Publications

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

Weigend, F. C., Clarke, D. C., Obst, O., & Siegler, J. (2021) A hydraulic model outperforms work-balance models for predicting recovery kinetics from intermittent exercise. arXiv preprint arXiv:2108.04510.

Heeney, N.D., Lee, R.H., Hockin, B.C.D., Clarke, D.C., Sanatani, S., Armstrong, K., Sedlak, T. and Claydon, V.E. (2021) At-home determination of 24-h urine sodium excretion: Validation of chloride test strips and multiple spot samples. Autonomic Neuroscience, 233: 102797.

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.

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.
*contributed equally to this work

Landry, B. D., Clarke, D. C., Lee, M. J. 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 DC, Skiba PF. Rationale and resources for teaching mathematical modeling of athletic training and performanceAdvances in Physiology Education. 2013 37(2):134-152. See commentary by Dr. Skiba here.

Huang SC, Clarke DC, Labadorf A, Chouinard CR, Gordon W, Lauffenburger DA, Fraenkel E. Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogenically induced signalingPLoS Computational Biology. 2013 Feb 9(2): e1002887. doi:10.1371/journal.pcbi.1002887.

Clarke DC, Morris MK, Lauffenburger DA. Normalization and statistical analysis of multiplexed bead-based immunoassay data using mixed-effects modelingMolecular and Cellular Proteomics. 2013 Jan; 12(1): 245-62.

Clarke DC, Lauffenburger DA. Multi-pathway network analysis of human epithelial cell responses in inflammatory environmentsBiochemical Society Transactions. 2012 Feb 1;40(1):133-8.

Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuliPLoS Computational Biology. 2011 Mar;7(3):e1001099.

Clarke DC, Liu X. Measuring the absolute abundance of the Smad transcription factors using quantitative immunoblottingMethods in Molecular Biology. 2010; 647:357-76.

Clarke DC, Brown ML, Erickson RA, Shi Y, Liu X. Transforming growth factor-β depletion is the primary determinant of Smad signaling kineticsMolecular and Cellular Biology. 2009 May;29(9):2443-55.

Clarke DC, Liu X. Decoding the quantitative nature of TGF-β/Smad signalingTrends in Cell Biology. 2008 Sep;18(9):430-42.

Zhu S, Wang W, Clarke DC, Liu X. Activation of Mps1 promotes transforming growth factor-β-independent Smad signalingJournal of Biological Chemistry. 2007 Jun 22;282(25):18327-38.

Clarke DC, Betterton MD, Liu X. Systems theory of Smad signallingSystems Biology (Stevenage). 2006 Nov;153(6):412-24.

Clarke DC, Miskovic D, Han XX, Calles-Escandon J, Glatz JF, Luiken JJ, Heikkila JJ, Bonen A. Overexpression of membrane-associated fatty acid binding protein (FABPpm) in vivo increases fatty acid sarcolemmal transport and metabolismPhysiological Genomics. 2004 Mar 12;17(1):31-7.

Bonen A, Benton CR, Campbell SE, Chabowski A, Clarke DC, Han XX, Glatz JF, Luiken JJ. Plasmalemmal fatty acid transport is regulated in heart and skeletal muscle by contraction, insulin and leptin, and in obesity and diabetesActa Physiologica Scandinavica. 2003 Aug;178(4):347-56.