Robust control of biochemical reaction networks via stochastic morphing
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Guy-Bart Stan | Tomislav Plesa | Thomas E. Ouldridge | Wooli Bae | G. Stan | T. Ouldridge | Wooli Bae | Tomislav Pleša | Tomislav Plesa
[1] Stefan Engblom,et al. On the Stability of Stochastic Jump Kinetics , 2012, 1202.3892.
[2] S. Leibler,et al. Bacterial Persistence as a Phenotypic Switch , 2004, Science.
[3] Ankit Gupta,et al. Antithetic proportional-integral feedback for reduced variance and improved control performance of stochastic reaction networks , 2018, Journal of The Royal Society Interface.
[4] Na Liu,et al. Dynamic Actuation of DNA-Assembled Plasmonic Nanostructures in Microfluidic Cell-Sized Compartments , 2020, Nano letters.
[5] Domitilla Del Vecchio,et al. Stochastic analysis of genetic feedback controllers to reprogram a pluripotency gene regulatory network , 2019, 2019 American Control Conference (ACC).
[6] Domitilla Del Vecchio,et al. Control theory meets synthetic biology , 2016, Journal of The Royal Society Interface.
[7] Paul C. Bressloff,et al. Stochastic switching in biology: from genotype to phenotype , 2017 .
[8] Dominic Scalise,et al. DNA Strand Buffers. , 2018, Journal of the American Chemical Society.
[9] Friedrich C. Simmel,et al. Membrane-Assisted Growth of DNA Origami Nanostructure Arrays , 2015, ACS nano.
[10] Gentian Buzi,et al. Glycolytic Oscillations and Limits on Robust Efficiency , 2011, Science.
[11] S. Swain. Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences , 1984 .
[12] S. Leibler,et al. Robustness in simple biochemical networks , 1997, Nature.
[13] Christian A. Yates,et al. Inherent noise can facilitate coherence in collective swarm motion , 2009, Proceedings of the National Academy of Sciences.
[14] T. Kepler,et al. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. , 2001, Biophysical journal.
[15] Richard M. Murray,et al. Design and Implementation of a Biomolecular Concentration Tracker , 2014, ACS synthetic biology.
[16] R. Metzler,et al. Strong defocusing of molecular reaction times results from an interplay of geometry and reaction control , 2018, Communications Chemistry.
[17] François Képès,et al. Periodic transcriptional organization of the E.coli genome. , 2004, Journal of molecular biology.
[18] Ankit Gupta,et al. A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks , 2013, PLoS Comput. Biol..
[19] Thomas G. Kurtz,et al. Stochastic Analysis of Biochemical Systems , 2015 .
[20] T. Fujii,et al. High-resolution mapping of bifurcations in nonlinear biochemical circuits. , 2016, Nature chemistry.
[21] E. Winfree,et al. Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. , 2014, Nature chemistry.
[22] L. Mirny,et al. How gene order is influenced by the biophysics of transcription regulation , 2007, Proceedings of the National Academy of Sciences.
[23] C. W. Gardiner,et al. Handbook of stochastic methods - for physics, chemistry and the natural sciences, Second Edition , 1986, Springer series in synergetics.
[24] T. Ha,et al. A rule of seven in Watson-Crick base pairing of mismatched sequences , 2012, Nature Structural &Molecular Biology.
[25] Radek Erban,et al. Chemical reaction systems with a homoclinic bifurcation: an inverse problem , 2015, Journal of Mathematical Chemistry.
[26] Erik Winfree,et al. Enzyme-free nucleic acid dynamical systems , 2017, Science.
[27] Vadim I. Utkin,et al. A singular perturbation analysis of high-gain feedback systems , 1977 .
[28] Eduardo Sontag,et al. Modular cell biology: retroactivity and insulation , 2008, Molecular systems biology.
[29] Thomas E. Ouldridge,et al. Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration , 2019, Biological Cybernetics.
[30] Flavio Romano,et al. Modelling toehold-mediated RNA strand displacement. , 2014, Biophysical journal.
[31] James Chappell,et al. Creating small transcription activating RNAs. , 2015, Nature chemical biology.
[32] Peter Ruoff,et al. Predicting perfect adaptation motifs in reaction kinetic networks. , 2008, The journal of physical chemistry. B.
[33] Grigorios A. Pavliotis,et al. Multiscale Methods: Averaging and Homogenization , 2008 .
[34] RADEK ERBAN,et al. Noise-induced mixing and multimodality in reaction networks , 2018, European Journal of Applied Mathematics.
[35] Alan Garfinkel,et al. Multi-scale modeling in biology: how to bridge the gaps between scales? , 2011, Progress in biophysics and molecular biology.
[36] R. Milo,et al. Cell Biology by the Numbers , 2015 .
[37] A. Turberfield,et al. A DNA-fuelled molecular machine made of DNA , 2022 .
[38] M. Khammash,et al. Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks. , 2016, Cell systems.
[39] E. Cox,et al. Gene location and DNA density determine transcription factor distributions in Escherichia coli , 2012, Molecular systems biology.
[40] Thomas E. Ouldridge,et al. DNA nanotechnology: understanding and optimisation through simulation , 2014, 1411.1927.
[41] Domitilla Del Vecchio,et al. Realizing “integral control” in living cells: How to overcome leaky integration due to dilution? , 2017, bioRxiv.
[42] R. Holliday. A mechanism for gene conversion in fungi. , 1964, Genetical research.
[43] Domitilla Del Vecchio,et al. A Blueprint for a Synthetic Genetic Feedback Controller to Reprogram Cell Fate. , 2017, Cell systems.
[44] A. Turberfield,et al. Programmable energy landscapes for kinetic control of DNA strand displacement , 2014, Nature Communications.
[45] Mark Thomas Holtzapple,et al. Foundations of Engineering , 1999 .
[46] Pengyu Y. Ren,et al. Measuring DNA hybridization kinetics in live cells using a time-resolved 3D single-molecule tracking method. , 2019, Journal of the American Chemical Society.
[47] D. Y. Zhang,et al. Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.
[48] D. Gillespie. Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .
[49] Thomas E. Ouldridge,et al. High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits , 2017, 1708.01792.
[50] S. Leibler,et al. Mechanisms of noise-resistance in genetic oscillators , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[51] Radek Erban,et al. Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks , 2015, Journal of The Royal Society Interface.
[52] J. Collins,et al. Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.
[53] T. Kurtz. The Relationship between Stochastic and Deterministic Models for Chemical Reactions , 1972 .
[54] M. Elowitz,et al. A synthetic oscillatory network of transcriptional regulators , 2000, Nature.
[55] Teruo Fujii,et al. Predator-prey molecular ecosystems. , 2013, ACS nano.
[56] James E Ferrell,et al. Perfect and Near-Perfect Adaptation in Cell Signaling. , 2016, Cell systems.
[57] Ralf Metzler,et al. Distance matters: the impact of gene proximity in bacterial gene regulation. , 2013, Physical review letters.
[58] Johan Paulsson,et al. Stochastic Switching of Cell Fate in Microbes. , 2015, Annual review of microbiology.
[59] C. Joo,et al. Fueling protein–DNA interactions inside porous nanocontainers , 2007, Proceedings of the National Academy of Sciences.
[60] J. S. Parkinson,et al. A model of excitation and adaptation in bacterial chemotaxis. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[61] D. Lilley,et al. Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic. , 2004, Biophysical journal.
[62] Andrea Ciliberto,et al. Antagonism and bistability in protein interaction networks. , 2008, Journal of theoretical biology.
[63] Maximilian T. Strauss,et al. Single Particle Tracking and Super-Resolution Imaging of Membrane-Assisted Stop-and-Go Diffusion and Lattice Assembly of DNA Origami. , 2019, ACS nano.
[64] Teruo Fujii,et al. High-throughput and long-term observation of compartmentalized biochemical oscillators. , 2015, Chemical communications.
[65] J. Doudna,et al. A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.
[66] John J Tyson,et al. Exploring the roles of noise in the eukaryotic cell cycle , 2009, Proceedings of the National Academy of Sciences.
[67] Ankit Gupta,et al. Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks. , 2014, Cell systems.
[68] Guy-Bart Stan,et al. Host-aware synthetic biology , 2019, Current Opinion in Systems Biology.
[69] D. Endy. Foundations for engineering biology , 2005, Nature.
[70] Arup K Chakraborty,et al. Stochastic bimodalities in deterministically monostable reversible chemical networks due to network topology reduction. , 2009, The Journal of chemical physics.
[71] Andrew D. Ellington,et al. Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers , 2014, Nucleic acids research.
[72] Guy-Bart Stan,et al. Characterization of Biologically Relevant Network Structures form Time-series Data , 2018, 2018 IEEE Conference on Decision and Control (CDC).
[73] Xi Chen,et al. Expanding the rule set of DNA circuitry with associative toehold activation. , 2012, Journal of the American Chemical Society.
[74] Radek Erban,et al. Test Models for Statistical Inference: Two-Dimensional Reaction Systems Displaying Limit Cycle Bifurcations and Bistability , 2016, 1607.07738.
[75] N. Kampen,et al. Stochastic processes in physics and chemistry , 1981 .
[76] Erik Winfree,et al. Stochastic Chemical Reaction Networks for Robustly Approximating Arbitrary Probability Distributions , 2018, Theor. Comput. Sci..
[77] Luca Cardelli,et al. Molecular Filters for Noise Reduction , 2018, Biophysical journal.
[78] D. Lilley,et al. Structural dynamics of individual Holliday junctions , 2003, Nature Structural Biology.
[79] Radek Erban,et al. Noise control for molecular computing , 2018, Journal of The Royal Society Interface.
[80] Baojun Wang,et al. Scaling up genetic circuit design for cellular computing: advances and prospects , 2018, Natural Computing.
[81] Pavel Loskot,et al. Determining the Transcription Rates Yielding Steady-State Production of mRNA in the Lac Genetic Switch of Escherichia coli , 2018, J. Comput. Biol..
[82] Fan Hong,et al. Strand displacement: a fundamental mechanism in RNA biology? , 2019, 1903.12199.
[83] 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.
[84] G. Seelig,et al. DNA as a universal substrate for chemical kinetics , 2010, Proceedings of the National Academy of Sciences.
[85] D. Gillespie. A rigorous derivation of the chemical master equation , 1992 .
[86] R. Erban,et al. Stochastic Modelling of Reaction–Diffusion Processes , 2019 .
[87] Farren J. Isaacs,et al. Engineered riboregulators enable post-transcriptional control of gene expression , 2004, Nature Biotechnology.