A synthetic oscillatory network of transcriptional regulators

Citations

Cited by:

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. 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.
3. 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).
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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).
14. 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.
15. 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).
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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).
24. 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.
25. Thomas B. Kepler & Timothy C. Elston, 2001. "Stochasticity in Transcriptional Regulation: Origins, Consequences and Mathematical Representations," Working Papers 01-06-033, Santa Fe Institute.
26. 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).
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. Kuznetsov, A. & Afraimovich, V., 2012. "Heteroclinic cycles in the repressilator model," Chaos, Solitons & Fractals, Elsevier, vol. 45(5), pages 660-665.
34. 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).
35. 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.
36. 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.
37. 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.
38. 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.
39. 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.
40. 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.
41. 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.
42. 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.
43. 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.
44. 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.
45. 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.
46. 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.
47. Kanakov, Oleg & Chen, Shangbin & Zaikin, Alexey, 2024. "Learning by selective plasmid loss for intracellular synthetic classifiers," Chaos, Solitons & Fractals, Elsevier, vol. 179(C).
48. 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.
49. Ankit Gupta & Mustafa Khammash, 2022. "Frequency spectra and the color of cellular noise," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
50. Duncan Ingram & Guy-Bart Stan, 2023. "Modelling genetic stability in engineered cell populations," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
51. 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.
52. Mario A Marchisio & Jörg Stelling, 2011. "Automatic Design of Digital Synthetic Gene Circuits," PLOS Computational Biology, Public Library of Science, vol. 7(2), pages 1-13, February.
53. 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.
54. Jung Hun Park & Gábor Holló & Yolanda Schaerli, 2024. "From resonance to chaos by modulating spatiotemporal patterns through a synthetic optogenetic oscillator," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
55. Volkov, Evgeny & Hellen, Edward H., 2021. "The effect of characteristic times on collective modes of two quorum sensing coupled identical ring oscillators," Chaos, Solitons & Fractals, Elsevier, vol. 151(C).
56. Konstantinos I Papadimitriou & Guy-Bart V Stan & Emmanuel M Drakakis, 2013. "Systematic Computation of Nonlinear Cellular and Molecular Dynamics with Low-Power CytoMimetic Circuits: A Simulation Study," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-24, February.
57. 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.
58. Nasimul Noman & Taku Monjo & Pablo Moscato & Hitoshi Iba, 2015. "Evolving Robust Gene Regulatory Networks," PLOS ONE, Public Library of Science, vol. 10(1), pages 1-21, January.
59. Inés P Mariño & Alexey Zaikin & Joaquín Míguez, 2017. "A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-25, August.
60. Zhdanov, Vladimir P., 2012. "Periodic perturbation of genetic oscillations," Chaos, Solitons & Fractals, Elsevier, vol. 45(5), pages 577-587.
61. Rutger Hermsen & Bas Ursem & Pieter Rein ten Wolde, 2010. "Combinatorial Gene Regulation Using Auto-Regulation," PLOS Computational Biology, Public Library of Science, vol. 6(6), pages 1-13, June.
62. Dhiman, Aman & Poria, Swarup, 2018. "Allee effect induced diversity in evolutionary dynamics," Chaos, Solitons & Fractals, Elsevier, vol. 108(C), pages 32-38.
63. Bottani, Samuel & Grammaticos, Basile, 2008. "A simple model of genetic oscillations through regulated degradation," Chaos, Solitons & Fractals, Elsevier, vol. 38(5), pages 1468-1482.
64. Scharf, Yael, 2017. "A chaotic outlook on biological systems," Chaos, Solitons & Fractals, Elsevier, vol. 95(C), pages 42-47.
65. Alex J. H. Fedorec & Neythen J. Treloar & Ke Yan Wen & Linda Dekker & Qing Hsuan Ong & Gabija Jurkeviciute & Enbo Lyu & Jack W. Rutter & Kathleen J. Y. Zhang & Luca Rosa & Alexey Zaikin & Chris P. Bar, 2024. "Emergent digital bio-computation through spatial diffusion and engineered bacteria," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
66. Luna Rizik & Loai Danial & Mouna Habib & Ron Weiss & Ramez Daniel, 2022. "Synthetic neuromorphic computing in living cells," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
67. 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.
68. Yue, Dandan & Guan, Zhi-Hong & Li, Tao & Liao, Rui-Quan & Liu, Feng & Lai, Qiang, 2017. "Event-based cluster synchronization of coupled genetic regulatory networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 482(C), pages 649-665.
69. 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).
70. Tai-Yin Chiu & Hui-Ju K Chiang & Ruei-Yang Huang & Jie-Hong R Jiang & François Fages, 2015. "Synthesizing Configurable Biochemical Implementation of Linear Systems from Their Transfer Function Specifications," PLOS ONE, Public Library of Science, vol. 10(9), pages 1-27, September.
71. 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.
72. Kroll, K.M. & Ferrantini, A. & Domany, E., 2010. "Introduction to biology and chromosomal instabilities in cancer," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(20), pages 4374-4388.
73. Lorenzo Pasotti & Nicolò Politi & Susanna Zucca & Maria Gabriella Cusella De Angelis & Paolo Magni, 2012. "Bottom-Up Engineering of Biological Systems through Standard Bricks: A Modularity Study on Basic Parts and Devices," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-10, July.
74. Hasegawa, Takanori & Niida, Atsushi & Mori, Tomoya & Shimamura, Teppei & Yamaguchi, Rui & Miyano, Satoru & Akutsu, Tatsuya & Imoto, Seiya, 2016. "A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models," Computational Statistics & Data Analysis, Elsevier, vol. 94(C), pages 63-74.