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Construction of a genetic toggle switch in Escherichia coli

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Cited by:

  1. Nagarajan, Radhakrishnan, 2007. "Delay estimation in a two-node acyclic network," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 376(C), pages 725-737.
  2. Christoph Schmal & Peter Reimann & Dorothee Staiger, 2013. "A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana," PLOS Computational Biology, Public Library of Science, vol. 9(3), pages 1-16, March.
  3. Chen Jia & Ramon Grima, 2024. "Holimap: an accurate and efficient method for solving stochastic gene network dynamics," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  4. T. Ochiai & J. C. Nacher, 2007. "Stochastic analysis of autoregulatory gene expression dynamics," Mathematical and Computer Modelling of Dynamical Systems, Taylor & Francis Journals, vol. 14(4), pages 377-388, November.
  5. Stefano Ciliberti & Olivier C Martin & Andreas Wagner, 2007. "Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology," PLOS Computational Biology, Public Library of Science, vol. 3(2), pages 1-10, February.
  6. Takako Kaneko-Kawano & Fugo Takasu & Honda Naoki & Yuichi Sakumura & Shin Ishii & Takahiro Ueba & Akinori Eiyama & Aiko Okada & Yoji Kawano & Kenji Suzuki, 2012. "Dynamic Regulation of Myosin Light Chain Phosphorylation by Rho-kinase," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-10, June.
  7. Luca Cardelli & Rosa D Hernansaiz-Ballesteros & Neil Dalchau & Attila Csikász-Nagy, 2017. "Efficient Switches in Biology and Computer Science," PLOS Computational Biology, Public Library of Science, vol. 13(1), pages 1-16, January.
  8. Liu, Xian & Wang, Jinzhi & Huang, Lin, 2007. "Global synchronization for a class of dynamical complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 386(1), pages 543-556.
  9. Tobias May & Lee Eccleston & Sabrina Herrmann & Hansjörg Hauser & Jorge Goncalves & Dagmar Wirth, 2008. "Bimodal and Hysteretic Expression in Mammalian Cells from a Synthetic Gene Circuit," PLOS ONE, Public Library of Science, vol. 3(6), pages 1-7, June.
  10. Oleg Kanakov & Roman Kotelnikov & Ahmed Alsaedi & Lev Tsimring & Ramón Huerta & Alexey Zaikin & Mikhail Ivanchenko, 2015. "Multi-Input Distributed Classifiers for Synthetic Genetic Circuits," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-17, May.
  11. Xu, Yong & Zhu, Ya-nan & Shen, Jianwei & Su, Jianbin, 2014. "Switch dynamics for stochastic model of genetic toggle switch," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 416(C), pages 461-466.
  12. Shivang Hina-Nilesh Joshi & Chentao Yong & Andras Gyorgy, 2022. "Inducible plasmid copy number control for synthetic biology in commonly used E. coli strains," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  13. Vladimir Kazeev & Mustafa Khammash & Michael Nip & Christoph Schwab, 2014. "Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains," PLOS Computational Biology, Public Library of Science, vol. 10(3), pages 1-19, March.
  14. Javier Macia & Romilde Manzoni & Núria Conde & Arturo Urrios & Eulàlia de Nadal & Ricard Solé & Francesc Posas, 2016. "Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia," PLOS Computational Biology, Public Library of Science, vol. 12(2), pages 1-24, February.
  15. Thomas B. Kepler & Timothy C. Elston, 2001. "Stochasticity in Transcriptional Regulation: Origins, Consequences and Mathematical Representations," Working Papers 01-06-033, Santa Fe Institute.
  16. Jamiree Harrison & Enoch Yeung, 2021. "Stability Analysis of Parameter Varying Genetic Toggle Switches Using Koopman Operators," Mathematics, MDPI, vol. 9(23), pages 1-25, December.
  17. Samanthe M Lyons & Wenlong Xu & June Medford & Ashok Prasad, 2014. "Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems," PLOS Computational Biology, Public Library of Science, vol. 10(3), pages 1-16, March.
  18. Lida Xu & Zhilin Qu, 2012. "Roles of Protein Ubiquitination and Degradation Kinetics in Biological Oscillations," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-11, April.
  19. Vojislav Gligorovski & Ahmad Sadeghi & Sahand Jamal Rahi, 2023. "Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  20. Sara Hooshangi & William E Bentley, 2011. "LsrR Quorum Sensing “Switch” Is Revealed by a Bottom-Up Approach," PLOS Computational Biology, Public Library of Science, vol. 7(9), pages 1-11, September.
  21. Ankit Gupta & Corentin Briat & Mustafa Khammash, 2014. "A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks," PLOS Computational Biology, Public Library of Science, vol. 10(6), pages 1-16, June.
  22. Graham Rockwell & Nicholas J Guido & George M Church, 2013. "Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective," PLOS Computational Biology, Public Library of Science, vol. 9(1), pages 1-15, January.
  23. Jaroslav Albert & Marianne Rooman, 2012. "Design Principles of a Genetic Alarm Clock," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-8, November.
  24. Alan Veliz-Cuba & Andrew J Hirning & Adam A Atanas & Faiza Hussain & Flavia Vancia & Krešimir Josić & Matthew R Bennett, 2015. "Sources of Variability in a Synthetic Gene Oscillator," PLOS Computational Biology, Public Library of Science, vol. 11(12), pages 1-23, December.
  25. Luis Mier-y-Terán-Romero & Mary Silber & Vassily Hatzimanikatis, 2010. "The Origins of Time-Delay in Template Biopolymerization Processes," PLOS Computational Biology, Public Library of Science, vol. 6(4), pages 1-15, April.
  26. Ioannis G Aviziotis & Michail E Kavousanakis & Andreas G Boudouvis, 2015. "Effect of Intrinsic Noise on the Phenotype of Cell Populations Featuring Solution Multiplicity: An Artificial lac Operon Network Paradigm," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-27, July.
  27. Buzzard, Gregery T., 2012. "Global sensitivity analysis using sparse grid interpolation and polynomial chaos," Reliability Engineering and System Safety, Elsevier, vol. 107(C), pages 82-89.
  28. Avraham E Mayo & Yaakov Setty & Seagull Shavit & Alon Zaslaver & Uri Alon, 2006. "Plasticity of the cis-Regulatory Input Function of a Gene," PLOS Biology, Public Library of Science, vol. 4(4), pages 1-1, March.
  29. Niklas Korsbo & Henrik Jönsson, 2020. "It’s about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology," PLOS Computational Biology, Public Library of Science, vol. 16(6), pages 1-29, June.
  30. Duncan Ingram & Guy-Bart Stan, 2023. "Modelling genetic stability in engineered cell populations," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  31. Ashty S. Karim & Dylan M. Brown & Chloé M. Archuleta & Sharisse Grannan & Ludmilla Aristilde & Yogesh Goyal & Josh N. Leonard & Niall M. Mangan & Arthur Prindle & Gabriel J. Rocklin & Keith J. Tyo & L, 2024. "Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  32. Zhou Fang & Ankit Gupta & Sant Kumar & Mustafa Khammash, 2024. "Advanced methods for gene network identification and noise decomposition from single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  33. Patrick R. Conrad & Youssef M. Marzouk & Natesh S. Pillai & Aaron Smith, 2016. "Accelerating Asymptotically Exact MCMC for Computationally Intensive Models via Local Approximations," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(516), pages 1591-1607, October.
  34. Zhou, Peipei & Cai, Shuiming & Liu, Zengrong & Chen, Luonan & Wang, Ruiqi, 2013. "Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems," Chaos, Solitons & Fractals, Elsevier, vol. 50(C), pages 115-126.
  35. Bonassi Fernando V. & You Lingchong & West Mike, 2011. "Bayesian Learning from Marginal Data in Bionetwork Models," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-27, October.
  36. Zachary R Fox & Brian Munsky, 2019. "The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments," PLOS Computational Biology, Public Library of Science, vol. 15(1), pages 1-23, January.
  37. Carl Song & Hilary Phenix & Vida Abedi & Matthew Scott & Brian P Ingalls & Mads Kærn & Theodore J Perkins, 2010. "Estimating the Stochastic Bifurcation Structure of Cellular Networks," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-11, March.
  38. Zhdanov, Vladimir P., 2011. "Periodic perturbation of the bistable kinetics of gene expression," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 390(1), pages 57-64.
  39. Evgeni V Nikolaev & Eduardo D Sontag, 2016. "Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory," PLOS Computational Biology, Public Library of Science, vol. 12(4), pages 1-33, April.
  40. Kudtarkar, Santosh Kumar & Dhadwal, Renu, 2023. "Noise induced bistability in a fluctuating environment," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 615(C).
  41. Lu, Wen & Zhang, Yuhao & Qian, Yu & Pandey, Vikas & Qu, Zhilin & Zhang, Zhaoyang, 2021. "Bursting and complex oscillatory patterns in a gene regulatory network model," Chaos, Solitons & Fractals, Elsevier, vol. 152(C).
  42. Andreas Petrides & Glenn Vinnicombe, 2018. "Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains," PLOS Computational Biology, Public Library of Science, vol. 14(5), pages 1-23, May.
  43. Zomorrodi, Ali R. & Maranas, Costas D., 2014. "Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits," European Journal of Operational Research, Elsevier, vol. 237(2), pages 665-676.
  44. Tomas Tokar & Jozef Ulicny, 2013. "The Mathematical Model of the Bcl-2 Family Mediated MOMP Regulation Can Perform a Non-Trivial Pattern Recognition," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-8, December.
  45. Wu, Juan & Xu, Yong & Ma, Shaojuan, 2019. "Realizing the transformation of logic gates in a genetic toggle system under Lévy noise," Chaos, Solitons & Fractals, Elsevier, vol. 119(C), pages 171-179.
  46. William Lopes & Daniel R. Amor & Jeff Gore, 2024. "Cooperative growth in microbial communities is a driver of multistability," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  47. Keun-Young Kim & Jin Wang, 2007. "Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch," PLOS Computational Biology, Public Library of Science, vol. 3(3), pages 1-13, March.
  48. Liu, Xian & Wang, Jinzhi & Huang, Lin, 2007. "Stabilization of a class of dynamical complex networks based on decentralized control," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 383(2), pages 733-744.
  49. Luís António Menezes Carreira & Filipe Tostevin & Ulrich Gerland & Lotte Søgaard-Andersen, 2020. "Protein-protein interaction network controlling establishment and maintenance of switchable cell polarity," PLOS Genetics, Public Library of Science, vol. 16(6), pages 1-30, June.
  50. Chen, Aimin & Wang, Pei & Zhou, Tianshou & Tian, Tianhai, 2022. "Balance of positive and negative regulation for trade-off between efficiency and resilience of high-dimensional networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 603(C).
  51. Mark Hallen & Bochong Li & Yu Tanouchi & Cheemeng Tan & Mike West & Lingchong You, 2011. "Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks," PLOS Computational Biology, Public Library of Science, vol. 7(10), pages 1-16, October.
  52. Deng, Liyuan & Huo, Siyu & Chen, Aihua & Liu, Zonghua, 2024. "Coupling resonance of signal responses induced by heterogeneously mixed positive and negative couplings in cognitive subnetworks," Chaos, Solitons & Fractals, Elsevier, vol. 180(C).
  53. Duan, Dongli & Bai, Xue & Rong, Yisheng & Hou, Gege & Hang, Jiale, 2022. "Controlling of nonlinear dynamical networks based on decoupling and re-coupling method," Chaos, Solitons & Fractals, Elsevier, vol. 163(C).
  54. Betz, Ulrich A.K. & Arora, Loukik & Assal, Reem A. & Azevedo, Hatylas & Baldwin, Jeremy & Becker, Michael S. & Bostock, Stefan & Cheng, Vinton & Egle, Tobias & Ferrari, Nicola & Schneider-Futschik, El, 2023. "Game changers in science and technology - now and beyond," Technological Forecasting and Social Change, Elsevier, vol. 193(C).
  55. Singh, Vijai & Chaudhary, Dharmendra Kumar & Mani, Indra & Dhar, Pawan Kumar, 2016. "Recent advances and challenges of the use of cyanobacteria towards the production of biofuels," Renewable and Sustainable Energy Reviews, Elsevier, vol. 60(C), pages 1-10.
  56. Weiyue Ji & Handuo Shi & Haoqian Zhang & Rui Sun & Jingyi Xi & Dingqiao Wen & Jingchen Feng & Yiwei Chen & Xiao Qin & Yanrong Ma & Wenhan Luo & Linna Deng & Hanchi Lin & Ruofan Yu & Qi Ouyang, 2013. "A Formalized Design Process for Bacterial Consortia That Perform Logic Computing," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-9, February.
  57. Marc Weber & Javier Buceta, 2013. "Stochastic Stabilization of Phenotypic States: The Genetic Bistable Switch as a Case Study," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-8, September.
  58. Das, Saureesh, 2022. "Recurrence quantification and bifurcation analysis of electrical activity in resistive/memristive synapse coupled Fitzhugh–Nagumo type neurons," Chaos, Solitons & Fractals, Elsevier, vol. 165(P1).
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  61. Linlin Tang & Zhijin Tian & Jin Cheng & Yijing Zhang & Yongxiu Song & Yan Liu & Jinghao Wang & Pengfei Zhang & Yonggang Ke & Friedrich C. Simmel & Jie Song, 2023. "Circular single-stranded DNA as switchable vector for gene expression in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
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