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Matni, Nikolai and Ames, Aaron D., et el. (2024) A Quantitative Framework for Layered Multirate Control: Toward a Theory of Control Architecture ; IEEE Control Systems; Vol. 44; No. 3; 52-94; 10.1109/mcs.2024.3382388
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Rochart, Roger and Liu, Quanying, et el. (2020) Heart rate and blood pressure decreases after a motor task in pre‐symptomatic AD ; Alzheimer's & Dementia; Vol. 16; No. S5, pt 2; Art. No. e045521; 10.1002/alz.045521
Liu, Quanying and Nakahira, Yorie, et el. (2020) WheelCon: A Wheel Control-Based Gaming Platform for Studying Human Sensorimotor Control ; Journal of Visualized Experiments; No. 162; Art. No. e61092; 10.3791/61092
Khazaei, Tahmineh and Williams, Rory L., et el. (2020) Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community ; Science Advances; Vol. 6; No. 33; Art. No. eaba0353; PMCID PMC7423363; 10.1126/sciadv.aba0353
Keating, Sarah M. and Waltemath, Dagmar, et el. (2020) SBML Level 3: an extensible format for the exchange and reuse of biological models ; Molecular Systems Biology; Vol. 16; No. 8; Art. No. e9110; 10.15252/msb.20199110
Siami, Milad and Motee, Nader, et el. (2020) Fundamental Limits and Tradeoffs in Autocatalytic Pathways ; IEEE Transactions on Automatic Control; Vol. 65; No. 2; 733-740; 10.1109/tac.2019.2921671
Wang, Yuh-Shyang and Matni, Nikolai, et el. (2019) A System Level Approach to Controller Synthesis ; IEEE Transactions on Automatic Control; Vol. 64; No. 10; 4079-4093; 10.1109/tac.2018.2890753
Alderson, David L. and Doyle, John C., et el. (2019) Lessons from "a first-principles approach to understanding the internet's router-level topology" ; ACM SIGCOMM Computer Communication Review; Vol. 49; No. 5; 96-103; 10.1145/3371934.3371964
Olsman, Noah and Baetica, Ania-Ariadna, et el. (2019) Hard Limits and Performance Tradeoffs in a Class of Antithetic Integral Feedback Networks ; Cell Systems; Vol. 9; No. 1; 49-63; 10.1016/j.cels.2019.06.001
Anderson, James and Doyle, John C., et el. (2019) System level synthesis ; Annual Reviews in Control; Vol. 47; 364-393; 10.1016/j.arcontrol.2019.03.006
Olsman, Noah and Xiao, Fangzhou, et el. (2019) Architectural Principles for Characterizing the Performance of Antithetic Integral Feedback Networks ; iScience; Vol. 14; 277-291; PMCID PMC6479019; 10.1016/j.isci.2019.04.004
Mavroudis, Panteleimon D. and Scheff, Jeremy D., et el. (2019) Impact of Stochasticity and Its Control on a Model of the Inflammatory Response ; Computation; Vol. 7; Art. No. 3; 10.3390/computation7010003
Wu, Ning and Bi, Yingjie, et el. (2018) A Control-Theoretic Approach to In-Network Congestion Management ; IEEE/ACM Transactions on Networking; Vol. 26; No. 6; 2443-2456; 10.1109/tnet.2018.2866785
Wang, Yuh-Shyang and Matni, Nikolai, et el. (2018) Separable and Localized System Level Synthesis for Large-Scale Systems ; IEEE Transactions on Automatic Control; Vol. 63; No. 12; 4234-4249; 10.1109/TAC.2018.2819246
Olsman, Noah and Xiao, Fangzhou, et el. (2018) Evaluation of Hansen et al.: Nuance Is Crucial in Comparisons of Noise ; Cell Systems; Vol. 7; No. 4; 352-355; 10.1016/j.cels.2018.10.003
Leong, Yoke Peng and Doyle, John C. (2017) Effects of Delays, Poles, and Zeros on Time Domain Waterbed Tradeoffs and Oscillations ; IEEE Control Systems Letters; Vol. 1; No. 1; 122-127; 10.1109/LCSYS.2017.2710327
Csete, Marie and Doyle, John (2017) 15th International Conference on Complex Acute Illness (ICCAI) Society for Complex Acute Illness: August 10–14, 2016 at the Beckman Institute, Caltech ; Journal of Critical Care; Vol. 38; 340; 10.1016/j.jcrc.2016.11.011
Jonsson, Vanessa D. and Blakely, Collin M., et el. (2017) Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution ; Scientific Reports; Vol. 7; Art. No. 44206; PMCID PMC5347024; 10.1038/srep44206
Das, Anup and Sampson, Aaron L., et el. (2017) Interpretation of the Precision Matrix and Its Application in Estimating Sparse Brain Connectivity during Sleep Spindles from Human Electrocorticography Recordings ; Neural Computation; Vol. 29; No. 3; 603-642; PMCID PMC5424817; 10.1162/NECO_a_00936
Kempes, Christopher P. and Wang, Lawrence, et el. (2016) Evolutionary tradeoffs in cellular composition across diverse bacteria ; ISME Journal; Vol. 10; No. 9; 2145-2157; 10.1038/ismej.2016.21
Doyle, John C. (2016) Even Noisy Responses Can Be Perfect If Integrated Properly ; Cell Systems; Vol. 2; No. 2; 73-75; 10.1016/j.cels.2016.02.012
Nair, Jayakrishnan and Andreasson, Martin, et el. (2016) On Channel Failures, File Fragmentation Policies, and Heavy-Tailed Completion Times ; IEEE/ACM Transactions on Networking; Vol. 24; No. 1; 529-541; 10.1109/TNET.2014.2375920
Lamperski, Andrew and Doyle, John C. (2015) The ℋ_2 Control Problem for Quadratically Invariant Systems With Delays ; IEEE Transactions on Automatic Control; Vol. 60; No. 7; 1945-1950; 10.1109/TAC.2014.2363917
Sojoudi, Somayeh and Low, Steven H., et el. (2014) Buffering Dynamics and Stability of Internet Congestion Controllers ; IEEE/ACM Transactions on Networking; Vol. 22; No. 6; 1808-1818; 10.1109/TNET.2013.2287198
Csete, Marie and Doyle, John (2014) The mathematician's control toolbox for management of type 1 diabetes ; Interface Focus; Vol. 4; No. 5; Art. No. 20140042; PMCID PMC4142019; 10.1098/rsfs.2014.0042
Li, Na and Cruz, Jerry, et el. (2014) Robust efficiency and actuator saturation explain healthy heart rate control and variability ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 111; No. 33; E3476-E3485; PMCID PMC4143073; 10.1073/pnas.1401883111
Matni, Nikolai and Leong, Yoke Peng, et el. (2014) Resilience in Large Scale Distributed Systems ; Procedia Computer Science; Vol. 28; 285-293; 10.1016/j.procs.2014.03.036
Caporale, Lynn Helena and Doyle, John (2013) In Darwinian evolution, feedback from natural selection leads to biased mutations ; Annals of the New York Academy of Sciences; Vol. 1305; 18-28; 10.1111/nyas.12235
Scheff, Jeremy D. and Mavroudis, Panteleimon D., et el. (2013) A multiscale modeling approach to inflammation: A case study in human endotoxemia ; Journal of Computational Physics; Vol. 244; 279-289; 10.1016/j.jcp.2012.09.024
Chen, Lijun and Ho, Tracey, et el. (2012) Congestion Control for Multicast Flows With Network Coding ; IEEE Transactions on Information Theory; Vol. 58; No. 9; 5908-5921; 10.1109/TIT.2012.2204170
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Page, Morgan T. and Alderson, David, et el. (2011) The magnitude distribution of earthquakes near Southern California faults ; Journal of Geophysical Research B; Vol. 116; Art. No. B12309; 10.1029/2010JB007933
Doyle, John C. and Csete, Marie (2011) Architecture, constraints, and behavior ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. S3; 15624-15630; PMCID PMC3176601; 10.1073/pnas.1103557108
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Chandra, Fiona A. and Buzi, Gentian, et el. (2011) Glycolytic Oscillations and Limits on Robust Efficiency ; Science; Vol. 333; No. 6039; 187-192; 10.1126/science.1200705
Gayme, Dennice F. and McKeon, Beverley J., et el. (2011) Amplification and nonlinear mechanisms in plane Couette flow ; Physics of Fluids; Vol. 23; No. 6; 065108; 10.1063/1.3599701
Buzi, Gentian and Topcu, Ufuk, et el. (2011) Analysis of autocatalytic networks in biology ; Automatica; Vol. 47; No. 6; 1123-1130; 10.1016/j.automatica.2011.02.040
Chen, Lijun and Low, Steven H., et el. (2011) Cross-layer design in multihop wireless networks ; Computer Networks; Vol. 55; No. 2; 480-496; 10.1016/j.comnet.2010.09.005
Sandberg, Henrik and Delvenne, Jean-Charles, et el. (2011) On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements ; IEEE Transactions on Automatic Control; Vol. 56; No. 2; 293-308; 10.1109/TAC.2010.2056450
Lavaei, Javad and Babakhani, Aydin, et el. (2011) Solving Large-Scale Hybrid Circuit-Antenna Problems ; IEEE Transactions on Circuits and Systems I: Regular Papers; Vol. 58; No. 2; 374-387; 10.1109/TCSI.2010.2072010
Chen, Lijun and Low, Steven H., et el. (2010) Random Access Game and Medium Access Control Design ; IEEE/ACM Transactions on Networking; Vol. 18; No. 4; 1303-1316; 10.1109/TNET.2010.2041066
Alderson, David L. and Doyle, John C. (2010) Contrasting Views of Complexity and Their Implications For Network-Centric Infrastructures ; IEEE Transactions on Systems Man and Cybernetics - Part A Systems and Humans; Vol. 40; No. 4; 839-852; 10.1109/TSMCA.2010.2048027
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Willinger, Walter and Alderson, David, et el. (2009) Mathematics and the Internet: A Source of Enormous Confusion and Great Potential ; Notices of the American Mathematical Society; Vol. 56; No. 5; 586-599
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Bohland, Jason and Wu, Caizhi, et el. (2009) A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale ; PLoS Computational Biology; Vol. 5; No. 3; Art. No. e1000334; PMCID PMC2655718; 10.1371/journal.pcbi.1000334
Arkin, Adam and Doyle, John (2008) Appreciation of the Machinations of the Blind Watchmaker ; IEEE Transactions on Automatic Control; Vol. 53; No. Specia; 8-9; 10.1109/TAC.2007.913342
Doyle, John and Csete, Marie (2007) Rules of engagement ; Nature; Vol. 446; No. 7138; 860; 10.1038/446860a
Martins, Nuno C. and Dahleh, Munther A., et el. (2007) Fundamental Limitations of Disturbance Attenuation in the Presence of Side Information ; IEEE Transactions on Automatic Control; Vol. 52; No. 1; 56-66; 10.1109/TAC.2006.887898
Chiang, Mung and Low, Steven H., et el. (2007) Layering as Optimization Decomposition: A Mathematical Theory of Network Architectures ; Proceedings of the IEEE; Vol. 95; No. 1; 255-312; 10.1109/JPROC.2006.887322
Kurata, Hiroyuki and El-Samad, Hana, et el. (2006) Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ; PLOS Computational Biology; Vol. 2; No. 7; 663-675; PMCID PMC1523291; 10.1371/journal.pcbi.0020059
El-Samad, Hana and Prajna, Stephen, et el. (2006) Advanced methods and algorithms for biological networks analysis ; Proceedings of the IEEE; Vol. 94; No. 4; 832-853; 10.1109/JPROC.2006.871776
Moritz, Max A. and Morais, Marco E., et el. (2005) Wildfires, complexity, and highly optimized tolerance ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 102; No. 50; 17912-17917; PMCID PMC1312407; 10.1073/pnas.0508985102
Tanaka, R. and Csete, M., et el. (2005) Highly optimised global organisation of metabolic networks ; Systems Biology; Vol. 152; No. 4; 179-184; 10.1049/ip-syb:20050042
Alderson, David and Li, Lun, et el. (2005) Understanding Internet topology: principles, models, and validation ; IEEE/ACM Transactions on Networking; Vol. 13; No. 6; 1205-1218; 10.1109/TNET.2005.861250
Brookings, Ted and Carlson, J. M., et el. (2005) Three mechanisms for power laws on the Cayley tree ; Physical Review E; Vol. 72; No. 5; Art. no. 056120; 10.1103/PhysRevE.72.056120
Doyle, John and Csete, Marie (2005) Motifs, Control, and Stability ; PLoS Biology; Vol. 3; No. 11; e392; PMCID PMC1283396; 10.1371/journal.pbio.0030392
Doyle, John C. and Anderson, David L., et el. (2005) The "robust yet fragile" nature of the Internet ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 102; No. 41; 14497-14502; PMCID PMC1240072; 10.1073/pnas.0501426102
Manning, M. and Carlson, J. M., et el. (2005) Highly optimized tolerance and power laws in dense and sparse resource regimes ; Physical Review E; Vol. 72; No. 1; Art. No. 016108; 10.1103/PhysRevE.72.016108
Wang, Jiantao and Li, Lun, et el. (2005) Cross-layer optimization in TCP/IP networks ; IEEE/ACM Transactions on Networking; Vol. 13; No. 3; 582-595; 10.1109/TNET.2005.850219
El-Samad, H. and Kurata, H., et el. (2005) Surviving heat shock: Control strategies for robustness and performance ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 102; No. 8; 2736-2741; PMCID PMC549435; 10.1073/pnas.403510102
Paganini, Fernando and Wang, Zhikui, et el. (2005) Congestion control for high performance, stability, and fairness in general networks ; IEEE/ACM Transactions on Networking; Vol. 13; No. 1; 43-56; 10.1109/TNET.2004.842216
Jin, Cheng and Wei, David X., et el. (2005) FAST TCP: from theory to experiments ; IEEE Network; Vol. 19; No. 1; 4-11; 10.1109/MNET.2005.1383434
Shapiro, Bruce E. and Hucka, Michael, et el. (2004) MathSBML: a package for manipulating SBML-based biological models ; Bioinformatics; Vol. 20; No. 16; 2829-2831; PMCID PMC1409765; 10.1093/bioinformatics/bth271
Doyle, John and Csete, Marie (2004) Imitation of life: How biology is inspiring computing [Book Review] ; Nature; Vol. 431; No. 7011; 908-909; 10.1038/431908a
Stelling, Jörg and Sauer, Uwe, et el. (2004) Robustness of Cellular Functions ; Cell; Vol. 118; No. 6; 675-685; 10.1016/j.cell.2004.09.008
Papachristodoulou, Antonis and Li, Lun, et el. (2004) Methodological frameworks for large-scale network analysis and design ; ACM SIGCOMM Computer Communication Review; Vol. 34; No. 3; 7-20; 10.1145/1031134.1031138
Hucka, M. and Finney, A., et el. (2004) Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project ; Systems Biology; Vol. 1; No. 1; 41-53; 10.1049/sb:20045008
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Hucka, M. and Finney, A., et el. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models ; Bioinformatics; Vol. 19; No. 4; 524-531; 10.1093/bioinformatics/btg015
Alderson, David and Doyle, John, et el. (2003) Toward an Optimization-Driven Framework for Designing and Generating Realistic Internet Topologies ; ACM SIGCOMM Computer Communication Review; Vol. 33; No. 1; 41-46; 10.1145/774763.774769
Gilman, Alfred G. and Simon, Melvin I., et el. (2002) Overview of the Alliance for Cellular Signaling ; Nature; Vol. 420; No. 6916; 703-706; 10.1038/nature01304
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Csete, Marie E. and Doyle, John C. (2002) Reverse Engineering of Biological Complexity ; Science; Vol. 295; No. 5560; 1664-1669; 10.1126/science.1069981
Zhou, Tong and Carlson, J. M., et el. (2002) Mutation, specialization, and hypersensitivity in highly optimized tolerance ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 99; No. 4; 2049-2054; PMCID PMC122317; 10.1073/pnas.261714399
Carlson, J. M. and Doyle, John (2002) Complexity and robustness ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 99; No. Suppl.; 2538-2545; PMCID PMC128573; 10.1073/pnas.012582499
Low, Steven H. and Paganini, Fernando, et el. (2002) Internet congestion control ; IEEE Control Systems Magazine; Vol. 22; No. 1; 28-43; 10.1109/37.980245
Tangmunarunkit, Hongsuda and Doyle, John, et el. (2001) Does AS size determine degree in as topology? ; ACM SIGCOMM Computer Communication Review; Vol. 31; No. 5; 7-8; 10.1145/1037107.1037108
Doyle, John (2001) Beyond the spherical cow ; Nature; Vol. 411; No. 6834; 151-152; 10.1038/35075703
Robert, Carl and Carlson, J. M., et el. (2001) Highly optimized tolerance in epidemic models incorporating local optimization and regrowth ; Physical Review E; Vol. 63; No. 5; Art. no. 056122; 10.1103/PhysRevE.63.056122
Doyle, John and Carlson, J. M. (2000) Power Laws, Highly Optimized Tolerance, and Generalized Source Coding ; Physical Review Letters; Vol. 84; No. 24; 5656-5659; 10.1103/PhysRevLett.84.5656
Primbs, James A. and Nevistić, Vesna, et el. (2000) A receding horizon generalization of pointwise min-norm controllers ; IEEE Transactions on Automatic Control; Vol. 45; No. 5; 898-909; 10.1109/9.855550
Yi, Tau-Mu and Huang, Yun, et el. (2000) Robust perfect adaptation in bacterial chemotaxis through integral feedback control ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 97; No. 9; 4649-4653; PMCID PMC18287
Carlson, J. M. and Doyle, John (2000) Highly Optimized Tolerance: Robustness and Design in Complex Systems ; Physical Review Letters; Vol. 84; No. 11; 2529-2532; 10.1103/PhysRevLett.84.2529
Becker, Carolyn L. and Doyle, John (1999) A necessary and sufficient minimality condition for uncertain systems ; IEEE Transactions on Automatic Control; Vol. 44; No. 10; 1802-1813; 10.1109/9.793720
Carlson, J. M. and Doyle, John (1999) Highly optimized tolerance: A mechanism for power laws in designed systems ; Physical Review E; Vol. 60; No. 2; 1412-1427; 10.1103/PhysRevE.60.1412
Lundström, Petter and Skogestad, Sigurd, et el. (1999) Two-degree-of-freedom controller design for an ill-conditioned distillation process using µ-synthesis ; IEEE Transactions on Control Systems Technology; Vol. 7; No. 1; 12-21; 10.1109/87.736744
Lu, Wei-Min and Doyle, John C. (1997) Robustness analysis and synthesis for nonlinear uncertain systems ; IEEE Transactions on Automatic Control; Vol. 42; No. 12; 1654-1662; 10.1109/9.650015
Young, Peter M. and Doyle, John C. (1997) A lower bound for the mixed µ problem ; IEEE Transactions on Automatic Control; Vol. 42; No. 1; 123-128; 10.1109/9.553696
Beck, Carolyn L. and Doyle, John, et el. (1996) Model reduction of multidimensional and uncertain systems ; IEEE Transactions on Automatic Control; Vol. 41; No. 10; 1466-1477; 10.1109/9.539427
Doyle, John and Murray, Richard (1996) Robust Nonlinear Control Theory with Applications to Aerospace Vehicles ; IFAC Proceedings Volumes; Vol. 29; No. 1; 7624-7629; 10.1016/s1474-6670(17)58916-8
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Lu, Wei-Min and Doyle, John C. (1994) ℋ∞ control of nonlinear systems via output feedback: controller parameterization ; IEEE Transactions on Automatic Control; Vol. 39; No. 12; 2517-2521; 10.1109/9.362834
Balas, Gary J. and Doyle, John C. (1994) Robustness and performance trade-offs in control design for flexible structures ; IEEE Transactions on Control Systems Technology; Vol. 2; No. 4; 352-361; 10.1109/87.338656
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Packard, A. and Doyle, J. (1993) The complex structured singular value ; Automatica; Vol. 29; No. 1; 71-109; 10.1016/0005-1098(93)90175-S
Smith, Roy S. and Doyle, John C. (1992) Model validation: a connection between robust control and identification ; IEEE Transactions on Automatic Control; Vol. 37; No. 7; 942-952; 10.1109/9.148346
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