Dr Alys Rachel Clark

BA(Hons) Oxf., MSc PhD Adel.

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Senior Research Fellow

Biography

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

Current

PhD

  • Wendy Kang A computational model of integrative lung physiology for studying nasal high flow therapy.
  • Hamed Minaeizaeim Computing abnormalities in chest x-ray.
  • Rojan Saghian Modelling the uterine circulation to understand the causes and consequences of inadequate spiral artery remodelling.
  • 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
  • Luca Parisi Developing and validating a novel integrated computational model of the human lung to understand the pathophysiology of Acute Respiratory Distress Syndrome
  • Zay Yar Win Patient-specific computational models of lung mechanics and gas exchange to optimise invasive mechanical ventilation


Completed

PhD

ME

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

 

Distinctions/Honours

2012 - Aotearoa Foundation Postdoctoral Fellowship

2014 - Rutherford Discovery Fellowship

2017 - ANZIAM JH Michell 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)

  • 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: Amir Haji Rassouliha, Poul Nielsen, Merryn Tawhai, Andrew Taberner
  • CLARK, A. R., & TAWHAI, M. H. (2018). TEMPORAL AND SPATIAL HETEROGENEITY IN PULMONARY PERFUSION: A MATHEMATICAL MODEL TO PREDICT INTERACTIONS BETWEEN MACRO- AND MICRO-VESSELS IN HEALTH AND DISEASE. The ANZIAM Journal, 59 (04), 562-580. 10.1017/S1446181118000111
    Other University of Auckland co-authors: Merryn Tawhai
  • Kang, W., Tawhai, M. H., Clark, A. R., Sá RC, Geier, E. T., Prisk, G. K., & Burrowes, K. S. (2018). In silico modeling of oxygen-enhanced MRI of specific ventilation. Physiological reports, 6 (7)10.14814/phy2.13659
    Other University of Auckland co-authors: Kelly Burrowes, Merryn Tawhai

Identifiers

Contact details

Primary office location

UNISERVICES HOUSE - Bldg 439
Level 7, Room 717
70 SYMONDS ST
AUCKLAND 1010
New Zealand

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