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Doyle, III FJ, Petzold LR, Smith KS, Taylor SR, Webb AB.  2010.  Velocity Response Curves Support the Role of Continuous Entrainment in Circadian Clocks. JOURNAL OF BIOLOGICAL RHYTHMS. 25:138-149.
Doyle, III FJ, Shoemaker J, Bagheri N, Mirsky H, Petzold L, Gunawan R, Hildebrandt S, Taylor S.  2010.  Systems Analysis for Systems Biology. SYSTEMS BIOMEDICINE: CONCEPTS AND PERSPECTIVES. :249-272.
Doyle, III FJ, Shoemaker JE, Gunawan R, Mirsky H, Stelling J, Taylor SR, Bagheri N, Kwei E.  2009.  Automatic Control in Systems Biology. SPRINGER HANDBOOK OF AUTOMATION. :1335-1360.
Doyle FJ, Mahadevan R, Gadkar KG.  2005.  Batch control of genetic alterations for optimal metabolic engineering. PROCEEDINGS OF THE AMERICAN CONTROL CONFERENCE. :3108-3114.
Doyle FJ, Harrison CA, Crowley TJ.  2003.  Hybrid model-based approach to batch-to-batch control of particle size distribution in emulsion polymerization. COMPUTERS & CHEMICAL ENGINEERING. 27:1153-1163.
Doyle, III FJ.  2012.  Zone Model Predictive Control of an Artificial Pancreas. :8-9.
Doyle, III FJ, Pinto MA, Immanuel CD.  2007.  A feasible solution technique for higher-dimensional population balance models. COMPUTERS & CHEMICAL ENGINEERING. 31:1242-1256.
Doyle, III FJ, Herzog ED, Tsai CA, Granados-Fuentes D, Mazuski C, Harang R, Petzold LR, Meeker K, Kim J, An S.  2013.  A neuropeptide speeds circadian entrainment by reducing intercellular synchrony. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 110:E4355-E4361.
Doyle, III FJ, Wang Y.  2011.  The exponential synchronization of Kuramoto oscillator networks in the presence of combined global and local cues. Proceedings of the American Control Conference.
Doyle, III FJ, B. Bequette W, Dassau E, Buckingham BA.  2008.  Detection of a Meal Using Continuous Glucose Monitoring implications for an artificial beta-cell. DIABETES CARE. 31:295-300.
Doyle FJ, Saffer DR.  2005.  Efficient linear programming formulations of model predictive control for cross-directional control of a paper machine. INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH. 44:2134-2144.
Doyle FJ, Gilles ED, Stelling J.  2004.  Robustness properties of circadian clock architectures. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 101:13210-13215.
Doyle, III FJ, Gondhalekar R, Dassau E.  2014.  State Estimation with Sensor Recalibrations and Asynchronous Measurements for MPC of an Artificial Pancreas to Treat T1DM. 47:224-230.
Doyle, III FJ, Pinsker JE, Dassau E, Seborg DE, Gondhalekar R, Bradley PK, Huyett L, Lee JBok, Bevier WC, Zisser HC.  2016.  Randomized Crossover Comparison of Personalized MPC and PID Control Algorithms for the Artificial Pancreas. DIABETES CARE. 39:1135-1142.
Doyle, III FJ, Pistikopoulos EN, Dua P.  2009.  Multi-objective blood glucose control for type 1 diabetes. MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING. 47:343-352.
Doyle, III FJ, Zisser H, Seborg DE, Palerm CC, Jovanovic L, Bevier WC, Finan DA.  2008.  Identification of empirical dynamic models from type 1 diabetes subject data. Proceedings of the American Control Conference. :2099-+.
Doyle, III FJ, B. Bequette W, Forlenza GP, Ly TT, Howsmon DP, Pinsker JE, Mauritzen E, Cameron F, Dassau E, Deshpande S et al..  2017.  Application of Zone Model Predictive Control Artificial Pancreas During Extended Use of Infusion Set and Sensor: A Randomized Crossover-Controlled Home-Use Trial. DIABETES CARE. 40:1096-1102.
Doyle FJ, Mahadevan R.  2003.  Efficient optimization approaches to nonlinear model predictive control. INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL. 13:309-329.
Doyle, III FJ, Mercangoz M.  2007.  Distributed model predictive control of an experimental four-tank system. JOURNAL OF PROCESS CONTROL. 17:297-308.
Doyle, III FJ, Herzog ED, Thoroughman KA, Taylor SR, Webb AB.  2012.  Weakly Circadian Cells Improve Resynchrony. PLOS COMPUTATIONAL BIOLOGY. 8
Doyle, III FJ, Hori Y, Wang Y, Hara S.  2014.  Intercellular Delay Regulates the Collective Period of Repressively Coupled Gene Regulatory Oscillator Networks. IEEE TRANSACTIONS ON AUTOMATIC CONTROL. 59:211-216.
Doyle FJ, McFarlane R, BenAmor S.  2004.  Polymer grade transition control using advanced real-time optimization software. JOURNAL OF PROCESS CONTROL. 14:349-364.
Doyle, III FJ, Rodriguez-Fernandez M, Timmer J, Klett H, Leon LR, Dineen S.  2015.  Modeling the inflammatory response in the hypothalamus ensuing heat stroke: Iterative cycle of model calibration, identifiability analysis, experimental design and data collection. MATHEMATICAL BIOSCIENCES. 260:35-46.
Doyle, III FJ, Wang Y.  2012.  Optimal Phase Response Functions for Fast Pulse-Coupled Synchronization in Wireless Sensor Networks. IEEE TRANSACTIONS ON SIGNAL PROCESSING. 60:5583-5588.
Doyle, III F.J, Stelling J., Bagheri N..  2007.  Circadian phase entrainment via nonlinear model predictive control. INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL. 17:1555-1571.