Control-theoretic methods for biological networks
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Franco Blanchini | Eduardo D. Sontag | Giulia Giordano | Hana EI-Samad | Eduardo Sontag | F. Blanchini | G. Giordano | Hana EI-Samad | Giulia Giordano
[1] Hidde de Jong,et al. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..
[2] P. Haccou. Mathematical Models of Biology , 2022 .
[3] M. Khammash,et al. Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks. , 2016, Cell systems.
[4] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[5] H. Kitano. Systems Biology: A Brief Overview , 2002, Science.
[6] Eduardo Sontag,et al. Fold-change detection and scalar symmetry of sensory input fields , 2010, Proceedings of the National Academy of Sciences.
[7] D. E. Atkinson,et al. Biological feedback control at the molecular level. , 1965, Science.
[8] Eduardo Sontag. A technique for determining the signs of sensitivities of steady states in chemical reaction networks. , 2013, IET systems biology.
[9] Eduardo D. Sontag,et al. Synchronization of Interconnected Systems With Applications to Biochemical Networks: An Input-Output Approach , 2009, IEEE Transactions on Automatic Control.
[10] Declan G. Bates,et al. Feedback Control in Systems Biology , 2011 .
[11] B. Ross Barmish,et al. New Tools for Robustness of Linear Systems , 1993 .
[12] Franco Blanchini,et al. Polyhedral Lyapunov functions structurally ensure global asymptotic stability of dynamical networks iff the Jacobian is non-singular , 2017, Autom..
[13] H. Kitano. Towards a theory of biological robustness , 2007, Molecular systems biology.
[14] Tsuyoshi Murata,et al. {m , 1934, ACML.
[15] Eduardo D. Sontag,et al. Mathematical Control Theory: Deterministic Finite Dimensional Systems , 1990 .
[16] David Angeli,et al. Chemical networks with inflows and outflows: A positive linear differential inclusions approach , 2009, Biotechnology progress.
[17] Gaetano Zampieri,et al. Diffeomorphisms with Banach space domains , 1992 .
[18] Antonis Papachristodoulou,et al. Advanced Methods and Algorithms for Biological Networks Analysis , 2006, Proceedings of the IEEE.
[19] Nicole Radde,et al. Graphical methods for analysing feedback in biological networks – A survey , 2010, Int. J. Syst. Sci..
[20] Franco Blanchini,et al. Structurally robust biological networks , 2011, BMC Systems Biology.
[21] N. Balaban. Persistence: mechanisms for triggering and enhancing phenotypic variability. , 2011, Current opinion in genetics & development.
[22] J. Lei. Monotone Dynamical Systems , 2013 .
[23] Uri Alon,et al. Response regulator output in bacterial chemotaxis , 1998, The EMBO journal.
[24] M. Feinberg. Chemical reaction network structure and the stability of complex isothermal reactors—II. Multiple steady states for networks of deficiency one , 1988 .
[25] Eduardo D. Sontag,et al. Symmetry invariance for adapting biological systems , 2010, SIAM J. Appl. Dyn. Syst..
[26] Peter Takáč,et al. Linearly stable subharmonic orbits in strongly monotone time-periodic dynamical systems , 1992 .
[27] N. Wingreen,et al. Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response. , 2010, Molecular cell.
[28] Roman Srzednicki,et al. On rest points of dynamical systems , 1985 .
[29] E. Groisman,et al. The biology of the PmrA/PmrB two-component system: the major regulator of lipopolysaccharide modifications. , 2013, Annual review of microbiology.
[30] Thomas G. Kurtz,et al. Stochastic Analysis of Biochemical Systems , 2015 .
[31] Elisabeth Pécou,et al. The interaction graph structure of mass-action reaction networks , 2011, Journal of Mathematical Biology.
[32] Alex Groisman,et al. Incoherent Feedforward Control Governs Adaptation of Activated Ras in a Eukaryotic Chemotaxis Pathway , 2012, Science Signaling.
[33] H. Berg,et al. Chemotaxis in Escherichia coli analysed by Three-dimensional Tracking , 1972, Nature.
[34] James E Ferrell,et al. Feedback loops and reciprocal regulation: recurring motifs in the systems biology of the cell cycle. , 2013, Current opinion in cell biology.
[35] D. Vecchio,et al. Biomolecular Feedback Systems , 2014 .
[36] Steven W. Flavell,et al. A Circuit for Gradient Climbing in C. elegans Chemotaxis. , 2015, Cell reports.
[37] Franco Blanchini,et al. Compartmental flow control: Decentralization, robustness and optimality , 2016, Autom..
[38] Lubomír Bakule,et al. Decentralized control: An overview , 2008, Annu. Rev. Control..
[39] Franco Blanchini,et al. Network-Decentralized Control Strategies for Stabilization , 2015, IEEE Transactions on Automatic Control.
[40] Franco Blanchini,et al. Piecewise-linear Lyapunov functions for structural stability of biochemical networks , 2014, Autom..
[41] Franco Blanchini,et al. A Structural Classification of Candidate Oscillatory and Multistationary Biochemical Systems , 2014, Bulletin of mathematical biology.
[42] U. Alon. An introduction to systems biology : design principles of biological circuits , 2019 .
[43] Michael T. Laub,et al. Regulation of the bacterial cell cycle by an integrated genetic circuit , 2006, Nature.
[44] David Angeli,et al. New Approach to the Stability of Chemical Reaction Networks: Piecewise Linear in Rates Lyapunov Functions , 2014, IEEE Transactions on Automatic Control.
[45] Frédéric Grognard,et al. Global stability for a model of competition in the chemostat with microbial inputs , 2012 .
[46] Thorsten Mascher,et al. Stoichiometry and perturbation studies of the LiaFSR system of Bacillus subtilis , 2013, Molecular microbiology.
[47] S. Leibler,et al. Robustness in simple biochemical networks , 1997, Nature.
[48] Eduardo D. Sontag,et al. Oscillatory stimuli differentiate adapting circuit topologies , 2017, Nature Methods.
[49] Hiroaki Kitano,et al. Biological robustness , 2008, Nature Reviews Genetics.
[50] James E. Ferrell,et al. A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision , 2007, Nature.
[51] Eduardo D. Sontag,et al. Monotone and near-monotone biochemical networks , 2007, Systems and Synthetic Biology.
[52] David Angeli,et al. Monotone control systems , 2003, IEEE Trans. Autom. Control..
[53] Franco Blanchini,et al. Computing the structural influence matrix for biological systems , 2016, Journal of mathematical biology.
[54] David Angeli,et al. Oscillations in I/O Monotone Systems Under Negative Feedback , 2007, IEEE Transactions on Automatic Control.
[55] Katalin M. Hangos. Engineering Model Reduction and Entropy-based Lyapunov Functions in Chemical Reaction Kinetics , 2010, Entropy.
[56] Shinji Hara,et al. Coordinated Spatial Pattern Formation in Biomolecular Communication Networks , 2015, IEEE Transactions on Molecular, Biological and Multi-Scale Communications.
[57] U. Alon,et al. Robustness in bacterial chemotaxis , 2022 .
[58] J. Ferrell,et al. A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision , 2003, Nature.
[59] M. Feinberg,et al. Structural Sources of Robustness in Biochemical Reaction Networks , 2010, Science.
[60] F. Mazenc,et al. Polytopic Lyapunov functions for the stability analysis of persistence of competing species , 2005, Proceedings of the 44th IEEE Conference on Decision and Control.
[61] J. Ferrell,et al. Tuning the Activation Threshold of a Kinase Network by Nested Feedback Loops , 2009, Science.
[62] Yu-Jin Jung,et al. Expression of Th1-mediated immunity in mouse lungs induces a Mycobacterium tuberculosis transcription pattern characteristic of nonreplicating persistence , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[63] Giulia Giordano,et al. Structural Analysis and Control of Dynamical Networks , 2016 .
[64] Josef Hofbauer,et al. An index theorem for dissipative semiflows , 1990 .
[65] U. Alon. Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.
[66] Alessandro Bertuzzi,et al. MATHEMATICAL MODELING OF THE GLUCOSE-INSULIN SYSTEM: A REVIEW PAPER , 2011 .
[67] David Angeli,et al. Remarks on the invalidation of biological models using monotone systems theory , 2012, 2012 IEEE 51st IEEE Conference on Decision and Control (CDC).
[68] M. Khammash,et al. Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective. , 2002, Journal of theoretical biology.
[69] H. Freud. Mathematical Control Theory , 2016 .
[70] Kazuyuki Aihara,et al. Modeling Biomolecular Networks in Cells , 2010 .
[71] Eduardo A. Groisman,et al. The Pleiotropic Two-Component Regulatory System PhoP-PhoQ , 2001, Journal of bacteriology.
[72] Altug Iftar,et al. A linear programming based decentralized routing controller for congested highways , 1999, Autom..
[73] A. Oudenaarden,et al. A Systems-Level Analysis of Perfect Adaptation in Yeast Osmoregulation , 2009, Cell.
[74] J. Ferrell,et al. Ultrasensitivity part III: cascades, bistable switches, and oscillators. , 2014, Trends in biochemical sciences.
[75] Franco Blanchini,et al. Set-theoretic methods in control , 2007 .
[76] Bruce A. Francis,et al. The internal model principle of control theory , 1976, Autom..
[77] R. Jackson,et al. General mass action kinetics , 1972 .
[78] Pratik Datta,et al. Regulation of Central Metabolism Genes of Mycobacterium tuberculosis by Parallel Feed-Forward Loops Controlled by Sigma Factor E (σE) , 2010, Journal of bacteriology.
[79] Eduardo D. Sontag,et al. A Characterization of Scale Invariant Responses in Enzymatic Networks , 2012, PLoS Comput. Biol..
[80] Yi-Ju Hsieh,et al. Global regulation by the seven-component Pi signaling system. , 2010, Current opinion in microbiology.
[81] Roman Stocker,et al. Response rescaling in bacterial chemotaxis , 2011, Proceedings of the National Academy of Sciences.
[82] P. Olver. Nonlinear Systems , 2013 .
[83] David Angeli,et al. A tutorial on Chemical Reaction Networks dynamics , 2009, 2009 European Control Conference (ECC).
[84] Eliseo Ferrante,et al. Swarm robotics: a review from the swarm engineering perspective , 2013, Swarm Intelligence.
[85] J. K. Hale,et al. Competition for fluctuating nutrient , 1983 .
[86] Dongwoo Shin,et al. A Positive Feedback Loop Promotes Transcription Surge That Jump-Starts Salmonella Virulence Circuit , 2006, Science.
[87] Mario di Bernardo,et al. Global Entrainment of Transcriptional Systems to Periodic Inputs , 2009, PLoS Comput. Biol..
[88] V. Isaeva. Self-organization in biological systems , 2012, Biology Bulletin.
[89] Franco Blanchini,et al. Aggregates of Monotonic Step Response Systems: A Structural Classification , 2018, IEEE Transactions on Control of Network Systems.
[90] Eduardo Sontag,et al. Modular cell biology: retroactivity and insulation , 2008, Molecular systems biology.
[91] Hal L. Smith,et al. Competitive and Cooperative Systems: A Mini-review , 2003, POSTA.
[92] Hal L. Smith,et al. Monotone Dynamical Systems: An Introduction To The Theory Of Competitive And Cooperative Systems (Mathematical Surveys And Monographs) By Hal L. Smith , 1995 .
[93] David Richeson,et al. A fixed point theorem for bounded dynamical systems , 2001 .
[94] J. Tyson,et al. Design principles of biochemical oscillators , 2008, Nature Reviews Molecular Cell Biology.
[95] J. Doyle,et al. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[96] Edward J. Davison,et al. Decentralized control strategies for dynamic routing , 2002 .
[97] Eduardo D. Sontag,et al. Molecular Systems Biology and Control , 2005, Eur. J. Control.
[98] David Angeli,et al. Multi-stability in monotone input/output systems , 2003, Syst. Control. Lett..
[99] Murat Arcak,et al. Pattern Formation by Lateral Inhibition in Large-Scale Networks of Cells , 2013, IEEE Transactions on Automatic Control.