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A synthetic oscillatory network of transcriptional regulators

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  1. Padmaja, N. & Balasubramaniam, P., 2022. "Mixed H∞/passivity based stability analysis of fractional-order gene regulatory networks with variable delays," Mathematics and Computers in Simulation (MATCOM), Elsevier, vol. 192(C), pages 167-181.
  2. repec:plo:pcbi00:1003890 is not listed on IDEAS
  3. repec:plo:pone00:0129888 is not listed on IDEAS
  4. Irene Otero-Muras & Julio R Banga, 2016. "Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis," PLOS ONE, Public Library of Science, vol. 11(12), pages 1-26, December.
  5. Tian, Yufeng & Wang, Zhanshan, 2021. "A new result on H∞ performance state estimation for static neural networks with time-varying delays," Applied Mathematics and Computation, Elsevier, vol. 388(C).
  6. repec:plo:pcbi00:1003910 is not listed on IDEAS
  7. Rabajante, Jomar Fajardo & Talaue, Cherryl Ortega, 2015. "Equilibrium switching and mathematical properties of nonlinear interaction networks with concurrent antagonism and self-stimulation," Chaos, Solitons & Fractals, Elsevier, vol. 73(C), pages 166-182.
  8. Javier Santos-Moreno & Eve Tasiudi & Hadiastri Kusumawardhani & Joerg Stelling & Yolanda Schaerli, 2023. "Robustness and innovation in synthetic genotype networks," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  9. Juliane Liepe & Sarah Filippi & Michał Komorowski & Michael P H Stumpf, 2013. "Maximizing the Information Content of Experiments in Systems Biology," PLOS Computational Biology, Public Library of Science, vol. 9(1), pages 1-13, January.
  10. repec:plo:pcbi00:1006220 is not listed on IDEAS
  11. Jin Wang & Bo Huang & Xuefeng Xia & Zhirong Sun, 2006. "Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle," PLOS Computational Biology, Public Library of Science, vol. 2(11), pages 1-10, November.
  12. 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.
  13. 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.
  14. 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.
  15. Gabriele Lillacci & Mustafa Khammash, 2010. "Parameter Estimation and Model Selection in Computational Biology," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-17, March.
  16. Xue, Yu & Tu, Kairong & Liu, Chunyan & Zhang, Xian, 2024. "Non-fragile extended dissipative synchronization control for uncertain discrete-time neural networks with leakage and unbounded time-varying delays," Chaos, Solitons & Fractals, Elsevier, vol. 185(C).
  17. 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.
  18. Cheng, Guifang & Liu, Hao, 2024. "Asynchronous finite-time extended dissipative sliding mode control for semi-Markovian jump master–slave neural networks," Chaos, Solitons & Fractals, Elsevier, vol. 179(C).
  19. Takanori Hasegawa & Rui Yamaguchi & Masao Nagasaki & Satoru Miyano & Seiya Imoto, 2014. "Inference of Gene Regulatory Networks Incorporating Multi-Source Biological Knowledge via a State Space Model with L1 Regularization," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-19, August.
  20. Jacopo Gabrielli & Roberto Di Blasi & Cleo Kontoravdi & Francesca Ceroni, 2025. "Degradation bottlenecks and resource competition in transiently and stably engineered mammalian cells," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
  21. Martiny, Emil S. & Jensen, Mogens H. & Heltberg, Mathias S., 2022. "Detecting limit cycles in stochastic time series," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 605(C).
  22. 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.
  23. Bo-Wei Qin & Lei Zhao & Wei Lin, 2021. "A frequency-amplitude coordinator and its optimal energy consumption for biological oscillators," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  24. Margherita Carletti & Malay Banerjee, 2019. "A Backward Technique for Demographic Noise in Biological Ordinary Differential Equation Models," Mathematics, MDPI, vol. 7(12), pages 1-16, December.
  25. repec:plo:pone00:0090666 is not listed on IDEAS
  26. 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.
  27. 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.
  28. 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.
  29. Lukas Aufinger & Johann Brenner & Friedrich C. Simmel, 2022. "Complex dynamics in a synchronized cell-free genetic clock," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
  30. Ehigie, Julius O. & Luan, Vu Thai & Okunuga, Solomon A. & You, Xiong, 2022. "Exponentially fitted two-derivative DIRK methods for oscillatory differential equations," Applied Mathematics and Computation, Elsevier, vol. 418(C).
  31. repec:plo:pone00:0182385 is not listed on IDEAS
  32. 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.
  33. Thomas B. Kepler & Timothy C. Elston, 2001. "Stochasticity in Transcriptional Regulation: Origins, Consequences and Mathematical Representations," Working Papers 01-06-033, Santa Fe Institute.
  34. repec:plo:pone00:0122150 is not listed on IDEAS
  35. 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).
  36. 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.
  37. repec:plo:pbio00:0030343 is not listed on IDEAS
  38. Jianbang Wang & Zhenzhen Li & Itamar Willner, 2022. "Cascaded dissipative DNAzyme-driven layered networks guide transient replication of coded-strands as gene models," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
  39. 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.
  40. repec:plo:pcbi00:1000739 is not listed on IDEAS
  41. repec:plo:pbio00:1000513 is not listed on IDEAS
  42. 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.
  43. 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.
  44. Arjun Raj & Charles S Peskin & Daniel Tranchina & Diana Y Vargas & Sanjay Tyagi, 2006. "Stochastic mRNA Synthesis in Mammalian Cells," PLOS Biology, Public Library of Science, vol. 4(10), pages 1-13, September.
  45. Kuznetsov, A. & Afraimovich, V., 2012. "Heteroclinic cycles in the repressilator model," Chaos, Solitons & Fractals, Elsevier, vol. 45(5), pages 660-665.
  46. 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).
  47. 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.
  48. repec:plo:pmed00:0030208 is not listed on IDEAS
  49. Lucia Marucci & David A W Barton & Irene Cantone & Maria Aurelia Ricci & Maria Pia Cosma & Stefania Santini & Diego di Bernardo & Mario di Bernardo, 2009. "How to Turn a Genetic Circuit into a Synthetic Tunable Oscillator, or a Bistable Switch," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-10, December.
  50. Olivia Macovei, 2020. "Conceptual Delimitations related to the Philosophical Approaches on Synthetic Biology," Logos Universalitate Mentalitate Educatie Noutate - Sectiunea Filosofie si Stiinte umaniste/ Logos Universality Mentality Education Novelty - Section: Philosophy and Humanistic Sciences, Editura Lumen, Department of Economics, vol. 8(2), pages 83-104, December.
  51. 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.
  52. 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.
  53. Filippi Sarah & Barnes Chris P. & Cornebise Julien & Stumpf Michael P.H., 2013. "On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(1), pages 87-107, March.
  54. Miles Miller & Marc Hafner & Eduardo Sontag & Noah Davidsohn & Sairam Subramanian & Priscilla E M Purnick & Douglas Lauffenburger & Ron Weiss, 2012. "Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-18, July.
  55. Huang, Chengdai & Cao, Jinde & Xiao, Min, 2016. "Hybrid control on bifurcation for a delayed fractional gene regulatory network," Chaos, Solitons & Fractals, Elsevier, vol. 87(C), pages 19-29.
  56. Simeon D. Castle & Michiel Stock & Thomas E. Gorochowski, 2024. "Engineering is evolution: a perspective on design processes to engineer biology," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  57. Tian-Jiao Feng & Jie Mei & Rui-Wu Wang & Sabin Lessard & Yi Tao & Xiu-Deng Zheng, 2022. "Noise-Induced Quasi-Heteroclinic Cycle in a Rock–Paper–Scissors Game with Random Payoffs," Dynamic Games and Applications, Springer, vol. 12(4), pages 1280-1292, December.
  58. 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.
  59. repec:plo:pone00:0039355 is not listed on IDEAS
  60. Stefanie S. M. Meier & Elina Multamäki & Américo T. Ranzani & Heikki Takala & Andreas Möglich, 2024. "Leveraging the histidine kinase-phosphatase duality to sculpt two-component signaling," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  61. Kanakov, Oleg & Chen, Shangbin & Zaikin, Alexey, 2024. "Learning by selective plasmid loss for intracellular synthetic classifiers," Chaos, Solitons & Fractals, Elsevier, vol. 179(C).
  62. repec:plo:pone00:0042790 is not listed on IDEAS
  63. 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.
  64. Ankit Gupta & Mustafa Khammash, 2022. "Frequency spectra and the color of cellular noise," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  65. repec:plo:pone00:0016140 is not listed on IDEAS
  66. Aleksandra Eremina & Christian Schwall & Teresa Saez & Lennart Witting & Dietrich Kohlheyer & Bruno M. C. Martins & Philipp Thomas & James C. W. Locke, 2025. "Environmental and molecular noise buffering by the cyanobacterial clock in individual cells," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
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