Publications

1. Hunter, Peter J., Weiwei Ai, and David P. Nickerson. Energy-based bond graph models of glucose transport with SLC transporters. Biophysical Journal, Volume 124, Issue 2, 316 - 335, 2025
   
   
2. Means Shawn A., Hussan Jagir R., Garrett Amy S., Cheng Leo K. and Clark Alys Rachel, 2025, Electrical wave generation and spatial organization in uterine tissue J. R. Soc. Interface. 2220240638
   
   
3. Amy S Garrett , Mathias W Roesler, Omkar N Athavale, Peng Du, Shawn A Means, Alys R Clark, Leo K Cheng, 2024. Multichannel mapping of in vivo rat uterine myometrium exhibits both high and low frequency electrical activity in non-pregnancy. Sci Rep 2024 Mar 27;14(1):7316.
   
   
4. Athavale ON, Avci R, Clark AR, Di Natale MR, Wang X, Furness JB, Liu Z, Cheng LK, Du P. Neural regulation of slow waves and phasic contractions in the distal stomach: a mathematical model. J Neural Eng. 2024 Jan.
   
   
5. Athavale ON, DiNatale MR, Avci R, Clark AR, Furness JB, Cheng LK, Du P. Mapping the rat gastric slow wave conduction pathway: Bridging in vitro and in vivo methods, revealing a loosely-coupled region in the distal stomach. Am J Physiol Gastrointest Liver Physiol. 2024 Jun 11. PMID: 38860855.
   
   
6. Means, S.A., Roesler, M.W., Garrett, A.S., Cheng, L. and Clark, A.R., 2023. Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model. PLOS Computational Biology, 19(8), p.e1011359. 
   
   
7. Ebrahimi BS, Khwaounjoo P, Chan HF, Argus F, Ma X, Nash MP, Doi A, Dagan M, Kaye DM, Joseph T, McGiffin D, Tawhai MH. Patient-Specific Haemodynamic Modeling to Estimate the Extent of Microvascular Disease and Response to Pulmonary Endarterectomy in Chronic Thromboembolic Pulmonary Hypertension. Pulm Circ. 2025 Oct 14;15(4):e70176. PMID: 41104021; PMCID: PMC12521630.
   
   
8. Hunter, P., de Bono, B., Brooks, D., Christie, R., Hussan, J., Lin, M., & Nickerson, D. (2024). IEEE Reviews in Biomedical Engineering, vol. 18, pp. 300-315, 2025.
   
   
9. Kim, J., Yeung, T., Raghvani, R., Choisne, J., & Besier, T. (2025). Robust workflow for diaphyseal cortical bone thickness calculation. Journal of Biomechanics, 11303.
   
   
10. Alessandra Aldieri, Thiranja Prasad Babarenda Gamage, Antonino Amedeo La Mattina, Axel Loewe, Francesco Pappalardo, Marco Viceconti. Consensus statement on the credibility assessment of machine learning predictors, Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf100,
    
    
11. Haggie, L., Schmid, L., Rohrle, O., Besier, T., McMorland, A., & Saini, H. (2023). Linking cortex and contraction-Integrating models along the corticomuscular pathway. Front Physiol, 14, 1095260.
    
    
12. Xu Y, Bruling J, Carman L, Yeung T, Besier TF, Choisne J. A statistical shape and density model can accurately predict bone morphology and regional femoral bone mineral density variation in children. Bone. 2025;193:117419. 
    
    
13. Yahya, Y., Hunter, I., Besier, T., Taberner, A., & Ruddy, B. (2022). Shoulder Joint Stiffness in a Functional Posture at Various Levels of Muscle Activation. IEEE Trans Biomed Eng, 69(7), 2192-2201. https://doi.org/10.1109/TBME.2021.3138398
    
    
14. Ai, Weiwei, and David P. Nickerson (2021). A Quantitative Model of Human Jejunal Smooth Muscle Cell Electrophysiology. Physiome. Journal contribution.
    
    
15. Fong, Shelly, and Jeffrey J. Saucerman (2021). A kinetic model of β-adrenergic control in cardiac myocytes. Physiome Journal contribution. 
    
    
16. Ai, Weiwei, Limor Freifeld, and David P. Nickerson (2021). Mathematical model of excitation-contraction in a uterine smooth muscle cell. Physiome. Journal contribution. 
    
    
17. Simulating multi-scale pulmonary vascular function by coupling computational fluid dynamics with an anatomic network model. BS Ebrahimi, H Kumar, MH Tawhai, KS Burrowes, EA Hoffman, AR Clark. Frontiers in Network Physiology, 2021. 
    
    
18. P Khwaounjoo, A Dixon, A Hajirassouliha, E Lam Po Tang, M Webster, A Taberner, P Nielsen, M Nash, Y Cakmak (2023). Non-contact quantification of aortic stenosis and mitral regurgitation using carotid waveforms from skin displacements. Physiological Measurement.
    
    
19. Athavale ON, Avci R, Cheng LK, Du P. Computational models of autonomic regulation in gastric motility: Progress, challenges, and future directions. Frontiers in Neuroscience. 2023;17.
    
    
20. Mathias W Roesler, Amy S Garrett, Mark L Trew, Dane Gerneke, Satya Amirapu, Leo K Cheng, Alys R Clark, 2024. Three-dimensional virtual histology of the rat uterus musculature using micro-computed tomography. J Anat 2024 Sep 10.
    
    
21. Dowrick JM, Roy NC, Bayer S, Frampton CMA, Talley NJ, Gearry RB, Angeli‐Gordon TR. Unsupervised machine learning highlights the challenges of subtyping disorders of gut-brain interaction. Neurogastroenterol. Motil. 2024;36(12):e14898.

2024
 

• Sands G.B., Randles H. & Nielsen P.M.F. Incorporating Wearable Sensor Data into Research Workflows. Virtual Physiological Human (VPH): Data-Driven Simulation Technologies for Clinical Decision Making; 2024; Stuttgart, Germany. 

• Khwaounjoo, P., Dixon, A., HajiRassouliha, A., Po Tang, E. L., Webster, M., Taberner, A., Nielsen, P., Nash, M., Edwards, N. & Cakmak, Y. Non-Contact Quantification of Valvular Disease Using Carotid Waveforms From Skin Displacements—Echocardiography Pilot Study. in Heart Lung Circ S389 (2024).

• Carman L, Besier T, Choisne J, editors. Predicting paediatric lower limb bone geometry using bony landmarks. European Society for Movement Analysis in Adults and Children (ESMAC); 2024; Oslo, Norway.

• Besier T, Carman L, Choisne J, Passmore E, Modenese L, Carty C, editors. Harmonising historical clinical gait analysis data using personalised musculoskeletal models. European Society for Movement Analysis in Adults and Children (ESMAC); 2024; Oslo, Norway.

2023
 

• AW Dixon, SP Richardson, H Suami, TP Babarenda Gamage, PMF Nielsen, HM Reynolds (2023). Toward Development of a Portable System for 3D Fluorescence Lymphography. 45th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. 

• IEEE Engineering in Medicine and Biology Society - Predicting Patient Status in Chronic Thromboembolic Pulmonary Hypertension Using a Biophysical Model Sep 2023, Engineering in Medicine and Biology conference (EMBC) Shaarbaf Ebrahimi B, Khwaounjoo P, Argus F, Chan H, Nash M, Tawhai M

• B. Ebrahimi, ‘Predicting Patient Status in Chronic Thromboembolic Pulmonary Hypertension Using a Biophysical Model’, Annual Meeting of the IEEE Engineering in Medicine and Biology Society, Sydney Australia, July 2023

• Carman L., Besier T.F., Choisne J., Combined shape model of the lower limb in a paediatric population provides accurate bone shape estimation, CMBBE 2023.

• Garrett AS, Roesler MW, Athavale ON, Du P, Cheng L, Clark AR. Acute In Vivo Measurement of Uterine Smooth Muscle Electrophysiology in Rats SRI 2023: Scientific Program & Abstracts. Reprod. Sci. 30 (Suppl 1), 1–324 (2023). 

2021
 

• IUPS (International Union of Physiological Sciences) 2022 second Global Physiological Sciences Report: Physiology – Challenges and the Way Forward,  UPS Physiome Project, Peter Hunter.