniques and flexions of femoropoliteal arteries. 

Dr. Maureen Ross (PhD 2017-2021) - Co Supervisor - Novel imaging and bioprinting approaches for auricular cartilage reconstruction. Principally supervised by Prof Maria Woodruf (QUT).

Dr. Michael Chen (PhD 2017-2021) - Co Supervisor - Clinical applications of 3D printing in urological surgery. Principally supervised by Prof Maria Woodruf (QUT).

Dr. Rena Cruz (PhD 2017-2021) - Co Supervisor - Advanced 3D biofabrication appraoches for the treatment of microtia. Principally supervised by Prof Maria Woodruf (QUT).

Dr. Matthew Lanaro (PhD 2017-2021) - Co Supervisor - Multi-material multi-scale biofabrication approaches. Principally supervised by Prof Maria Woodruf (QUT).

Dr. Naomi Paxton (PhD 2017-2020) - Co Supervisor - Additive manufacturing patient-specific porous high-density polyethylene surgical implants. Principally supervised by Prof Maria Woodruf (QUT).


Tissue Engineering

The field of tissue engineering aims to recreate tissue within the laboratory. We engineer synthetic platforms and culture cells to mimic or controllably grow complex and functional tissue at high density and scale. This artificial tissue may have future applications for therapeutics and grafts, testing and optimising interventions, and cellular agriculture. Topics: Biomaterial Fabrication, Bioreactor Engineering, Stem Cell & Tissue Culture.

Biomedical Image Analysis

Imaging remains the gold standard technique to assess tissue quality and function. We capture microscopy and medical images and program algorithms and software to rapidly, automatically, and precisely diagnose our engineered tissue or patient tissue. This imaging data links our experiments to our computational models and to clinical data. Topics: Microscopy, MRI, CT, Segmentation, Statistical Shape Analyses, Co-Localisation, Motility & Fate Tracking

Computational Biology

Predictive models of cell and tissue behaviour are necessary to optimise tissue manufacturing or guide clinical decision-making. Leveraging image analyses and culture experiments, we program multiscale mathematical or statistical models in single-cell, tissue-wide, or multi-tissue systems to link experiments to theory to practice. Topics: Cell Population Models (DE's), Single-Cell Models (Agent-Based), Tissue Biomechanics (FEA).


Engineering Tissue Organisation Using Intelligent Additive Biomanufacturing

Australian Research Council DECRA Fellowship (2022-2025)

  • Engineering tissue organisation under 3D printed microconfinement (TBA - UQ)
  • Engineering tissue organisation under bioreactor mass transport (PhD Astrid Gloria Nausa Galeano - UQ)
  • Engineering cerebrovascular models for surgical decision-making (PhD Chloe De Nys - UQ)
  • Engineering vascular conduits to control mass transport for tissue regeneration (PhD Ryan McKinnon - UQ)

Biofabrication for Personalised Vascular Surgery Prognosis, Training, and Treatment 

Advanced Queensland Industry Research Fellowship (2019-2022)

  • Development of a numerical and experimental model to optimise graft anastomosis in peripheral arteries (PhD Sabrina Schoenborn - UQ)
  • Combining additive manufacturing and soft robotics for biomimetic tissue engineered constructs (PhD Brenna Devlin - QUT)
  • 3D-printed composite biomaterials for personalised vascular implants (PhD Trent Brooks-Richards - QUT)
  • Soft robotic devices for emulating vascular mechanobiology (MPhil Cody Fell - QUT)
  • A diagnostic software suite using machine learning to predict intracranial aneurysm rupture (MPhil Mitchell Johnson - UQ)

News and Past Events

January 21st, 2023: Nataly's preprint, "Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies a preeclampsia-like gene signature" has been uploaded to bioRxiv. Congrats to Nataly and all the collaborators! (Led by Arutha Kulasinghe, UQ TRI). 

December 23rd, 2022: Phani's paper, "Reproducibility of the computational fluid dynamic analysis of a cerebral aneurysm monitored over a decade" has been published in Scientific Reports. Congrats Phani! (Led by Zhiyong Li, QUT). This is a paper from our CERG consortium with Dr. Craig Winter, RBWH.

October 31st, 2022: Mark has been awarded a very spoooooky Ramaciotti Health Investment Grant entitled "Engineering high-density tissue bioreactors for the affordable manufacture of cell therapies" for 2023-2024, more details can be found here

October 19th, 2022: Sabrina Schoenborn's paper, "Fluid-Structure Interaction Within Models of Patient-Specific Arteries: Compuational Simulations and Experimental Validations" has been published in IEEE Reviews in Biomedical Engieneering. Congrats Sabrina! (Collaboration with Prof Selene Pirola, TU Delft and Prof Mia Woodruff, QUT)


October 12th, 2022: Ashley Murphy has been awarded our school's Health Safety and Wellness Award for establishing and directing new cell culture practices in our shared biomedical engineering laboratory. Congrats Ash!

October 4th, 2022: Ashley Murphy has been awarded a EAIT ECR grant "HemaChip: Fetal liver microenvironments to enhance hematopoietic stem cell expansion" for 2023, which will support future work engineering microfluidic hydrogels to screen HSPC expansion factors. Congrats Ash!
September 13th, 2022: We welcomed Prof. Dieter Veit from RWTH Aachen to discuss future collaborations in textile manufacturing for biomedical engineering. 
Mark, Prof. Dieter Veit, and Sabrina
June 28th, 2022: David Forrestal's paper, "Personalised Volumetric Tissue Generation By Enhancing Multiscale Mass Transport Through 3D Printed Scaffolds in Perfused Bioreactors" has been published in Advanced Healthcare Materials. Congrats David! (Led by Prof Mia Woodruff, QUT)

June 6th, 2022: David Killian's paper, "3D Plotting of Calcium Phosphate Cement and Melt Electrowriting of Polycaprolactone Microfibers in One Scaffold" has been published in Journal of Functional Biomaterials. Congrats David! (Led by Prof Michael Gelinsky, TUD, Germany)

May 4th, 2022: Our recent review article in Biomaterials has been highlighted as a news story in GEN magazine (Genetic Engineering and Biotechnology) to describe new developments in computerised image analyses for cell and tissue bioprocess intensification and bioreactor engineering. 

April 27th, 2022: Ryan McKinnon joins us for his PhD on "Engineering vascular conduits in grafts to control mass transport for tissue regeneration" in collaboration with the Princess Alexandra Hospital. Ryan joins us after working as a molecular biologist at BD Biosciences and research assistant at Griffith University. Welcome Ryan!

April 2022: Ash, Chloe, Sabrina, Mark, and Ryan (L->R)

April 22nd, 2022: Sabrina has passed her mid-term PhD candidature review! Congrats Sabrina!

April 7th, 2022: Mark and Mia Woodruff's collaborative review paper 'Image analyses for engineering advanced tissue biomanufacturing processes' has been published at Biomaterials!

April 4th, 2022: Chloe De Nys joins us for her PhD on "Engineering Cerebrovascular Models for Surgical Decision Making" in collaboration with the Royal Brisbane & Women's Hospital and Herston Biofabrication Institute. Chloe joins us after a degree in Chemical Engineering from UQ. Welcome Chloe!
April 3rd, 2022: Cody Fell's paper 'Soft pneumatic actuators for mimicking multi-axial femoropopliteal artery mechanobiology' has been published at Biofabrication!  (collaboration with Prof Mia Woodruff, QUT).

March 11th, 2022: Mark has been awarded a HaBS - EAIT ECR Collaboration Seen Funding Grant with Dr Pingping Han, Prof Saso Ivanovski, and Dr Melanie Robitaille entitled 'Modelling implant osseointegration and mechanotransduction.' Excited to develop transfected mechosensitive reporter cell lines for live imaging analyses of cell-implant integration!
February 14th, 2022: Dr Ashley Murphy, previously from CSIRO and Monash, has started with us as a Postdoctoral Research Fellow in tissue biomanufacturing! Welcome, Ash! Personal Webpage, LinkedIn, Twitter.

January 21st, 2022: In collaboration with Assistant Professor Hon Fai Chan, Mark recieved a SPARC collaboration grant from the Chinese University of Hong Kong on 'Mechanicaly Programmable Cell Culture Platforms for Cell and Tissue Modelling.'
November 15th-19th, 2021: Cody, Sabrina, and Mark delivered oral presentations virtually at TERMIS-WC. BMSE Lab members were honored to recieve 4 oral presentations out of 4 abstract submissions! A perfect record!
  • Cody in When biofabrication meets bioreactors: implementing construct maturation and functional tissue culture 
  • Sabrina in Biomechanics of 3D (Bio)printed Materials
  • Mark in Frontiers of Bioprocessing and Automation in Tissue Engineering & Regenerative Medicine (keynote) and Advanced Spatiotemporal Imaging for Regenerative Medicine (chair)

October 26th, 2021: Mark delivered a pre-recorded talk at the Effective Altruism UQ event Alternative Meats at 6pm.

October 22nd, 2021: Mark delivered an invited talk at the Queensland Cardiovascular Research Network (QCVRN) at 4:15pm.

September 29th, 2021: Mark's paper 'A spatiotemporal microenvironment model to improve design of a three-dimensional bioreactor for red cell production' has been published in Tissue Engineering Part A  (led by Prof Sakis Mantalaris, Georgia Tech).

September 28th, 2021: Sabrina and Trent presented their PhD projects at the International Society of Biofabrication Conference! Sabrina presented 'Numerical and Experimental Platform for the Characterisation of Patient Specific Small-Diameter Vascular Graft Anastomoses for Translation to Tissue Engineering' and Trent presented 'Towards Patient-Specific Vascular Stents: Additive Manufacturing of Poly(ɛ-Caprolactone) Mechanically Enhanced with Graphene Oxide'.

September 24th, 2021: Matt's paper developing 'A quantitative analysis of cell bridging kinetics on a scaffold using computer vision algorithms' has been published in Acta Biomaterialia (led by Prof Mia Woodruff, QUT).

September 5th, 2021: Habib's paper reviewing 'The effects of COVID-19 on the placenta during pregnancy' has been published in Frontiers in Immunology (led by Dr Arutha Kulasinghe, UQ).

August 18th, 2021: Mark was awarded a DECRA entitled 'Engineering tissue organisation using intelligent additive biomanufacturing' which will run from March 2022 through 2025. 

August 5th, 2021: Mark welcomed his first child into the world, Giulia Letizia Allenby! Bring on the sleepless nights!

August 3rd, 2021: Alex's paper on 'Model-based data analysis of tissue growth in thin 3D printed scaffolds' has been published in the Journal of Theoretical Biology (led by Prof Matthew Simpson, QUT).

July 20th, 2021: Maureen's paper using 'Using melt-electrowritten microfibres for tailoring scaffold mechanics of 3D bioprinted chondrocyte-laden constructs' has been published in Bioprinting (led by Prof Mia Woodruff, QUT)

July 10th, 2021: Jared's paper on 'A deep learning method for automatic segmentation of the bony orbit in MRI and CT images' has been published in Scientific Reports (led by Dr. David Alonso-Caneiro, QUT)

July 5th, 2021: The BMSE Lab started at UQ!