Design principles of biochemical oscillators

Cited by (1,000)

Items 701–800 of 1,000

1. The cyanobacterial circadian clock
   Yong-Gang Chang, Andy LiWang · 2025 · npj Biological Timing and Sleep
2. Light-mediated communication in responsive materials ranging from individual self-oscillators to feedback-driven network
   Hong-Shuang Guo, Kai Li, Jianfeng Yang, Dengfeng Li, Fan Liu, Hao Zeng · 2025 · Nature Communications
3. A mathematical model for the role of dopamine-D2 self-regulation in the production of ultradian rhythms
   An Qi Zhang, Martin Roland Ralph, Adam R. Stinchcombe · 2024 · PLoS Computational Biology
4. Chaos and Robustness in a Single Family of Genetic Oscillatory Networks
   Daniel Y. Fu, Patrick Tan, Alexey S. Kuznetsov, Yaroslav I. Molkov · 2014 · PLoS ONE
5. Bayesian Parameter Inference by Markov Chain Monte Carlo with Hybrid Fitness Measures: Theory and Test in Apoptosis Signal Transduction Network
   Yohei Murakami, Shoji Takada · 2013 · PLoS ONE
6. An amplified derepression controller with multisite inhibition and positive feedback
   Gorana Drobac, Qaiser Waheed, Behzad Heidari, Peter Ruoff · 2021 · PLoS ONE
7. Discovering design principles for biological functionalities: Perspectives from systems biology
   Priyan Bhattacharya, Karthik Raman, Arun Kumar Tangirala · 2022 · Journal of Biosciences
8. Temporal pH waveforms generated in an enzymatic reaction network in batch and cell-sized microcompartments
   Masaki Itatani, Gábor Holló, Paola Albanese, Nadia Valletti, Sándor Kurunczi, Róbert Horváth, Federico Rossi, István Lagzi · 2025 · Cell Reports Physical Science
9. Influence of parameter values on the oscillation sensitivities of two p53–Mdm2 models
   Christian Cuba Samaniego, Alexander R. Valle, Giancarlo Ayala‐Charca, Elizabeth Villota, Alberto M. Coronado · 2015 · Systems and Synthetic Biology
10. Diffusive coupling can discriminate between similar reaction mechanisms in an allosteric enzyme system
    Ronny Straube, Ernesto M. Nicola · 2010 · BMC Systems Biology
11. Mathematical modeling of fission yeast Schizosaccharomyces pombe cell cycle: exploring the role of multiple phosphatases
    P. Anbumathi, Sharad Bhartiya, Kareenhalli Viswanath Venkatesh · 2011 · Systems and Synthetic Biology
12. Intrinsic noise induced state transition in coupled positive and negative feedback genetic circuit
    Pei Wang, Jinhu Lü, Yuhuan Zhang, MACIEJ J. OGORZAŁEK · 2011 · IEEE International Conference on Systems Biology
13. Mutual regulation causes co-entrainment between a synthetic oscillator and the bacterial cell cycle
    Marta Dies, Leticia Galera-Laporta, Jordi García‐Ojalvo · 2015 · Integrative Biology
14. Systems and Synthetic Biology Applied to Health
    Tiago Antônio de Oliveira Mendes, Filippo Castiglione, Paolo Tieri, Liza Figueiredo Felicori · 2016 · Elsevier eBooks
15. A thermodynamic description for physiological transmembrane transport
    Marco Arieli Herrera-Valdez · 2018 · F1000Research
16. Kinetic Model of Translational Autoregulation
    Tyng, Vivian, Kellman, Michael E. · 2019 · The Journal of Physical Chemistry B
17. Complementary phase responses via functional differentiation of dual negative feedback loops
    Koichiro Uriu, Hajime Tei · 2021 · PLoS Computational Biology
18. Oscillatory Behaviors of Delayed p53 Regulatory Network with microRNA 192 in DNA Damage Response
    Chunyan Gao, Fangqi Chen · 2021 · International Journal of Bifurcation and Chaos
19. Design of non-autonomous pH oscillators and the existence of chemical beat phenomenon in a neutralization reaction
    Hugh Shearer Lawson, Gábor Holló, Norbert Német, Satoshi Teraji, Hideyuki Nakanishi, Róbert Horváth, István Lagzi · 2021 · Scientific Reports
20. The finding and researching algorithm for potentially oscillating enzymatic systems
    Tatiana N. Lakhova, Казанцев Федор Владимирович, Sergey Alexandrovich Lashin, Yu. G. Matushkin · 2021 · Vavilov Journal of Genetics and Breeding
21. The Problem of Engines in Statistical Physics
    Robert Alicki, David Gelbwaser-Klimovsky, Alejandro Jenkins · 2021 · Entropy
22. Resonant amplification of enzymatic chemical oscillations by oscillating flow
    Oleg E. Shklyaev, Anna C. Balazs · 2021 · Chaos An Interdisciplinary Journal of Nonlinear Science
23. Tick, Tock, Circadian Clocks
    Jae Kyoung Kim · 2021 · Springer eBooks
24. Stability and bifurcation analysis of a delayed genetic oscillator model
    Chunyan Gao, Fangqi Chen · 2021 · Nonlinear Dynamics
25. Improved estimation for energy dissipation in biochemical oscillations
    Zhiyu Cao, Zhonghuai Hou · 2022 · The Journal of Chemical Physics
26. Cesium: A public database of evolved oscillatory reaction networks
    Lillian T. Tatka, Wesley Luk, Timothy C. Elston, Joseph L. Hellerstein, Herbert M. Sauro · 2023 · Biosystems
27. Deficiency, kinetic invertibility, and catalysis in stochastic chemical reaction networks
    Shesha Gopal Marehalli Srinivas, Matteo Polettini, Massimiliano Esposito, Francesco Avanzini · 2023 · The Journal of Chemical Physics
28. Polylysine‐Coated Surfaces Drive Competition in Chemical Reaction Networks to Enable Molecular Information Processing
    A. Hazal Koyuncu, Jacopo Movilli, Sevil Sahin, Dmitrii V. Kriukov, Jurriaan Huskens, Albert S. Y. Wong · 2023 · ChemSystemsChem
29. A Brief History of Eukaryotic Cell Cycle Research
    Fatima Cvrčková · 2018 · Plant cell monographs
30. Autonomous Chemical Modulation and Unidirectional Coupling in Two Oscillatory Chemical Systems
    Gábor Holló, István Lagzi · 2019 · The Journal of Physical Chemistry A
31. Coupling protocol of interlocked feedback oscillators in circadian clocks
    Md Mamunur Rashid, Hiroyuki Kurata · 2020 · Journal of The Royal Society Interface
32. Coupled Feedback Loops Involving PAGE4, EMT and Notch Signaling Can Give Rise to Non-Genetic Heterogeneity in Prostate Cancer Cells
    Divyoj Singh, Federico Bocci, Prakash Kulkarni, Mohit Kumar Jolly · 2021 · Entropy
33. Dynamic modeling of yeast meiotic initiation
    Debjit Ray, Yongchun Su, Ping Ye · 2013 · BMC Systems Biology
34. Phase Responses of Oscillating Components in a Signaling Pathway
    Masaki Nomura, Mariko Okada · 2013 · Frontiers in Physiology
35. Stability and Hopf bifurcation analysis in a delayed three-node circuit involving interlinked positive and negative feedback loops
    Guiyuan Wang, Zhuoqin Yang, Marc Turcotte · 2018 · Mathematical Biosciences
36. Dynamics of Gene Networks with Time Delays
    Anael Verdugo · 2010 · eCommons (Cornell University)
37. Neural network aided approximation and parameter inference of stochastic models of gene expression
    Qingchao Jiang, Xiaoming Fu, Shifu Yan, Runlai Li, Wenli Du, Zhixing Cao, Feng Qian, Ramon Grima · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
38. MODELLING NUCLEOCYTOPLASMIC TRANSPORT WITH APPLICATION TO THE INTRACELLULAR DYNAMICS OF THE TUMOR SUPPRESSOR PROTEIN P53
    Luna Dimitrio, Jean Clairambault, Roberto Natalini · 2012 · OpenGrey (Institut de l'Information Scientifique et Technique)
39. Mapping, Modeling, and Reprogramming Cell-Fate Decision-Making Systems
    Lucy Ham, Taylor E. Woodward, Megan A. Coomer, Michael P. H. Stumpf · 2025 · Annual Review of Biomedical Data Science
40. Extrinsic fluctuations in the p53 cycle
    Manuel Eduardo Hernández-García, Mariana Gómez-Schiavon, Jorge Velázquez-Castro · 2024 · The Journal of Chemical Physics
41. Time after time – circadian clocks through the lens of oscillator theory
    Marta del Olmo, Carolin Ector, Hanspeter Herzel · 2026 · FEBS Letters
42. Quantifying the Dynamics of Coupled Networks of Switches and Oscillators
    Matthew R. Francis, Elana Judith Fertig · 2012 · PLoS ONE
43. Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity
    Kazuhiro Maeda, Hiroyuki Kurata · 2014 · BMC Systems Biology
44. Design and analysis of a biomolecular positive-feedback oscillator
    Christian Cuba Samaniego, Elisa Franco, Giulia Giordano · 2018 · IEEE Conference on Decision and Control (CDC)
45. Elucidating the Implications of Diverse Dynamical Responses in p53 Protein
    Kajal Charan, Amitava Giri, Sandip Kar · 2022 · ChemPhysChem
46. Self-organization of Protein Patterns
    Erwin Frey, Fridtjof Brauns · 2022
47. Accurate Reduced Models for the pH Oscillations in the Urea–Urease Reaction Confined to Giant Lipid Vesicles
    Arthur V. Straube, Stefanie Winkelmann, Felix Höfling · 2023 · The Journal of Physical Chemistry B
48. Design of oscillatory dynamics in numerical simulations of compartment-based enzyme systems
    Anna S. Leathard, Paul A. Beales, Annette Fiona Taylor · 2023 · Chaos An Interdisciplinary Journal of Nonlinear Science
49. Complex role of time delay in dynamical coordination of neural progenitor fate decisions mediated by Notch pathway
    Yuan Zhang, Jinde Cao, Lixia Liu, Haihong Liu, Zhouhong Li · 2024 · Chaos Solitons & Fractals
50. How do multiple active cellular forces co-regulate wound shape evolution?
    Qianchun Wang, Shijie He, Baohua Ji · 2024 · Journal of the Mechanics and Physics of Solids
51. Energy-based analysis of biochemical oscillators using bond graphs and linear control theory
    P.J. Gawthrop, Michael Pan · 2025 · Royal Society Open Science
52. Design and analysis of a synthetic aptamer-based oscillator
    Christian Cuba Samaniego, Sho M Kitada, Elisa Franco · 2015 · Proceedings of the ... American Control Conference/Proceedings of the American Control Conference
53. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems
    Peipei Zhou, Shuiming Cai, Zengrong Liu, Luonan Chen, Ruiqi Wang · 2013 · Chaos Solitons & Fractals
54. The Usual Suspects 2019: of Chips, Droplets, Synthesis, and Artificial Cells
    Christoph Eilenberger, Sarah Spitz, Barbara Bachmann, Eva-Kathrin Ehmoser, Peter Ertl, Mario Rothbauer · 2019 · Micromachines
55. Oscillation Expression of NF-$\kappa$ B Driven by Transcription and Translation Time Delays
    Li Liu, Fang Yan, Haihong Liu · 2019 · IEEE Transactions on NanoBioscience
56. Feedback enrichment analysis for transcription factor-target genes in signaling pathways
    Kentaro Inoue · 2020 · Biosystems
57. Entrainment within hierarchical circadian oscillator networks
    Guangyuan Liao, Amitabha Bose · 2022 · Mathematical Biosciences
58. Generating Oscillatory Behavior by Applying a Magnetic Field during Electrocatalytic Oxidation of Glycerol
    Rui Gao, Mohamad S. Kodaimati, Kaitlyn M. Handy, Samuel E. Root, George M. Whitesides · 2022 · The Journal of Physical Chemistry C
59. Noise facilitates entrainment of a population of uncoupled limit cycle oscillators
    Vojtěch Kumpošt, Lennart Hilbert, Ralf Mikut · 2023 · Journal of The Royal Society Interface
60. A theory of synchrony for active compartments with delays coupled through bulk diffusion
    Bin Xu, Paul C. Bressloff · 2016 · Physica D Nonlinear Phenomena
61. Asymmetry in Signal Oscillations Contributes to Efficiency of Periodic Systems
    Seul-A Bae, Alison Acevedo, Ioannis P. Androulakis · 2016 · Critical Reviews in Biomedical Engineering
62. Role of intercellular coupling and delay on the synchronization of genetic oscillators
    Supravat Dey, Lee Tracey, Abhyudai Singh · 2021 · Proceedings of the ... American Control Conference/Proceedings of the American Control Conference
63. Multiple Time Delays Induced Dynamics of p53 Gene Regulatory Network
    Yuanhong Bi, Yanan Li, Jianmin Hou, Quansheng Liu · 2021 · International Journal of Bifurcation and Chaos
64. A synthetic population-level oscillator in non-microfluidic environments
    Fei Gu, Wei Jiang, Fangbing Kang, Tianyuan Su, Xiaoya Yang, Qingsheng Qi, Quanfeng Liang · 2023 · Communications Biology
65. Dissecting Long-Term Glucose Metabolism Identifies New Susceptibility Period for Metabolic Dysfunction in Aged Mice
    Anuradha Chauhan, Heike Weiß, Franziska Koch, Saleh Mohamed Ibrahim, Julio Vera, Olaf Wolkenhauer A, Markus Tiedge · 2015 · PLoS ONE
66. Transient amplification limits noise suppression in biochemical networks
    John Dixon, Anika Lindemann, Jonathan McCoy · 2016 · Physical review. E
67. Computational Models to Decipher Cell-Signaling Pathways
    Anne Poupon, Éric Reiter · 2014 · Elsevier eBooks
68. The Hallmarks of Cancer Revisited Through Systems Biology and Network Modelling
    Charles Auffray, Trey Ideker, David J. Galas, Leroy Hood · 2011 · Springer eBooks
69. Stability and Hopf Bifurcation Analysis in a Delayed Myc/E2F/miR-17-92 Network Involving Interlinked Positive and Negative Feedback Loops
    Guiyuan Wang, Zhuoqin Yang · 2018 · Discrete Dynamics in Nature and Society
70. Two Challenges of Systems Biology
    William S. Hlavacek · 2011 · Wiley eBooks
71. Integrative systems and synthetic biology of cell-matrix adhesion sites
    Eli Zamir · 2016 · Cell Adhesion & Migration
72. Synthetic Biology: An Emerging Approach for Strain Engineering
    Jie Sun, Hal S. Alper · 2016 · Industrial Biotechnology
73. A free-running oscillator times and executes centriole biogenesis
    Mustafa G. Aydogan, Thomas L. Steinacker, Mohammad Mofatteh, Lisa Gartenmann, Alan Wainman, Saroj Saurya, Paul T. Conduit, Felix Zhou, Michael A. Boemo, Jordan W. Raff · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
74. Excitability and Oscillations of Active Droplets
    Ivar S. Haugerud, Hidde Derk Vuijk, Job Boekhoven, Christoph A. Weber · 2026 · Physical Review Letters
75. Self-Oscillatory Neuron-like Devices for Unconventional Computing Applications
    Gonzalo Rivera‐Sierra, Juan Bisquert, Roberto Fenollosa · 2026 · Chemical Reviews
76. The impact of decoys on a genetic oscillator based on coupled positive-negative feedbacks
    Zhanhao Zhang, Supravat Dey, Abhyudai Singh · 2022 · IFAC-PapersOnLine
77. Towards Autonomous Materials–Challenges in Chemical Communication
    P. Jarne de Jong, Foteini Trigka, Michael Markus Lerch · 2024 · ChemSystemsChem
78. Bifurcations in coupled amyloid-β aggregation-inflammation systems
    Kalyan Sundar Chakrabarti, Davood Bakhtiari, Nasrollah Rezaei‐Ghaleh · 2024 · npj Systems Biology and Applications
79. Identify structures underlying out-of-equilibrium reaction networks with random graph analysis
    Éverton Fernandes da Cunha, Yanna J. Kraakman, Dmitrii V. Kriukov, Thomas van Poppel, Clara Stegehuis, Albert S. Y. Wong · 2025 · Chemical Science
80. Generic bifurcations in the dynamics of biochemical networks
    Steffen Waldherr, Frank Allgöwer, Nicole Erika Radde · 2010 · The proceedings of the IEEE Conference on Control Applications/The proceedings of the ... IEEE Conference on Control Applications
81. Cell Polarity: Netrin Calms an Excitable System
    Allison W. McClure, Daniel J. Lew · 2014 · Current Biology
82. ASYMMETRIC TRANSITION AND TIME-SCALE SEPARATION IN INTERLINKED POSITIVE FEEDBACK LOOPS
    Pencho Yordanov, Stefka Tyanova, M.‐Th. Hütt, Annick Lesne · 2011 · International Journal of Bifurcation and Chaos
83. Automated analysis of biological oscillator models using mode decomposition
    Tomasz Konopka · 2011 · Bioinformatics
84. A Vanadium‐Based Chemical Oscillator: Identification of Chemical Species Responsible for the Redox Reaction and Construction of a Simplified Model
    Kan Kanamori, Hiroshi Kataoka, Seiichi Matsugo · 2012 · European Journal of Inorganic Chemistry
85. Topological origin of global attractors in gene regulatory networks
    Yunjun Zhang, Qi Ouyang, Zhi Geng · 2014 · Science China Physics Mechanics and Astronomy
86. Cross‐Regulation of an Artificial Metalloenzyme
    Yasunori Okamoto, Thomas R. Ward · 2017 · Angewandte Chemie
87. Spatiotemporal feedforward between PKM2 tetramers and mTORC1 prompts mTORC1 activation
    Xia Yu, Shuming Wang, Chunbo Song, Ruo-yu Luo · 2022 · Physical Biology
88. Computational characterization of recombinase circuits for periodic behaviors
    Judith Landau, Christian Cuba Samaniego, Giulia Giordano, Elisa Franco · 2022 · iScience
89. Autoregulation of Transcription and Translation: A Qualitative Analysis
    Philip J. Murray · 2023 · Bulletin of Mathematical Biology
90. Periodic on-off operations of the self-cycling ethanol fermentation process: Stability analysis and optimal operation strategies
    Chi Zhai, Sichen Wu, Shilin Chen, Yang Chunxi · 2024 · Chemical Engineering and Processing - Process Intensification
91. Newton's cradle: Cell cycle regulation by two mutually inhibitory oscillators
    Calin-Mihai Dragoi, John J. Tyson, Béla Novák · 2024 · Mathematical Biosciences
92. Unclocklike Oscillators with Frequency Memory for the Entrainment of Biological Clocks
    Christian Mauffette Denis, Paul François · 2024 · PRX Life
93. Depth-dependent contributions of various vascular zones to cerebral autoregulation and functional hyperemia: An in-silico analysis
    Hadi Esfandi, Mahshad Javidan, Rozalyn M. Anderson, Ramin Pashaie · 2025 · PLoS ONE
94. The Importance of Stochastic Effects for Explaining Entrainment in the Zebrafish Circadian Clock
    Raphaela Heussen, David Whitmore · 2015 · Computational and Mathematical Methods in Medicine
95. Mechanistic Modeling of Inflammation
    Jeremy D. Scheff, Kubra Kamisoglu, Ioannis P. Androulakis · 2016 · AAPS advances in the pharmaceutical sciences series
96. Periodic Switching in a Recombinase-Based Molecular Circuit
    Christian Cuba Samaniego, Giulia Giordano, Elisa Franco · 2019 · IEEE Control Systems Letters
97. Multiple Realization in Systems Biology
    Wei Fang · 2020 · Philosophy of Science
98. Effects of an Imposed Flow on Chemical Oscillations Generated by Enzymatic Reactions
    Oleg E. Shklyaev, Victor V. Yashin, Anna C. Balazs · 2020 · Frontiers in Chemistry
99. Bridging the Gap Between Modeling of Tumor Growth and Clinical Imaging
    Behnaz Abdollahi, Neal Dunlap, Hermann B. Frieboes · 2013 · Springer eBooks
100. Functional tunability of biological circuits from additional toggle switches
     Changhong Shi, Tianshou Zhou, Zhanjiang Yuan · 2013 · IET Systems Biology