Dr. David C. Clarke

Research interests: quantitative exercise biology

The mission of my research program is to build predictive models of exercise-training adaptations to improve fundamental understanding of exercise biology and to optimize exercise training programs for health, fitness, rehabilitation or performance goals. The lab's research is organized into the following themes:

1. Exercise-responsive cell signaling
   We study how exercise duration and intensity are encoded as cell signaling network dynamics using computational modeling and cell-culture-based experimental techniques.
2. Sports analytics and modeling of wearable-sensor data
   We devise improved metrics and algorithms for analyzing data from portable exercise- and physical-activity-monitoring devices in order to determine ways to individually optimize training programs.
   
3. Evidence-based exercise programming
   We conduct systematic reviews and meta-analyses of published data to create tools that facilitate evidence-based exercise programming.
4. Clinical exercise physiology
   Student interests and requests for collaboration have motivated us to pursue several clinically relevant exercise physiology projects, such as mitochondrial disease, congenital heart disease, and relative energy deficiency in sports.       
   

Our research is interdisciplinary and is informed by the concepts and tools of exercise physiology, systems biology, and biomedical engineering. Each project typically involves the development, validation, and application of mathematical models. Keywords: exercise physiology, training programming, cell signal transduction, mathematical modeling, statistical modeling, systems biology, proteomics, sports analytics.

Publications:

A complete up-to-date list of publications is available on PubMed.

• McColl, T. J., Clarke, D. C. (2024). Kinetic modeling of leucine-mediated signaling and protein metabolism in human skeletal muscle. iScience. 27(1): 108364.
• Peng, K., Brodie, R. T., Swartz, T. B., Clarke, D. C. (2024). Bayesian inference of the impulse-response model of athlete training and performance. International Journal of Performance Analysis in Sport. 24(1): 74-89.
• Cormier, P., Tsai, M.-C., Meylan, C., Soares, V. H. T., Clarke, D. C., Klimstra, M. (2023). Minimal number of events required for acceleration-speed profiling in elite women’s soccer. International Journal of Sports Physiology and Performance. 18(12): 1457-1460.
• Eisenhardt, D., Kits, A., Madeleine, P., Samani. A., Clarke, D. C., Kristiansen, M. (2023). Augmented-reality swim goggles accurately and reliably measure swim performance metrics in recreational swimmers. Frontiers in Sports and Active Living. 5: 1188102.
• Yogev, A., Arnold, J., Clarke, D. C., Guenette, J. A., Sporer, B. C., Koehle, M. (2023). The effect of severe intensity bouts on muscle oxygen saturation responses in trained cyclists. Frontiers in Sports and Active Living. 5: 1086227
• Weigend, F. C., Clarke, D. C., Obst, O., Siegler, J. (2023). A hydraulic model outperforms work-balance models for predicting recovery kinetics from intermittent exercise. Annals of Operations Research. 325: 589–613.
• Mattman, A., Nadeau, E., Mezei, M. M., Cresswell, M., Zhao, S., Bosdet, T., Sin, D. D., Guenette, J. A., Dupuis, I., Allin, E., Clarke, D. C. (2022). Ketogenic diet for mitochondrial disease: potential role in treating the Multiple Symmetric Lipomatosis phenotype associated with the common MT-TK genetic mutation. Orphanet Journal of Rare Diseases. 17(1): 1-2.
• Peng, K., Clarke, D. C., Swartz, T. B. (2022) Bayesian approaches for critical velocity modelling of data from intermittent efforts. International Journal of Sports Science and Coaching. 17(4): 868-879.
• Yogev, A., Arnold, J., Clarke, D. C., Guenette, J. A., Sporer, B. C., Koehle, M. (2022). Comparing the respiratory compensation point with muscle oxygen saturation in locomotor and non-locomotor muscles using wearable NIRS spectrometry during whole body exercise. Frontiers in Physiology. 13: 818733.
• Charlton, B. T., Forsyth, S., Clarke, D. C. (2022). Low energy availability and relative energy deficiency in sport: what coaches should know. International Journal of Sports Science and Coaching. 17(2): 445-460.
• Skiba, P. F., Clarke, D. C. (2021). The W¢ balance model: mathematical and methodological considerations. International Journal of Sports Physiology and Performance. 16(11): 1561-1572. 
• Heeney, N. D., Lee, R. H., Hockin, B. C. D., Clarke, D. C., Sanatani, S., Armstrong, K., Sedlak, T., Claydon, V.E. (2021). At-home determination of 24-hour urine sodium excretion: validation of chloride test strips and multiple spot samples. Autonomic Neuroscience. 233: 102797.
• Coccimiglio, I. F., Clarke, D. C. (2020) ADP is the dominant controller of AMP-activated protein kinase activity dynamics in skeletal muscle during exercise. PLoS Computational Biology. 16 (7): e1008079.
• Maganja, S. A., Clarke, D. C., Lear, S. A., Mackey, D. C. (2020) Formative Evaluation of Consumer-Grade Activity Monitors Worn by Older Adults: Test-Retest Reliability and Criterion Validity of Step Counts. JMIR Formative Research. 4(8):e16537. doi: 10.2196/16537.
• Nadeau, E., Mezei, M. M., Cresswell, M., Zhao, S., Bosdet, T., Sin, D. D., Guenette, J. A., Dupuis, I., Allin, E., Clarke, D. C., Mattman, A. (2020) Self-initiated lifestyle interventions lead to potential insight into an effective, alternative, non-surgical therapy for mitochondrial disease associated multiple symmetric lipomatosis. Mitochondrion. Mar 29. pii: S1567-7249(19)30315-0.
• Puchowicz, M. J., Baker, J., Clarke, D. C. (2020) Development and field validation of an omni-domain power-duration model. Journal of Sports Sciences. 38(7):801-813.
• Puchowicz, M. J., Mizelman, E., Yogev, A., Koehle, M. S., Townsend, N. E., Clarke, D. C. (2018) The critical power model as a potential tool for anti-doping. Frontiers in Physiology. 9: 643.
• Morris, M. K., Clarke, D. C., Osimiri, L. C., Lauffenburger, D. A. (2016) Systematic analysis of quantitative logic model ensembles predicts drug combination effects on cell signaling networks. Clinical Pharmacology and Therapeutics – Pharmacometrics and Systems Pharmacology. 5(10): 544-553.
• Landry, B. D., Clarke, D. C., Lee, M. J. (2015) Studying Cellular Signal Transduction with OMIC Technologies. Journal of Molecular Biology. 427(21): 3416-40.
• Skiba, P. F., Fulford, J. Clarke, D. C., Vanhatalo, A., Jones, A. M. (2015) Intramuscular determinants of the ability to recover work capacity above critical power. European Journal of Applied Physiology. 115(4): 703-13.
• Skiba, P. F., Clarke, D., Vanhatalo, A., Jones, A. M. (2014) Validation of a novel intermittent W′ model for cycling using field data. International Journal of Sports Physiology and Performance. 9(6): 900-4.
• Skiba, P. F., Jackman, S., Clarke, D., Vanhatalo, A., Jones, A. M. (2014) Effect of work and recovery durations on W' reconstitution during intermittent exercise. Medicine and Science in Sports and Exercise. 46(7):1433-40.
• Clarke, D. C., Skiba, P. F. (2013) Rationale and resources for teaching mathematical modeling of athletic training and performance. Advances in Physiology Education. 37(2): 134-152.

Teaching:

• BPK 310 – Exercise/Work Physiology
• BPK 443 – Advanced Exercise Programming