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 Engineering, Biomedical 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 blood, blood 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 the following thesis projects for UQ honours and masters degree research projects:
- Integrating equipment and sensors into stem cell bioreactors for human tissue engineering
- Programming single-cell analyses from 3D microscopy images of lab-grown tissue
- Bioprocess model-based optimisation of dynamic stem cell bioreactors
- Examining coronavirus-driven cell mutations and long COVID treatments by microscopic image analysis
Due to the experimental data our team is generating, we are interested in recruiting and collaborating with computational researchers in bioimage analysis, bioprocess modelling, and biomechanical simulations. We are 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
m.allenby@uq.edu.auUQ 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. Depite being 5 years post-PhD, Mark has published over 40 papers, principally supervised 6 PhDs and 2 MPhil/RAs, co-supervised 7 PhDs and has been awarded more than $2.8m of funding as chief investigator across 17 competitive funding rounds in 4 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.
Email: m.allenby@uq.edu.au
Dr Rose Ann Franco, Postdoctoral Research Fellow
Rose Ann joined the BioMimetic Systems Engineering (BMSE) Lab as a Graduate Research Officer in April 2023 and became a postdoc with the conferral of her PhD in September 2023. Under the supervision of Dr. Mark Allenby, she will be working on the enrichment of endothelial colony forming cells (ECFCs) from mononuclear cell (MNC) populations isolation from peripehral and umbilical cord blood, and vascularisation of organoid models derived from MNCs. Prior to this, Rose Ann worked on guided chondrogenesis of bone marrow stromal cells in micropellet cultures using signalling molecules, pathway inhibition, and gene silencing as the focus of her PhD project at the Queensland University of Technology. Her research experience also included biomaterials fabrication and evaluation of its regenerative capabilities using in vitro and animal models at Soonchunhyang University, South Korea and microbial-derived nanocellulose production for tissue-engineering applications at University of the Philippines.
Email: roseann.franco@uq.edu.au
Ms Chloe De Nys, 2nd Year PhD Student
Chloe is a second-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 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.
Email: c.denys@uq.net.au
Mr Ryan McKinnon, 2nd 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.
Email: r.mckinnon@uq.net.au
Ms Astrid Nausa Galeano, 2nd Year PhD Student
Astrid is a second-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.
Email: g.nausagaleano@uq.edu.au
Ms Susana Costas Maia, Visiting MPhil Student
Susana is a second-year Biomedical Sciences Masters Student from Maastricht University in the Netherlands, who recently joined the BioMimetic Systems Engineering (BMSE) Laboratory as a visiting researcher. She will be working under the supervision of Dr. Mark Allenby and PhD student Astrid Nausa Galeano on optimizing MEW-PCL scaffold design for blood cell therapy manufacturing. Susana has a bachelor's degreee in Forensic Laboratory Sciences from CESPU in Portugal, where she took part in a research project in pharmacognosy, evaluating if the species in pan masala counteract the carcinogenic potential and neurotoxicity of the Betel nut (Areca catechu L.).
Email: s.costamaia@uq.edu.au
Mr Harrison Krek, Honors Thesis Researcher
Harry is undertaking a Bachelor of Engineering in Electrical Engineering, preforming his final year honours research project in programming real-time video fluorescence microscopy image analyses and models of 3D tissue angiogenesis under the supervision of Mark and Ash Murphy.
Email: h.krek@uq.net.au
Ms Alyssa Detterman, MBiotech Researcher
Alyssa is pursuing a Masters of Biotechnology at UQ while assisting the BioMimetic Systems Engineering Lab. She Graduated from The University of Texas at Austin with a Bachelors of Science in Environmental Science in Biology, where she assisted the Chemical Engineering Institute for Cellular and Metabolic Biology within the Alper Lab to research the enxymatic degredation of polyethylene terephthalate.
Email: a.detterman@uqconnect.edu.au
Co-Supervisions
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).
Alumni
Dr. Ashley Murphy (2022-2024) Postdoctoral Fellow - Advanced microfluidic hydrogel chips to controllably organise gradient microvascular, adipose, and hematopoietic tissue formation. In partial collaboration with Australian Red Cross Lifeblood (Dr Rebecca Griffiths). Won an ECR EAIT Seed Grant and a Marie Curie Postdoctoral Fellowship, currently at Maastricht University.
Dr. Sabrina Schoenborn (PhD, 2021-2023) PhD Candidate - Fluid-structure interactions in peripheral arteries: biomechanical coupling of in-silico, in-vitro, and cellular models with application to patient-specific femoral-popliteal bypass graft anastomoses. In collaboration with Princess Alexandra Hospital (Dr Yogeesan Sivakumaran - Vascular Surgery, Dr Thomas Lloyd - Radiology). Won a 2021 Bionics Queensland Start-Up Challenge. Currently Biomechanics Lead Engineer at Convergence Medical.
Mr. William Parker (BE (Hons), 2023) Honors Thesis Researcher - Unruptured intracranial aneurysm detection. Principally supervised by Mark and Ms. Chloe De Nys (UQ). Currently in MedTech industry.
Mr. Mingyang (Aaron) Yuan (MEng, 2022-2023) Masters Research Student - Biomechanics of soft robotic bioreactors. Principally supervised by Ms. Sabrina Schoenborn (UQ). Currently a PhD candidate at QUT (Zhiyong Li, Yi-Chin Toh).
Ms. Amé Badenhorst (BE (Hons), 2022-2023) Summer Research Student - Quantitative analysis of tissue vascularisation. Principally supervised by Dr. Ashley Murphy (UQ). Currently a ChE-BME student at UQ.
Mr. Trent Brooks-Richards (PhD, 2018-2022) - Co Supervisor - 3D printed composite biomaterials for personalised vascular implants. Principally supervised by Prof Maria Woodruff and Dr Naomi Paxton (QUT). Currently in industry.
Mr. Mitchell Johnson (MPhil, 2020-2021) - Principal Supervisor - Medical image analysis of intracranial aneurysms. Currently a frontend engineer at Canva.
Mr. Cody Fell (MPhil 2019-2020) - Principal Supervisor - Soft robotic devices for emulating vascular mechanobiology. Currently a PhD Student at Rice University (Omid Veiseh).
Ms. Victoria Nguyen (MSci, 2019) - Principal Supervisor - Histological imaging techniques and flexions of femoropoliteal arteries. Currently a pathologist technician at Sullivan Nicolades.
Dr. Maureen Ross (PhD 2017-2021) - Co Supervisor - Novel imaging and bioprinting approaches for auricular cartilage reconstruction. Principally supervised by Prof Maria Woodruf (QUT). Currently Medical Engineering Lead at VitalTrace.
Dr. Michael Chen (PhD 2017-2021) - Co Supervisor - Clinical applications of 3D printing in urological surgery. Principally supervised by Prof Maria Woodruf (QUT). Currently a clinical urologist.
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). Currently a medical engineer.
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). Currently a Senior Research Fellow at 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).
News and Past Events
April 8th, 2024: Sabrina successfully passed her final PhD viva for her thesis "Fluid-Structure Interactions in Peripheral Arteries: Biomechanical Coupling of In-Silico, In-Vitro, and Cellular Models with Application to Patient-Specific Femoral-Popliteal Bypass Graft Anastomoses". A special thanks to PhD examiners Prof Barry Doyle, Susann Beier, and Geoff Wang. Congratulations DOCTOR Schoenborn!
April 1st, 2024: Ashley has successfully been awarded a Marie Curie Postdoctoral Fellowship at TU Einhoven! An amazing culmination to Ash's incredible time at our lab from 2022-2024 where he has established our group to such a high standard of research preformance, collegiality, and safety. Congratulations Ash - we will miss you so much in Europe!
November 16th, 2023: Astrid successfully passed her PhD confirmation milestone for her thesis "Bioengineering a Bone Marrow Mimicry for Cell Therapy Manufacturing." She has had an incredible first year and we look forward to celebrating her future successes!
September 19th, 2023: Ash's paper, "In vitro microvascular engineering approaches and strategies for interstitial tissue integration" has been published in Acta Biomaterialia. Congrats to Ash!
September 6th, 2023: Sabrina's paper, "Fluid-structure interactions of peripheral arteries using a coupled in silico and in vitro approach" has been published in Computers in Biology and Medicine. Congrats to Sabrina, Tomas, Kai-Chieh, David, Mia, and Selene! (collaboration with Tomas, Kai-Chieh at RWTH Aachen; David Fletcher at USyd; Selene Pirola at TU Delft; Mia Woodruff at QUT)
August 21st, 2023: Victoria's paper, "Quantitative and large-format histochemistry to characterize peripheral artery compositional gradients" has been published in Microscopy Research & Technique. Congrats to Victoria, Trent, Ed, and Mia! (collaboration with Mia Woodruff, QUT).
May 31st, 2023: Two successful confirmation seminars (Chloe, Ryan) and a successful progress review (Sabrina) capped off by a night out of dinner, drinks, and mini golf. Chloe won the coveted visor with a record score of 22. Congratulations Sabrina, Chloe, and Ryan on a wonderful year.
May 30th, 2023: Brenna's preprint, "Advancing scaffold biomimicry: engineering mechanics in microfiber scaffolds with independently controlled architecture using melt electrowriting" has been uploaded to bioRxiv. Congrats to Brenna, Ted, Naomi, and Mia! (led by Mia Woodruff, QUT).
May 11th, 2023: Rena's paper, "An automated parametric ear model to improve frugal 3D scanning methods for the advanced manufacturing of high-quality prosthetic ears" has been published by Computers in Biology and Medicine. Congrats to Rena! (Led by Sean Powell, QUT).
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 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!
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)
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 22nd, 2022: Sabrina has passed her mid-term PhD candidature review! Congrats Sabrina!
- 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!
