Dr Mark Allenby

ARC DECRA & Senior Lecturer

School of Chemical Engineering
Faculty of Engineering, Architecture and Information Technology

Overview

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.

Research Interests

  • 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, Microscopy and Analysis.
  • 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) in Python, R, MATLAB, and ANSYS.
  • 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 in Python, R, MATLAB, and ImageJ.

Qualifications

  • Doctor of Philosophy, Imperial College

Publications

  • 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 ... Allenby, Mark (2024). Minimal information for studies of extracellular vesicles (MISEV2023): from basic to advanced approaches: Position paper. Journal of Extracellular Vesicles, 13 (2) e12404. doi: 10.1002/jev2.12404

  • 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

  • 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

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Grants

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Supervision

  • Doctor Philosophy

  • Doctor Philosophy

  • Doctor Philosophy

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Publications

Book Chapter

  • Paxton, Naomi C., Wong, Cynthia S., Desselle, Mathilde R., Allenby, Mark C. and Woodruff, Maria A. (2020). Bone morphogenetic protein–assisted bone regeneration and applications in biofabrication. Biomaterials for organ and tissue regeneration: new technologies and future prospects. (pp. 363-391) edited by Nihal Engin Vrana, Helena Knopf-Marques and Julien Barthes. Duxford, United Kingdom: Woodhead Publishing. doi: 10.1016/b978-0-08-102906-0.00016-7

  • Allenby, Mark C., Dos Santos, Susana Brito, Panoskaltsis, Nicki and Mantalaris, Athanasios (2019). Differentiation of human pluripotent stem cells for red blood cell production. Bioreactors for stem cell expansion and differentiation. (pp. 47-62) edited by Joaquim M. S. Cabral and Cláudia Lobato da Silva. Boca Raton, FL, United States: CRC Press. doi: 10.1201/9780429453144-3

Journal Article

Conference Publication

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Principal Advisor

  • Doctor Philosophy — Principal Advisor

  • Doctor Philosophy — Principal Advisor

  • Doctor Philosophy — Principal Advisor