Dr Alys Rachel Clark

BA(Hons) Oxf., MSc PhD Adel.

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Senior Research Fellow


Alys Clark obtained her Bachelor of Arts (Honours) in Mathematical Sciences from the University of Oxford and her Masters and PhD degrees in Applied Mathematics at the University of Adelaide. She joined the ABI in 2008 as a Postdoctoral Research Fellow in the Lung Research Group and now is one of the lead researchers in that group, as well as leading an active research group in reproductive health and development. Alys is a current awardee of a RSNZ Rutherford Discovery Fellowship (2014), and the JH Michell Medal for Applied Mathematics (2017).


Research | Current

Alys’ research interests focus on understanding how we get oxygen from our environment, before and after birth, and using this new knowledge to improve diagnosis and treatment strategies when things go wrong. Alys develops computational models of lungs, placenta and ovaries, which account for complexities in their structure and can predict the impact of disease on organ function. Her expertise lies in developing efficient and reliable methods for modelling physical processes that occur simultaneously in complex networks of tissue and blood vessels.

Placental health 

Abnormal vascular stucture in the uterus and placenta have been implicated in serious complications of pregnancy, such as intra-uterine growth restriction and pre-eclampsia. We aim to construct structural and functional models of the placenta uterus throughout pregnancy that can help to detect problems earlier and more reliably.

Lung health

The impact of lung disease on daily life is considerable, with sufferers often unable to go about activities without becoming short of breath. Lung disease often starts small, via tiny changes in lung tissue structure, and is often undectable in conventional CT imaging until significant damage is done. We aim to develop new models predicting the impact of lung disease on an individual, and new image analysis tools to improve detection of disease before it becomes severe. Importantly, we consider how age (young and old) modifies disease impact, and so should be considered in treatment planning. 

Project linkages

Postgraduate supervision



  • Vijayalakshmi Srinivasan In silico models of fetal growth restriction to aid clinical translation
  • Sayak Ray Model and image-based approaches to understanding utero-placental vascular development.
  • Anandita Umapathy Mesenchymal stem cell transplantation as a potential therapy for fetal growth restriction
  • Joyce John A computer-based quantitative CT Analysis for prediction of disease progression and mortality in interstitial lung disease
  • Behad Ebrahimi A tool for prediction of patient status in pulmonary hypertension
  • Hamed Minaeizaeim Computing abnormalities in chest x-ray.
  • Yuwen Zhang Integration of dynamic lung imaging with structure-based models of lung function
  • Michael Gravatt Modelling the collective behaviour of swimming microorganisms
  • Win Min Tun Oxygen and shear stress in placental vascular development
  • Nurul Izza Ismail Cellular and molecular mechanisms of maternal immune response in early pregnancy
  • Zay Yar Win Patient-specific computational models of lung mechanics and gas exchange to optimise invasive mechanical ventilation


  • Monika Byrne Modelling Human Feto-Placental Circulation Based on Imaging
  • Ali Moulvi How do mum and fetus interact in early pregnancy? The shear stress response of the placental syncytiotrophoblast 



  • Rojan Saghian Modelling the uterine circulation to understand the causes and consequences of inadequate spiral artery remodelling.
  • Wendy Kang A computational model of integrative lung physiology for studying nasal high flow therapy.
  • Mabelle Lin A computational model of the placental chorionic villous.
  • Yik Ching (Joshua) Lee Predicting pulmonary hypertension.


  • Fung Chan Multimodal lung image registration.
  • Arthur Postles Arterial wall shear stress in acute and chronic pulmonary embolism.



2012 - Aotearoa Foundation Postdoctoral Fellowship

2014 - Rutherford Discovery Fellowship

2017 - ANZIAM JH Michell Medal

2018 - University of Auckland Research Excellence Medal

Areas of expertise

Alys' areas of expertise include

  • Multi-scale modelling of blood flow, air flow and nutrient transport mechanisms.
  • Image analysis, including functional interpretation of images with computational models.
  • Modelling structure-function relationships in complex vascular networks through life.

Selected publications and creative works (Research Outputs)

  • Clark, A., & Tawhai, M. (2019). Pulmonary Vascular Dynamics. Comprehensive Physiology, 9 (3), 1081-1100. 10.1002/cphy.c180033
    Other University of Auckland co-authors: Merryn Tawhai
  • Zhang, Y., Osanlouy, M., Clark, A. R., Kumar, H., King, C., Wilsher, M. L., ... Tawhai, M. H. (2019). Pulmonary lobar segmentation from computed tomography scans based on a statistical finite element analysis of lobe shape. Progress in Biomedical Optics and Imaging - Proceedings of SPIE. 10.1117/12.2512642
    Other University of Auckland co-authors: Haribalan Kumar, Merryn Tawhai
  • Saw, S. N., Tay, J. J. H., Poh, Y. W., Yang, L., Tan, W. C., Tan, L. K., ... Yap, C. H. (2018). Altered Placental Chorionic Arterial Biomechanical Properties During Intrauterine Growth Restriction. Scientific reports, 8 (1)10.1038/s41598-018-34834-5
  • Subramaniam, K., Clark, A. R., Hoffman, E. A., & Tawhai, M. H. (2018). Metrics of lung tissue heterogeneity depend on BMI but not age. Journal of applied physiology (Bethesda, Md. : 1985), 125 (2), 328-339. 10.1152/japplphysiol.00510.2016
    Other University of Auckland co-authors: Merryn Tawhai
  • Gravatt, M., Suresh, V., Clark, A., & Clarke, R. (2018). Importance of irrotational components of swimming flows on the stability of a suspension of weakly-squirming microorganisms. IMA JOURNAL OF APPLIED MATHEMATICS, 83 (4), 720-742. 10.1093/imamat/hxy020
    URL: http://hdl.handle.net/2292/42655
    Other University of Auckland co-authors: Richard Clarke, Vinod Suresh
  • James, J. L., Saghian, R., Perwick, R., & Clark, A. R. (2018). Trophoblast plugs: impact on utero-placental haemodynamics and spiral artery remodelling. Human reproduction (Oxford, England)10.1093/humrep/dey225
    URL: http://hdl.handle.net/2292/44889
    Other University of Auckland co-authors: Jo James
  • Clark, A. R., James, J. L., Stevenson, G. N., & Collins, S. L. (2018). Understanding abnormal uterine artery Doppler waveforms: A novel computational model to explore potential causes within the utero-placental vasculature. Placenta, 66, 74-81. 10.1016/j.placenta.2018.05.001
    Other University of Auckland co-authors: Jo James
  • Richardson, S., Babarenda Gamage, T. P., HajiRassouliha, A., Jackson, T., Hedges, K., Clark, A., ... Nielsen, P. M. F. (2018). Towards a real-time full-field stereoscopic imaging system for tracking lung surface deformation under pressure controlled ventilation. Computational Biomechanics for Medicine: Measurements, Models, and Predictions (pp. 119-130). 10.1007/978-3-319-75589-2_12
    Other University of Auckland co-authors: Thiranja Babarenda Gamage, Amir Haji Rassouliha, Poul Nielsen, Merryn Tawhai, Andrew Taberner


Contact details

Primary office location

Level 7, Room 717
New Zealand

Social links

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