Dr Mark Allenby

ARC DECRA & Senior Lecturer

School of Chemical Engineering

m.allenby@uq.edu.au

Researcher biography

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.

Publications

Book Chapters (2)

Journal Articles (45)

Conference Papers (5)

Book Chapters

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 Articles

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

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 ... Guanzon, Dominic (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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Totton, Nikki, Bradburn, Mike, Hoo, Zhe Hui, Lewis, Jen, Hind, Daniel, Girling, Carla, Shepherd, Elizabeth, Nightingale, Julia, Daniels, Thomas, Dewar, Jane, Dawson, Sophie, Carroll, Mary, Allenby, Mark, Edenborough, Frank, Curley, Rachael, Carolan, Charlotte and Wildman, Martin (2021). Prospectively predicting Pseudomonas aeruginosa infection/s using routine data from the UK cystic fibrosis register. Health Science Reports, 4 (4) e381, 1-9. doi: 10.1002/hsr2.381

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

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

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

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 (2021). The effects of COVID-19 on the placenta during pregnancy. Frontiers in Immunology, 12 743022. doi: 10.3389/fimmu.2021.743022

Ross, Maureen T., Kilian, David, Lode, Anja, Ren, Jiongyu, Allenby, Mark C., Gelinsky, Michael and Woodruff, Maria A. (2021). Using melt-electrowritten microfibres for tailoring scaffold mechanics of 3D bioprinted chondrocyte-laden constructs. Bioprinting, 23 e00158, 1-13. doi: 10.1016/j.bprint.2021.e00158

Allenby, Mark C., Okutsu, Naoki, Brailey, Kate, Guasch, Joana, Zhang, Qiming, Panoskaltsis, Naoki and Mantalaris, Athanasios (2021). A spatiotemporal microenvironment model to improve design of a 3D bioreactor for red cell production. Tissue Engineering. Part A, 28 (1-2), 38-53. doi: 10.1089/ten.TEA.2021.0028

Allenby, Mark C., Liang, Ee Shern, Harvey, James, Woodruff, Maria A., Prior, Marita, Winter, Craig D. and Alonso-Caneiro, David (2021). Detection of clustered anomalies in single-voxel morphometry as a rapid automated method for identifying intracranial aneurysms. Computerized Medical Imaging and Graphics, 89 101888, 1-12. doi: 10.1016/j.compmedimag.2021.101888

Paxton, Naomi C., Dinoro, Jeremy, Ren, Jiongyu, Ross, Maureen T., Daley, Ryan, Zhou, Renwu, Bazaka, Kateryna, Thompson, Robert G., Yue, Zhilian, Beirne, Stephen, Harkin, Damien G., Allenby, Mark C., Wong, Cynthia S., Wallace, Gordon G. and Woodruff, Maria A. (2021). Additive manufacturing enables personalised porous high-density polyethylene surgical implant manufacturing with improved tissue and vascular ingrowth. Applied Materials Today, 22 100965, 100965. doi: 10.1016/j.apmt.2021.100965

Nightingale, Renee C., Ross, Maureen T., Cruz, Rena L.J., Allenby, Mark C., Powell, Sean K. and Woodruff, Maria A. (2021). A protocol for clinically accessible three-dimensional ear scanning using smartphones. Plastic and Reconstructive Surgery, 148 (5), 863e-865e. doi: 10.1097/PRS.0000000000008469

Nightingale, Renee C., Ross, Maureen T., Cruz, Rena L.J., Allenby, Mark C., Powell, Sean K. and Woodruff, Maria A. (2021). Frugal 3D scanning using smartphones provides an accessible framework for capturing the external ear. Journal of Plastic, Reconstructive and Aesthetic Surgery, 74 (11), 3066-3072. doi: 10.1016/j.bjps.2021.03.131

Nightingale, Renee Christine, Ross, Maureen Therese, Allenby, Mark Colin, Woodruff, Maria Ann and Powell, Sean Keiran (2020). A Method for Economical Smartphone-Based Clinical 3D Facial Scanning. Journal of Prosthodontics, 29 (9), 818-825. doi: 10.1111/jopr.13274

Cruz, Rena L. J., Ross, Maureen T., Skewes, Jacob, Allenby, Mark C., Powell, Sean K. and Woodruff, Maria A. (2020). An advanced prosthetic manufacturing framework for economic personalised ear prostheses. Scientific Reports, 10 (1) 11453. doi: 10.1038/s41598-020-67945-z

Buenzli, Pascal R., Lanaro, Matthew, Wong, Cynthia S., McLaughlin, Maximilian P., Allenby, Mark C., Woodruff, Maria A. and Simpson, Matthew J. (2020). Cell proliferation and migration explain pore bridging dynamics in 3D printed scaffolds of different pore size. Acta Biomaterialia, 114, 285-295. doi: 10.1016/j.actbio.2020.07.010

Paxton, Naomi C., Daley, Ryan, Forrestal, David P., Allenby, Mark C. and Woodruff, Maria A. (2020). Auxetic tubular scaffolds via melt electrowriting. Materials and Design, 193 108787, 108787. doi: 10.1016/j.matdes.2020.108787

Paxton, Naomi C., Lanaro, Matthew, Bo, Arixin, Crooks, Nathan, Ross, Maureen T., Green, Nicholas, Tetsworth, Kevin, Allenby, Mark C., Gu, YuanTong, Wong, Cynthia S., Powell, Sean K. and Woodruff, Maria A. (2020). Design tools for patient specific and highly controlled melt electrowritten scaffolds. Journal of the Mechanical Behavior of Biomedical Materials, 105 103695, 103695. doi: 10.1016/j.jmbbm.2020.103695

Angelopoulos, Ioannis, Allenby, Mark C., Lim, Mayasari and Zamorano, Mauricio (2020). Engineering inkjet bioprinting processes toward translational therapies. Biotechnology and Bioengineering, 117 (1), 272-284. doi: 10.1002/bit.27176

Paxton, Naomi C., Allenby, Mark C., Lewis, Philip M. and Woodruff, Maria A. (2019). Biomedical applications of polyethylene. European Polymer Journal, 118, 412-428. doi: 10.1016/j.eurpolymj.2019.05.037

Paxton, Naomi C., Ren, Jiongyu, Ainsworth, Madison J., Solanki, Anu K., Jones, Julian R., Allenby, Mark C., Stevens, Molly M. and Woodruff, Maria A. (2019). Rheological characterization of biomaterials directs additive manufacturing of strontium-substituted bioactive glass/polycaprolactone microfibers. Macromolecular Rapid Communications, 40 (11) 1900019, 1900019. doi: 10.1002/marc.201900019

Allenby, Mark C. and Woodruff, Maria A. (2019). Biofabrication of personalised anatomical models and tools for the clinic. Journal of Cystic Fibrosis, 18 (2), 161-162. doi: 10.1016/j.jcf.2019.02.005

Tahlawi, Asma, Klontzas, Michail E., Allenby, Mark C., Morais, José C. F., Panoskaltsis, Nicki and Mantalaris, Athanasios (2019). RGD-functionalized polyurethane scaffolds promote umbilical cord blood mesenchymal stem cell expansion and osteogenic differentiation. Journal of Tissue Engineering and Regenerative Medicine, 13 (2) term.2784, 232-243. doi: 10.1002/term.2784

Allenby, Mark C., Panoskaltsis, Nicki, Tahlawi, Asma, Dos Santos, Susana Brito and Mantalaris, Athanasios (2019). Dynamic human erythropoiesis in a three-dimensional perfusion bone marrow biomimicry. Biomaterials, 188, 24-37. doi: 10.1016/j.biomaterials.2018.08.020

Misener, Ruth, Allenby, Mark C., Fuentes-Garí, María, Gupta, Karan, Wiggins, Thomas, Panoskaltsis, Nicki, Pistikopoulos, Efstratios N. and Mantalaris, Athanasios (2018). Stem cell biomanufacturing under uncertainty: a case study in optimizing red blood cell production. AI Ch E Journal, 64 (8), 3011-3022. doi: 10.1002/aic.16042

Totti, Stella, Allenby, Mark C., Dos Santos, Susana Brito, Mantalaris, Athanasios and Velliou, Eirini G. (2018). A 3D bioinspired highly porous polymeric scaffolding system for: in vitro simulation of pancreatic ductal adenocarcinoma. RSC Advances, 8 (37), 20928-20940. doi: 10.1039/c8ra02633e

Allenby, Mark C., Tahlawi, Asma, Morais, José C. F., Li, Kang, Panoskaltsis, Nicki and Mantalaris, Athanasios (2018). Ceramic hollow fibre constructs for continuous perfusion and cell harvest from 3D hematopoietic organoids. Stem Cells International, 2018 6230214, 1-14. doi: 10.1155/2018/6230214

Allenby, Mark C., Misener, Ruth, Panoskaltsis, Nicki and Mantalaris, Athanasios (2017). A quantitative three-dimensional image analysis tool for maximal acquisition of spatial heterogeneity data. Tissue Engineering - Part C: Methods, 23 (2), 108-117. doi: 10.1089/ten.tec.2016.0413

Allison, Brittany J., Allenby, Mark C., Bryant, Shane S., Min, Jae Eun, Hieromnimon, Mark and Joyner, P. Matthew (2017). Antibacterial activity of fractions from three Chumash medicinal plant extracts and in vitro inhibition of the enzyme enoyl reductase by the flavonoid jaceosidin. Natural Product Research, 31 (6), 707-712. doi: 10.1080/14786419.2016.1217201

Shah, Umang V., Allenby, Mark C., Williams, Daryl R. and Heng, Jerry Y. Y. (2012). Crystallization of proteins at ultralow supersaturations using novel three-dimensional nanotemplates. Crystal Growth and Design, 12 (4), 1772-1777. doi: 10.1021/cg201190c

Conference Papers

Dos Santos, Joana, Enfield, Louise, Dos Santos, Susana Brito, Allenby, Mark C., Zemenides, Sophie, Mantalaris, Athanasios and Panoskaltsis, Nicki (2017). Primary Chronic Lymphocytic Leukemia Cells Can be Maintained Long-Term in Serum-Free, Cytokine-Free 3D Culture. 59th Annual Meeting of the American-Society-of-Hematology (ASH), Atlanta Ga, Dec 09-12, 2017. WASHINGTON: AMER SOC HEMATOLOGY.

dos Santos, Susana Brito, Allenby, Mark C., Mantalaris, Athanasios and Panoskaltsis, Nicki (2016). Early Erythroid Development Is Enhanced with Hypoxia and Terminal Maturation with Normoxia in a 3D Ex Vivo Physiologic Eythropoiesis Model. 58th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH), San Diego Ca, Dec 03-06, 2016. WASHINGTON: AMER SOC HEMATOLOGY.

Allenby, Mark C., Tahlawi, Asma, Misener, Ruth, dos Santos, Susana Brito, Mantalaris, Athanasios and Panoskaltsis, Nicki (2016). Spatiotemporal Mapping of Erythroid, Stromal, and Osteogenic Niche Formation to Support Physiologic Red Cell Production in a Three-Dimensional Hollow Fibre Perfusion Bioreactor. 58th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH), San Diego, CA, United States, 3-6 December 2016. Washington, DC, United States: American Society of Hematology. doi: 10.1182/blood.V128.22.3885.3885

Allenby, Mark C., Tahlawi, Asma, dos Santos, Susana Brito, Misener, Ruth, Hwang, Yu-Shik, Panoskaltsis, Nicki and Mantalaris, Athanasios (2015). DEVELOPMENT OF AN EX VIVO BONE MARROW MIMICRY MICROENVIRONMENT IN A NOVEL 3D HOLLOW FIBRE BIOREACTOR. 44th Annual Scientific Meeting of the International-Society-for-Experimental-Hematology (ISEH), Kyoto Japan, Sep 17-19, 2015. NEW YORK: ELSEVIER SCIENCE INC. doi: 10.1016/j.exphem.2015.06.075

Allison, B., Hester, V., Fleming, M., Allenby, M., Bryant, S. and Joyner, P.M. (2015). Investigation of in vitro bioactivity of extracts and secondary metabolites of Chumash native American medicinal plants. American Society of Pharmacognosy Annual Meeting, Copper Mountain, CO United States, 25–29 July 2015. Stuttgart, Germany: Georg Thieme Verlag. doi: 10.1055/s-0035-1556315