Publications

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

Underlined names indicate Lab trainees.

Peer-reviewed journal publications

Regnier, K., Beaupre, L. P. R., Coccimiglio, I. F., McColl, T. J., Clarke, D. C., Gurd, B. J. Bioinformatic analysis of differentially expressed long non-coding RNAs in skeletal muscle following aerobic and resistance exercise. Genes. 17(1): 110; https://doi.org/10.3390/genes17010110

Kits, A., Chhatre Elder, N., Eisenhardt, D., Hamedani, Y. D., Hoskinson, R., Madeleine, P., Samani, A., Kristiansen, M., Clarke, D. C. Smart swim goggles accurately measure heart rate during swim training: A criterion validation study. Journal of Sports Sciences, 1–14. https://doi.org/10.1080/02640414.2025.2610787

De Souza, A. M., Armstrong, K.R., Hoskins, K., Tran, N., Naylor, K. C., Romans, H. V., Potts, J. E., Hosking, M. C., Clarke, D. C. (2025). Aerobic fitness is related to sports participation in children with congenital heart disease.  Pediatric Cardiology. Vol:1-9. https://doi.org/10.1007/s00246-025-04014-0

Alfonso Martin, C., Clarke, D. C., Capdevila, L. (2025) Individual training prescribed by heart rate variability, heart rate and well-being scores in experienced cyclists. Scientific Reports. 15: 34023. https://doi.org/10.1038/s41598-025-13540-z

Eisenhardt, D., Kits, A., Madeleine, P., Samani, A., Clarke, D. C., Kristiansen, M. V. (2025) Compliance to prescribed training among recreational swimmers using augmented-reality swim goggles: A randomized controlled trial. Journal of Sports Sciences. 1-13. https://doi.org/10.1080/02640414.2025.2540661

Jeong, M., McColl, T. J., Clarke, D. C. (2025) Mechanisms of muscle atrophy in type 2 diabetes mellitus: Factors dysregulating muscle protein synthesis and breakdown. Applied Physiology, Nutrition, and Metabolism. 50: 1-22. https://doi.org/10.1139/apnm-2025-0017

Mayerhofer, P., Napier, C., Clarke, D. C., Bajic, I., Donelan, J. M. (2025) Neural networks can accurately identify individual runners from their foot kinematics but fail to predict their running performance. Journal of Biomechanics. 185: 112663. https://doi.org/10.1016/j.jbiomech.2025.112663

Sitko, S., Hopker, J., Townsend, N., Pinotti, M., Zabala, M., Artetxe, X., Gallo, G., Mateo-March, M., Sanders, D., Grappe, F., Carceller, A., Clarke, D. C., Valenzuela, P., van Erp, T., Viribay, A. (2025) Antidoping 2.0. Is adding power data to the biological passport the next step? Experts viewpoint. International Journal of Sports Physiology and Performance. 20: 172-175. https://doi.org/10.1123/ijspp.2024-0088

Yin, D., Engracia, M. V., Edema, M. K., Clarke, D. C. (2024). A PubMed search filter for efficiently retrieving exercise training studies. BMC Medical Research Methodology. 24: 302. https://doi.org/10.1186/s12874-024-02414-z

McColl, T. J., Clarke, D. C. (2024). Progress in physiologically based pharmacokinetic-pharmacodynamic models of amino acids in humans. Current Opinion in Clinical Nutrition and Metabolic Care. https://doi-org/10.1097/mco.0000000000001067

Yogev, A., Arnold, J., Nelson, H., Rosenblat, M. A., Clarke, D. C., Guenette, J. A., Sporer, B. C., Koehle, M. (2024). The effects of endurance training on muscle oxygen desaturation during incremental exercise tests: A systematic review and meta-analysis. Frontiers in Sports and Active Living. 6: 1406987. https://doi.org/10.3389/fspor.2024.1406987

Sitko, S., Hopker, J., Townsend, N., Pinotti, M., Zabala, M., Artetxe, X., Gallo, G., Mateo-March, M., Sanders, D., Grappe, F., Carceller, A., Clarke, D. C., Valenzuela, P., van Erp, T., Viribay, A. (2024) Antidoping 2.0. Is adding power data to the biological passport the next step? Experts viewpoint. International Journal of Sports Physiology and Performance. 20: 172-175. https://doi.org/10.1123/ijspp.2024-0088

Mizelman, E., Pearson, A., Chu, D., Clarke, D. C. (2024). Critical speed models of high-resolution speed-duration profiles describe peak running demands in soccer. International Journal of Sports Science and Coaching. 19(5), 2056-2066. https://doi.org/10.1177/17479541241246951

McColl, T. J., Clarke, D. C. (2024). Kinetic modeling of leucine-mediated signaling and protein metabolism in human skeletal muscle. iScience. 27(1): 108364. https://doi.org/10.1016/j.isci.2023.108634

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. https://doi.org/10.1080/24748668.2023.2268480; Preprint: SportRxiv, https://doi.org/10.51224/SRXIV.246

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. doi: 10.1123/ijspp.2023-0223

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. https://doi.org/10.3389/fspor.2023.1188102

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. https://doi.org/10.3389/fspor.2023.1086227

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. https://doi.org/10.1007/s10479-022-04947-2

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. https://doi.org/10.1186/s13023-021-02164-x

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. https://doi.org/10.1177/17479541221100311

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. https://doi.org/10.3389/fphys.2022.818733.

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. https://doi.org/10.1177%2F17479541211054458.

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. https://doi.org/10.1123/ijspp.2021-0205

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. https://doi.org/10.1016/j.autneu.2021.102797

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. https://doi.org/10.1371/journal.pcbi.1008079

Maganja, S. A., Clarke, D. C., Lear, S. A., Mackey, D. C. (2020). Test-Retest Reliability and Criterion Validity of Step Counts from Consumer-Grade Activity Monitors Worn by Older Adults. JMIR Formative Research. 4(8): e16537. https://doi.org/10.2196/16537

Nadeau, E., Mezeib, M., Cresswell, M., Zhao, S., Bosdet, T., Sin, D., Guenette, J. A., Allin, E., Dupuis, I., 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. 52:183-189. https://doi.org/10.1016/j.mito.2020.03.009

Puchowicz, M. J., Baker, J. R., Clarke, D. C. (2020) Development and field validation of an omni-domain power-duration model. Journal of Sport Sciences. 38(7):801-813. https://doi.org/10.1080/02640414.2020.1735609

Puchowicz, M. J., Mizelman, E., Yogev, A., Koehle, M., Townsend, N. E., Clarke, D. C. (2018) The critical power model as a potential tool for anti-doping. Frontiers in Physiology. 9: article 643. 21 pgs. https://doi.org/10.3389/fphys.2018.00643

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. doi:10.1002/psp4.12104
*Contributed equally

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.

Leon L. R.*, Dineen, S., Blaha, M.D., Rodriguez-Fernandez, M., Clarke, D. C. (2013) Attenuated thermoregulatory, metabolic and liver acute phase protein response to heat stroke in TNF-receptor knockout mice. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology. 305(12): R1421-32.
*Lead & corresponding author

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.
*Lead & corresponding author

Huang, S. C., Clarke, D. C., Labadorf, A., Chouinard, C. R., Gordon, W., Lauffenburger, D. A., Fraenkel, E. (2013) Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogenically induced signaling. PLoS Computational Biology. Feb 9(2): e1002887. doi:10.1371/journal.pcbi.1002887.

Clarke, D. C., Morris, M. K., Lauffenburger, D. A. (2013) Normalization and statistical analysis of multiplexed bead-based immunoassay data using mixed-effects models. Molecular and Cellular Proteomics. 12(1): 245-62.

Clarke, D. C., Lauffenburger, D. A. (2012). Multi-pathway network analysis of human epithelial cell responses in inflammatory environments. Biochemical Society Transactions. 40(1):133-8.

Morris, M. K., Saez-Rodriguez, J., Clarke, D. C., Sorger, P., Lauffenburger, D. A. (2011). Training signaling pathway maps to biochemical data with constrained fuzzy logic: Quantitative analysis of liver cell responses to inflammatory stimuli. PLoS Computational Biology. 7: e1001099. doi:10.1371/journal.pcbi.1001099

Clarke, D. C., Brown, M. L., Erickson, R. A., Shi, Y., Liu, X. (2009). Transforming Growth Factor-β depletion is the primary determinant of Smad signaling kinetics. Molecular and Cellular Biology. 29(9): 2443-2455.

Clarke, D. C. and Liu, X. (2008). Decoding the quantitative nature of Transforming Growth Factor-β signaling. Trends in Cell Biology. 18(9): 430-42.

Zhu, S., Wang, W., Clarke, D. C., Liu, X. (2007). Activation of Mps1 promotes Transforming Growth Factor-β-independent Smad signaling. J. Biol. Chem. 282(25): 18327-18338.

Clarke, D. C., Betterton, M. D., Liu, X. (2006). Systems theory of Smad signalling. Systems Biology (Stevenage). 153(6): 412-424.

Clarke, D. C. (2004) Restoring physiology to the undergraduate biology curriculum: a call to action. Advances in Physiology Education. 28(1-4):128. https://doi.org/10.1152/advan.00008.2004

Clarke, D. C., Miskovic, D., Han, X.-X., Calles-Escandon, J., Glatz, J. F. C., Luiken, J. J. F. P., Heikkila, J. J., Bonen, A. (2004). Overexpression of plasma-membrane-associated fatty acid binding protein (FABPpm) in vivo increases fatty acid sarcolemmal transport and metabolism. Physiol. Genomics. 17: 31-37.

Book chapters

Clarke, D. C. and Liu, X. (2010). Measuring the absolute abundance of the Smad transcription factors using quantitative immunoblotting. Methods in Molecular Biology. 647: 357-376. DOI: 10.1007/978-1-60761-738-9_22.

Technical reports

Clarke, D. C., Dumont, K. D. (2021). Manipulating and monitoring atmospheric and culture medium conditions using the Baker Ruskinn SCI-tive hypoxia workstation and the Lucid Scientific oxygen sensing system. White paper for The Baker Company, Inc. 15 pages. https://bakerco.com/images/uploads/assets/Baker_Ruskinn_SCI-tive_Hypoxia_White_Paper.pdf

Clarke, D. C. (2020). A proposed framework for the development of the sport data science discipline within Canadian high-performance sport. Submitted to Own The Podium. December 2020.

Industry publications

Peretz, D., Khuu, C., Bautista Jr., A., Clarke, D. C., and Gao, Q. (2013). Validation and application of Bio-Plex Pro™ Cell Signaling Assays. Bio-Rad Bulletin 6331.

Non-peer-reviewed and lay publications

Clarke, D.C., and Ricci, M. (2009). Calculated performance: Using quantitative models to optimize your training. Triathlete Magazine, January 2009 edition, p.119.

Selected presentations