Dr Mark Allenby
Dr

Mark Allenby

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Background

Dr Mark C Allenby is a Senior Lecturer in Biomedical Engineering (2021-ongoing) and an ARC DECRA Fellow (2022-2025) within UQ's School of Chemical Engineering. Mark is also an Adjunct Senior Lecturer at QUT and previously an Advance Queensland Fellow (2019-2022). Mark has principally supervised 5 PhDs and 2 MPhil/RAs, co-supervised 7 PhDs, and has been awarded over $2.8M of funding as chief investigator across 20 competitive funding rounds in 4 years. Mark received a PhD and MSc in chemical engineering from Imperial College London, UK and bachelors degrees in mathematics and chemistry from Pepperdine University, USA. Mark's leadership is exhibited by the:

Research Interests: Mark leads the BioMimetic Systems Engineering (BMSE) Lab. In the BMSE Lab, we combine Tissue Engineering, Biomedical Image Analysis, and Computational Biology to study and solve biological and medical problems using advanced cell culture and computer models. Initially, we will focus on Systems of Blood, Blood Vessels, and Vascularised Tissue as these are essential building blocks for human and mammalian function. Our work aligns with bioprocess 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, computationally model, experimentally engineer, optimise, control, scale, and automate dynamic systems of several entities such as multi-cellular tissues or cell-material and cell-fluid systems.

Academic Interests: Mark is the Convener of UQ's Biomedical Engineering (BME) major, ranked #2 in Australia. BME at UQ spans schools of Chemical Engineering (ChE; #1 in Australia), Electrical Engineering, and Mechanical Engineering, and engages with UQ's Faculty of Medicine and associated healthcare services. Mark is part of ChE teaching and scholarship committees, and Mark acts as the academic advisor for ChE-BME undergraduates. Mark is the creator and coordinator of Quantitative Methods in Biomedical Engineering, and is a lecturer of Process Modeling & Dynamics. Mark has previously taught courses in biomaterials, process modelling, and reaction engineering in ChE and BME departments at three universities in the UK and Australia.

Our BMSE Lab is currently looking for excellent computational researchers. These include candidates and collaborators with experience in microscopy and medical image processing, cell population dynamics simulation, and/or biomechanics simulations (Python, MATLAB, R, ANSYS) to analyse high-content experimental data. Postdoc candidates are welcome to contact us to explore fellowship applications. Interested PhD and MPhil candidates should consider applying with us to the UQ Annual HDR Scholarship Round. We are always recruiting masters and undergraduate thesis project students for thesis projects advertised on our lab website.

Availability

Dr Mark Allenby is:
Available for supervision
Media expert

Fields of research

Biofabrication Biomaterials Biomedical engineering Biomedical imaging Computational physiology Engineering Tissue engineering

Qualifications

  • Doctor of Philosophy, Imperial College

Research interests

  • Diagnostic Cell Culture Models to Screen Graft Versus Host Disease

    Bone marrow and organ transplants have been a lifesaving option for 200,000 patients per year. Patients and infants in need of blood, stem cells or solid organs often rely on donations from unrelated donors, despite their substantial risk of graft versus host disease (GVHD) which may lead to transplant rejection. By using rare stem cells from donated blood units, this project aims to engineer cell culture models which can accurately predict whether a patient would negatively react to a specific donor's cell or organ transplant, providing insights which could save thousands of Australian lives.  Researchers: Rose Ann Franco (Lead), Sara Chiaretti. Partners: Australian Red Cross Lifeblood, Queensland Cord Blood Bank at the Mater Hospital.  Funding: Australian Research Council, Ramaciotti Philanthropy, UQ Internal Funding.

  • Bone Marrow Mimicry Bioreactors for Blood Cell Therapy Manufacturing

    Cell therapies are widely considered to be the next step-change in clinical medicine, curing previously uncurable disease. However, many cell therapies cost $100,000 to $3,000,000 per dose, an expense which patients and healthcare systems cannot afford. If we could manufacture lab-grown cell therapies as efficiently as our body does, we could reduce the cost of cell therapies 10x-100x and deliver more curative treatments to more patients in need. Specifically, we are using our body's bone marrow as an inspiration for growing blood cell therapies such as blood stem cells (HSPCs) and red blood cells (RBCs).  Researchers: Astrid Nausa Galeano (Lead), Rose Ann Franco, Susana Costa Maia. Partners: Australian Red Cross Lifeblood, Queensland University of Technology, University of Maastricht.  Funding: Australian Research Council, Ramaciotti Philanthropy, UQ Internal Funding.

  • High-Content Microphysiological Systems for Cell Culture Screening

    3D culture systems can grow greater numbers of higher-quality cells at lower costs than traditional liquid suspension or 2D cultures, however the adoption of 3D culture systems in biopharmacuetical industries remains limited due to current dependenance on culture high content screening (HCS). Our lab is engineering the first experimental platforms and compuational models to preform HCS on 3D cell cultures for process optimisation and drug screening. Specifically, we are engineering live-imaged high-throughput hydrogel microchip platforms to optimise stem cell expansion and angiogenesis.  Researchers: Ryan McKinnon (Lead), Ashley Murphy, Rose Ann Franco.  Partners: Queensland Cord Blood Bank at the Mater, Royal Brisbane & Women's Hospital Dept of Haematology, Queensland University of Technology.  Funding: Australian Research Council, Ramaciotti Philanthropy, UQ Internal Funding.

  • Additive Manufacturing to Predict Patient-Specific Cardiovascular Disease

    The ability to diagnose and medically or surgically treat cardiovascular disease is particularly dependent on the anatomy and biology of our body's vessels. Additive manufacturing leverages medical imaging, computational simulations, and 3D printing to fabricate patient-specific models of cardiovascular disease useful for identifying disease, predicting disease progression, or simulating treatments. Specifically, we are computationally simulating and 3D printing perfusable cell culture models to simulate intracranial aneurysm rupture risk and predict peripheral artery graft success. Researchers: Chloe de Nys (Lead), Sabrina Schoenborn, Ryan McKinnon.  Partners: Royal Brisbane & Women's Hospital Dept of Neurosurgery, Herston Biofabrication Institute, Princess Alexandra Hospital Dept of Vascular Surgery, Queensland University of Technology.  Funding: Advance Queensland Industry Research Fellowship, Royal Brisbane & Women's Hospital Foundation, Bionics Gamechangers Australia, UQ Internal Funding.

Search Professor Mark Allenby’s works on UQ eSpace

51 works between 2012 and 2024
All (51) Journal Article (44) Book Chapter (2) Conference Publication (5)

1 - 20 of 51 works

2024

Journal Article

Time-of-Flight MRA of Intracranial Aneurysms with Interval Surveillance, Clinical Segmentation and Annotations

de Nys, Chloe M., Liang, Ee Shern, Prior, Marita, Woodruff, Maria A., Novak, James I., Murphy, Ashley R., Li, Zhiyong, Winter, Craig D. and Allenby, Mark C. (2024). Time-of-Flight MRA of Intracranial Aneurysms with Interval Surveillance, Clinical Segmentation and Annotations. Scientific Data, 11 (1) 555, 1-10. doi: 10.1038/s41597-024-03397-8

Time-of-Flight MRA of Intracranial Aneurysms with Interval Surveillance, Clinical Segmentation and Annotations

2024

Journal Article

Minimal information for studies of extracellular vesicles (MISEV2023): from basic to advanced approaches: Position paper

Welsh, Joshua A., Goberdhan, Deborah C. I., O'Driscoll, Lorraine, Buzas, Edit I., Blenkiron, Cherie, Bussolati, Benedetta, Cai, Houjian, Di Vizio, Dolores, Driedonks, Tom A. P., Erdbrugger, Uta, Falcon-Perez, Juan M., Fu, Qing-Ling, Hill, Andrew F., Lenassi, Metka, Lim, Sai Kiang, Mahoney, My G., Mohanty, Sujata, Moller, Andreas, Nieuwland, Rienk, Ochiya, Takahiro, Sahoo, Susmita, Torrecilhas, Ana C., Zheng, Lei, Zijlstra, Andries, Abuelreich, Sarah, Bagabas, Reem, Bergese, Paolo, Bridges, Esther M., Brucale, Marco ... Han, Pingping (2024). Minimal information for studies of extracellular vesicles (MISEV2023): from basic to advanced approaches: Position paper. Journal of Extracellular Vesicles, 13 (2) e12404, 1-84. doi: 10.1002/jev2.12404

Minimal information for studies of extracellular vesicles (MISEV2023): from basic to advanced approaches: Position paper

2024

Journal Article

Materials design innovations in optimizing cellular behavior on melt electrowritten (MEW) scaffolds

Devlin, Brenna L., Allenby, Mark C., Ren, Jiongyu, Pickering, Edmund, Klein, Travis J., Paxton, Naomi C. and Woodruff, Maria A. (2024). Materials design innovations in optimizing cellular behavior on melt electrowritten (MEW) scaffolds. Advanced Functional Materials, 34 (18) 2313092, 1-16. doi: 10.1002/adfm.202313092

Materials design innovations in optimizing cellular behavior on melt electrowritten (MEW) scaffolds

2024

Journal Article

Whole transcriptome profiling of placental pathobiology in SARS‐CoV‐2 pregnancies identifies placental dysfunction signatures

Stylianou, Nataly, Sebina, Ismail, Matigian, Nicholas, Monkman, James, Doehler, Hadeel, Röhl, Joan, Allenby, Mark, Nam, Andy, Pan, Liuliu, Rockstroh, Anja, Sadeghirad, Habib, Chung, Kimberly, Sobanski, Thais, O'Byrne, Ken, Almeida, Ana Clara Simoes Florido, Rebutini, Patricia Zadorosnei, Machado‐Souza, Cleber, Stonoga, Emanuele Therezinha Schueda, Warkiani, Majid E, Salomon, Carlos, Short, Kirsty, McClements, Lana, de Noronha, Lucia, Huang, Ruby, Belz, Gabrielle T, Souza‐Fonseca‐Guimaraes, Fernando, Clifton, Vicki and Kulasinghe, Arutha (2024). Whole transcriptome profiling of placental pathobiology in SARS‐CoV‐2 pregnancies identifies placental dysfunction signatures. Clinical & Translational Immunology, 13 (2) e1488, e1488. doi: 10.1002/cti2.1488

Whole transcriptome profiling of placental pathobiology in SARS‐CoV‐2 pregnancies identifies placental dysfunction signatures

2023

Journal Article

Quantitative and large-format histochemistry to characterize peripheral artery compositional gradients

Nguyen, V. A., Brooks-Richards, T. L., Ren, J., Woodruff, M. A. and Allenby, M. C. (2023). Quantitative and large-format histochemistry to characterize peripheral artery compositional gradients. Microscopy Research and Technique, 86 (12), 1642-1654. doi: 10.1002/jemt.24400

Quantitative and large-format histochemistry to characterize peripheral artery compositional gradients

2023

Journal Article

Fluid-structure interactions of peripheral arteries using a coupled in silico and in vitro approach

Schoenborn, S., Lorenz, T., Kuo, K., Fletcher, D. F., Woodruff, M. A., Pirola, S. and Allenby, M. C. (2023). Fluid-structure interactions of peripheral arteries using a coupled in silico and in vitro approach. Computers in Biology and Medicine, 165 107474, 1-11. doi: 10.1016/j.compbiomed.2023.107474

Fluid-structure interactions of peripheral arteries using a coupled in silico and in vitro approach

2023

Journal Article

In vitro microvascular engineering approaches and strategies for interstitial tissue integration

Murphy, A. R. and Allenby, M. C. (2023). In vitro microvascular engineering approaches and strategies for interstitial tissue integration. Acta Biomaterialia, 171, 114-130. doi: 10.1016/j.actbio.2023.09.019

In vitro microvascular engineering approaches and strategies for interstitial tissue integration

2023

Journal Article

An automated parametric ear model to improve frugal 3D scanning methods for the advanced manufacturing of high-quality prosthetic ears

Cruz, Rena LJ., Ross, Maureen T., Nightingale, Renee, Pickering, Edmund, Allenby, Mark C., Woodruff, Maria A. and Powell, Sean K. (2023). An automated parametric ear model to improve frugal 3D scanning methods for the advanced manufacturing of high-quality prosthetic ears. Computers in Biology and Medicine, 162 107033, 1-15. doi: 10.1016/j.compbiomed.2023.107033

An automated parametric ear model to improve frugal 3D scanning methods for the advanced manufacturing of high-quality prosthetic ears

2023

Journal Article

Reproducibility of the computational fluid dynamic analysis of a cerebral aneurysm monitored over a decade

Paritala, Phani Kumari, Anbananthan, Haveena, Hautaniemi, Jacob, Smith, Macauley, George, Antony, Allenby, Mark, Mendieta, Jessica Benitez, Wang, Jiaqiu, Maclachlan, Liam, Liang, EeShern, Prior, Marita, Yarlagadda, Prasad K D V, Winter, Craig and Li, Zhiyong (2023). Reproducibility of the computational fluid dynamic analysis of a cerebral aneurysm monitored over a decade. Scientific Reports, 13 (1) 219, 1-12. doi: 10.1038/s41598-022-27354-w

Reproducibility of the computational fluid dynamic analysis of a cerebral aneurysm monitored over a decade

2022

Journal Article

Fluid-structure interaction within models of patient-specific arteries: Computational simulations and experimental validations

Schoenborn, S., Pirola, S., Woodruff, M. A. and Allenby, M. C. (2022). Fluid-structure interaction within models of patient-specific arteries: Computational simulations and experimental validations. IEEE Reviews in Biomedical Engineering, PP (99), 1-18. doi: 10.1109/RBME.2022.3215678

Fluid-structure interaction within models of patient-specific arteries: Computational simulations and experimental validations

2022

Journal Article

Personalised volumetric tissue generation by enhancing multiscale mass transport through 3D printed scaffolds in perfused bioreactors

Forrestal, David P., Allenby, Mark C., Simpson, Benjamin, Klein, Travis J. and Woodruff, Maria A. (2022). Personalised volumetric tissue generation by enhancing multiscale mass transport through 3D printed scaffolds in perfused bioreactors. Advanced Healthcare Materials, 11 (24) 2200454, 1-15. doi: 10.1002/adhm.202200454

Personalised volumetric tissue generation by enhancing multiscale mass transport through 3D printed scaffolds in perfused bioreactors

2022

Journal Article

3D plotting of calcium phosphate cement and melt electrowriting of polycaprolactone microfibers in one scaffold: a hybrid additive manufacturing process

Kilian, David, von Witzleben, Max, Lanaro, Matthew, Wong, Cynthia S., Vater, Corina, Lode, Anja, Allenby, Mark C., Woodruff, Maria A. and Gelinsky, Michael (2022). 3D plotting of calcium phosphate cement and melt electrowriting of polycaprolactone microfibers in one scaffold: a hybrid additive manufacturing process. Journal of Functional Biomaterials, 13 (2) 75, 1-24. doi: 10.3390/jfb13020075

3D plotting of calcium phosphate cement and melt electrowriting of polycaprolactone microfibers in one scaffold: a hybrid additive manufacturing process

2022

Journal Article

Image analyses for engineering advanced tissue biomanufacturing processes

Allenby, Mark C. and Woodruff, Maria A. (2022). Image analyses for engineering advanced tissue biomanufacturing processes. Biomaterials, 284 121514, 121514. doi: 10.1016/j.biomaterials.2022.121514

Image analyses for engineering advanced tissue biomanufacturing processes

2022

Journal Article

Soft pneumatic actuators for mimicking multi-axial femoropopliteal artery mechanobiology

Fell, Cody, Brooks-Richards, Trent L., Woodruff, Mia A. and Allenby, Mark C. (2022). Soft pneumatic actuators for mimicking multi-axial femoropopliteal artery mechanobiology. Biofabrication, 14 (3) 035005, 035005. doi: 10.1088/1758-5090/ac63ef

Soft pneumatic actuators for mimicking multi-axial femoropopliteal artery mechanobiology

2022

Journal Article

Dissolvable 3D printed PVA moulds for melt electrowriting tubular scaffolds with patient-specific geometry

Brooks-Richards, Trent L., Paxton, Naomi C., Allenby, Mark C. and Woodruff, Maria A. (2022). Dissolvable 3D printed PVA moulds for melt electrowriting tubular scaffolds with patient-specific geometry. Materials and Design, 215 110466, 110466. doi: 10.1016/j.matdes.2022.110466

Dissolvable 3D printed PVA moulds for melt electrowriting tubular scaffolds with patient-specific geometry

2022

Journal Article

Ultrasound imaging offers promising alternative to create 3-D models for personalised auricular implants

Ross, Maureen T., Antico, Maria, McMahon, Katie L., Ren, Jiongyu, Powell, Sean K., Pandey, Ajay K., Allenby, Mark C., Fontanarosa, Davide and Woodruff, Maria A. (2022). Ultrasound imaging offers promising alternative to create 3-D models for personalised auricular implants. Ultrasound in Medicine and Biology, 48 (3), 450-459. doi: 10.1016/j.ultrasmedbio.2021.10.013

Ultrasound imaging offers promising alternative to create 3-D models for personalised auricular implants

2022

Journal Article

Corrigendum: The effects of COVID-19 on the placenta during pregnancy

Rad, Habib Sadeghi, Röhl, Joan, Stylianou, Nataly, Allenby, Mark C., Bazaz, Sajad Razavi, Warkiani, Majid E., Guimaraes, Fernando S F, Clifton, Vicki L. and Kulasinghe, Arutha (2022). Corrigendum: The effects of COVID-19 on the placenta during pregnancy. Frontiers in immunology, 13 998406, 998406. doi: 10.3389/fimmu.2022.998406

Corrigendum: The effects of COVID-19 on the placenta during pregnancy

2021

Journal Article

A deep learning method for automatic segmentation of the bony orbit in MRI and CT images

Hamwood, Jared, Schmutz, Beat, Collins, Michael J., Allenby, Mark C. and Alonso-Caneiro, David (2021). A deep learning method for automatic segmentation of the bony orbit in MRI and CT images. Scientific Reports, 11 (1) 13693, 1-12. doi: 10.1038/s41598-021-93227-3

A deep learning method for automatic segmentation of the bony orbit in MRI and CT images

2021

Journal Article

Model-based data analysis of tissue growth in thin 3D printed scaffolds

Browning, Alexander P., Maclaren, Oliver J., Buenzli, Pascal R., Lanaro, Matthew, Allenby, Mark C., Woodruff, Maria A. and Simpson, Matthew J. (2021). Model-based data analysis of tissue growth in thin 3D printed scaffolds. Journal of Theoretical Biology, 528 110852, 1-14. doi: 10.1016/j.jtbi.2021.110852

Model-based data analysis of tissue growth in thin 3D printed scaffolds

2021

Journal Article

A quantitative analysis of cell bridging kinetics on a scaffold using computer vision algorithms

Lanaro, Matthew, Mclaughlin, Maximilion P., Simpson, Matthew J., Buenzli, Pascal R., Wong, Cynthia S., Allenby, Mark C. and Woodruff, Maria A. (2021). A quantitative analysis of cell bridging kinetics on a scaffold using computer vision algorithms. Acta Biomaterialia, 136, 429-440. doi: 10.1016/j.actbio.2021.09.042

A quantitative analysis of cell bridging kinetics on a scaffold using computer vision algorithms

Current funding

  • 2022 - 2025
    Scalable high-density cell therapy manufacturing through engineering vascularised tissue biofactories
    Ramaciotti Health Investment Grants
    Open grant
  • 2022 - 2025
    Engineering Tissue Organisation Using Intelligent Additive Biomanufacturing
    ARC Discovery Early Career Researcher Award
    Open grant

Past funding

  • 2022 - 2023
    Mechanically Programmable Cell Culture Platforms for Cell and Tissue Modelling
    Strategic Partnerships for Research Collaboration Scheme
    Open grant
  • 2021 - 2022
    Biofabrication for personalised vascular surgery prognosis, training, and treatment
    Advance Queensland Industry Research Fellowships
    Open grant

Availability

Dr Mark Allenby is:
Available for supervision

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Supervision history

Current supervision

  • Doctor Philosophy

    Engineering cerebrovascular models for surgical decision-making

    Principal Advisor

  • Doctor Philosophy

    Engineering tissue organisation using intelligent additive biomanufacturing

    Principal Advisor

    Other advisors: Professor Justin Cooper-White

  • Doctor Philosophy

    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

    Principal Advisor

  • Doctor Philosophy

    Engineering vascular conduits in grafts to control mass transport for tissue regeneration

    Principal Advisor

Enquiries

Contact Dr Mark Allenby directly for media enquiries about:

  • BioImage Analysis
  • Bioprocess Modelling
  • Bioreactor Engineering
  • Cell Therapy Biomanufacturing
  • Tissue Engineering

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