Design principles of biochemical oscillators

Cited by (1,000)

Items 401–500 of 1,000

1. Circadian clocks optimally adapt to sunlight for reliable synchronization
   Yoshihiko Hasegawa, Masanori Arita · 2014
2. Mathematical analysis of robustness of oscillations in models of the mammalian circadian clock
   Xiangyu Yao, Benjamin Heidebrecht, Jing Chen, John J. Tyson · 2022 · PLoS Computational Biology
3. Phase‐Separated Droplets Can Direct the Kinetics of Chemical Reactions Including Polymerization, Self‐Replication and Oscillating Networks
   Iris B. A. Smokers, Brent S. Visser, Wojciech P. Lipiński, Karina K. Nakashima, Evan Spruijt · 2024 · ChemSystemsChem
4. Possible role of NF-κB in hormesis during ageing
   Salvatore Chirumbolo · 2012 · Biogerontology
5. Phosphorylation-mediated stabilization of Bora in mitosis coordinates Plx1/Plk1 and Cdk1 oscillations
   Oren Feine, Elvira Hukasova, Wytse Bruinsma, Raimundo Freire, Abraham Fainsod, Julian Gannon, Hiro M. Mahbubani, Arne Lindqvist, Michael Brandeis · 2014 · Cell Cycle
6. Designing synthetic networks in silico: a generalised evolutionary algorithm approach
   Robert W. Smith, Bob van Sluijs, Christian C. Fleck · 2017 · BMC Systems Biology
7. Control-theoretic methods for biological networks
   Franco Blanchini, Hana El Samad, Giulia Giordano, Eduardo D. Sontag · 2018 · IEEE Conference on Decision and Control (CDC)
8. The proneural wave in the Drosophila optic lobe is driven by an excitable reaction-diffusion mechanism
   David J. Jörg, Elizabeth E. Caygill, Anna E Hakes, Esteban G. Contreras, Andrea H. Brand, Benjamin D. Simons · 2019 · eLife
9. Single Cell Characterization of a Synthetic Bacterial Clock with a Hybrid Feedback Loop Containing dCas9-sgRNA
   John Henningsen, Matthaeus Schwarz‐Schilling, Andreas Leibl, Joaquı́n Gutiérrez, Sandra Sagredo, Friedrich Christian Simmel · 2020 · ACS Synthetic Biology
10. The Complexity of Cell-Biological Systems
    Olaf Wolkenhauer A, Allan Muir · 2011 · Elsevier eBooks
11. Architecture-Dependent Robustness and Bistability in a Class of Genetic Circuits
    Jiajun Zhang, Zhanjiang Yuan, Han‐Xiong Li, Tianshou Zhou · 2010 · Biophysical Journal
12. Amplitude Metrics for Cellular Circadian Bioluminescence Reporters
    Peter C. St. John, Stephanie R. Taylor, John H. Abel, Francis J. Doyle · 2014 · Biophysical Journal
13. A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference
    Jesper N. Tegner, Héctor Zenil, Narsis A. Kiani, Gordon Ball, David Gómez-Cabrero · 2016 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
14. Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle
    Ataur Katebi, Vivek Kohar, Mingyang Lu · 2020 · iScience
15. A modular approach for modeling the cell cycle based on functional response curves
    Jolan De Boeck, Jan Rombouts, Lendert Gelens · 2021 · PLoS Computational Biology
16. Coherence of oscillations in the weak-noise limit
    Benedikt Remlein, Volker Weissmann, Udo Seifert · 2022 · Physical review. E
17. Electrifying rhythms in plant cells
    Daniel Santa Cruz Damineli, Maria Teresa Portes, José Alberto Feijó · 2022 · Current Opinion in Cell Biology
18. Periodicity, mixed-mode oscillations, and multiple timescales in a phosphoinositide-Rho GTPase network
    Chee San Tong, X.J. Xǔ, Min Wu · 2023 · Cell Reports
19. Stochastic Oscillations Induced by Intrinsic Fluctuations in a Self-Repressing Gene
    Jingkui Wang, Marc Lefranc, Quentin Thommen · 2014 · Biophysical Journal
20. In vitro regulatory models for systems biology
    Anthony J. Genot, Teruo Fujii, Yannick Rondelez · 2013 · Biotechnology Advances
21. Dose-Response Aligned Circuits in Signaling Systems
    Long Yan, Qi Ouyang, Hongli Wang · 2012 · PLoS ONE
22. Quantifying Stochastic Noise in Cultured Circadian Reporter Cells
    Peter C. St. John, Francis J. Doyle · 2015 · PLoS Computational Biology
23. Serotyping, antibiotic susceptibility, and virulence genes screening of Escherichia coli isolates obtained from diarrheic buffalo calves in Egyptian farms
    Ashraf Samir Hakim, Shimaa T. Omara, Sohier M. Syame, Ehab A. Fouad · 2017 · Veterinary World
24. Thermodynamic costs of dynamic function in active soft matter
    Yong Dou, Kiran Dhatt-Gauthier, Kyle J. M. Bishop · 2018 · Current Opinion in Solid State and Materials Science
25. A new ultradian rhythm in mammalian cell dry mass observed by holography
    L. Ghenim, Cedric P. Allier, Patricia Obeïd, Lionel Hervé, Jean-Yves Fortin, Maxim Y. Balakirev, Xavier Gidrol · 2021 · Scientific Reports
26. Delay-induced anomalous fluctuations in intracellular regulation
    Andreas Grönlund, Per Lötstedt, Johan Elf · 2011 · Nature Communications
27. Costs and constraints from time-delayed feedback in small gene regulatory motifs
    Andreas Grönlund, Per Lötstedt, Johan Elf · 2010 · Proceedings of the National Academy of Sciences
28. Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators
    Sargis Karapetyan, Nicolas E. G. Buchler · 2015 · Physical Review E
29. Impact of time delays on oscillatory dynamics of interlinked positive and negative feedback loops
    Bo Yuan Huang, Xinyu Tian, Feng Liu, Wei Wang · 2016 · Physical review. E
30. Modeling the Dynamics of Cdc42 Oscillation in Fission Yeast
    Bin Xu, Alexandra Jilkine · 2018 · Biophysical Journal
31. Misaligned hormonal rhythmicity: Mechanisms of origin and their clinical significance
    Eder Zavala · 2022 · Journal of Neuroendocrinology
32. Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms
    Suchana Chakravarty, Christian I. Hong, Attila Csikász‐Nagy · 2023 · npj Systems Biology and Applications
33. NGN3 oscillatory expression controls the timing of human pancreatic endocrine differentiation
    Anzy Miller, Veronica Biga, Andrew Rowntree, Mariya Chhatriwala, Florence Woods, Benjamin Noble, Elli Marinopoulou, Anoushka Kamath, Ludovic Vallier, Nancy Papalopulu · 2025 · Developmental Cell
34. Control of MarRAB Operon in Escherichia coli via Autoactivation and Autorepression
    Mahendra Kumar Prajapat, Kirti Jain, Supreet Saini · 2015 · Biophysical Journal
35. Metabolic Regulation of the Ultradian Oscillator Hes1 by Reactive Oxygen Species
    Simona Ventre, Alessia Indrieri, Chiara Fracassi, Brunella Franco, Iván Conte, Luca Cardone, Diego di Bernardo · 2015 · Journal of Molecular Biology
36. Minimal Models for Cell-Cycle Control Based on Competitive Inhibition and Multisite Phosphorylations of Cdk Substrates
    Claude Gérard, John J. Tyson, Béla Novák · 2013 · Biophysical Journal
37. Role of Cdc42 dynamics in the control of fission yeast cell polarization
    Maitreyi E. Das, Fulvia Verde · 2013 · Biochemical Society Transactions
38. Realization of tristability in a multiplicatively coupled dual-loop genetic network
    Bo Yuan Huang, Yun Xia, Feng Liu, Wei Wang · 2016 · Scientific Reports
39. The 2-μm plasmid encoded protein Raf1 regulates both stability and copy number of the plasmid by blocking the formation of the Rep1–Rep2 repressor complex
    Syed Meraj Azhar Rizvi, Hemant Kumar Prajapati, Purba Nag, Santanu Ghosh · 2017 · Nucleic Acids Research
40. Effects of time delays on biological feedback systems and electromagnetic field exposures
    Frank Stephenson Barnes, Sahithi Kandala · 2018 · Bioelectromagnetics
41. Modulation of dynamic modes by interplay between positive and negative feedback loops in gene regulatory networks
    Liu-Suo Wang, Ning-Xi Li, Jingjia Chen, Xiao‐Peng Zhang, Feng Liu, Wei Wang · 2018 · Physical review. E
42. Homogeneous Time Constants Promote Oscillations in Negative Feedback Loops
    Franco Blanchini, Christian Cuba Samaniego, Elisa Franco, Giulia Giordano · 2018 · ACS Synthetic Biology
43. Computer simulations of the signalling network in FLT3 +-acute myeloid leukaemia – indications for an optimal dosage of inhibitors against FLT3 and CDK6
    Antoine Buetti‐Dinh, Ran Friedman · 2018 · BMC Bioinformatics
44. Neurodegeneration-associated FUS is a novel regulator of circadian gene expression
    Xin Jiang, Tao Zhang, Haifang Wang, Tao Wang, Meiling Qin, Puhua Bao, Ruiqi L. Wang, Yuwei Liu, Hung-Chun Chang, Jun Yan et al. · 2018 · Translational Neurodegeneration
45. On the importance of reaction networks for synthetic living systems
    Oliver R. Maguire, Wilhelm T. S. Huck · 2019 · Emerging Topics in Life Sciences
46. Robust oscillations in multi-cyclic Markov state models of biochemical clocks
    Clara del Junco, Suriyanarayanan Vaikuntanathan · 2020 · The Journal of Chemical Physics
47. Robust banded protoxylem pattern formation through microtubule-based directional ROP diffusion restriction
    Bas Jacobs, Jaap Molenaar, Eva E. Deinum · 2020 · Journal of Theoretical Biology
48. Models at the single cell level
    Raymond Cheong, Saurabh Paliwal, Andre Levchenko · 2009 · WIREs Systems Biology and Medicine
49. Inducing sustained oscillations in feedback-linearizable single-input nonlinear systems
    Carlos Fernando Aguilar-Ibañez, J.C. Martinez, José de Jesús Rubio, Miguel S. Suárez-Castañón · 2014 · ISA Transactions
50. Visualization of the spatial and temporal dynamics of MAPK signaling using fluorescence imaging techniques
    Taichiro Tomida · 2014 · The Journal of Physiological Sciences
51. Dynamical Scenarios for Chromosome Bi-orientation
    Tongli Zhang, Raquel A. Oliveira, Bernhard Schmierer, Béla Novák · 2013 · Biophysical Journal
52. Multistationarity in Biochemical Networks: Results, Analysis, and Examples
    Carsten Conradi, Casian Pantea · 2019 · Elsevier eBooks
53. An Inactivation Switch Enables Rhythms in a Neurospora Clock Model
    Abhishek Upadhyay, Michael Brunner, Hanspeter Herzel · 2019 · International Journal of Molecular Sciences
54. Minimal intervening control of biomolecular networks leading to a desired cellular state
    Sang‐Mok Choo, Sang‐Min Park, Kwang‐Hyun Cho · 2019 · Scientific Reports
55. Progress in integrative systems biology, physiology and medicine: towards a scale-relative biology
    Charles Auffray, Denis Noble, Laurent Nottale, Philip Turner · 2020 · The European Physical Journal A
56. A Simple Negative Interaction in the Positive Transcriptional Feedback of a Single Gene Is Sufficient to Produce Reliable Oscillations
    Jesús Miró-Bueno, Alfonso Rodríguez‐Patón · 2011 · PLoS ONE
57. Cycling expression and cooperative operator interaction in the trp operon of Escherichia coli
    Areli Hernández-Valdez, Moisés Santillán, Eduardo S. Zeron · 2009 · Journal of Theoretical Biology
58. Post-transcriptional regulatory feedback encodes JAK-STAT signal memory of interferon stimulation
    Eirini Kalliara, Małgorzata Kardyńska, James Bagnall, David G. Spiller, Werner Müller, Dominik Rückerl, Subhra Kumar Biswas, Jarosław Śmieja, Pawel Paszek · 2022 · Frontiers in Immunology
59. Change in RhoGAP and RhoGEF availability drives transitions in cortical patterning and excitability in Drosophila
    Jonathan A. Jackson, Marlis Denk-Lobnig, Katherine A. Kitzinger, Adam C. Martin · 2024 · Current Biology
60. Temperature-dependent fold-switching mechanism of the circadian clock protein KaiB
    Ning Zhang, Damini Sood, Spencer C. Guo, Nanhao Chen, Adam Antoszewski, Tegan L. Marianchuk, Supratim Dey, Yunxian Xiao, Lu Hong, Xiangda Peng et al. · 2024 · Proceedings of the National Academy of Sciences
61. A network-oriented perspective on cardiac calcium signaling
    Christopher H. George, Dimitris Parthimos, Nicole C. Silvester · 2012 · American Journal of Physiology-Cell Physiology
62. Delayed self-regulation and time-dependent chemical drive leads to novel states in epigenetic landscapes
    Mithun Kumar Mitra, Paul R. Taylor, Chris Hutchison, Tom C. B. McLeish, Buddhapriya Chakrabarti · 2014 · Journal of The Royal Society Interface
63. A method of ‘speed coefficients’ for biochemical model reduction applied to the NF- $$\upkappa $$ κ B system
    Simon West, Lloyd Bridge, Michael White, Pawel Paszek, Vadim Nadyrovich Biktashev · 2014 · Journal of Mathematical Biology
64. Chemical event chain model of coupled genetic oscillators
    David J. Jörg, Luis G. Morelli, Frank Jülicher · 2018 · Physical review. E
65. Roles of four feedback loops in mitochondrial permeability transition pore opening induced by Ca2+ and reactive oxygen species
    Hong Qi, Guoping Xu, Xiao-Long Peng, Xiang Li, Jianwei Shuai, Rui Xin Xu · 2020 · Physical review. E
66. Immobilization of Proteins of Cell Extract to Hydrogel Networks Enhances the Longevity of Cell-Free Protein Synthesis and Supports Gene Networks
    Xiaofei Ouyang, Xiaoyu Zhou, Sze Nga Lai, Qi Liu, Bo Zheng · 2021 · ACS Synthetic Biology
67. Theoretical Concept Study of Cooperative Abnormality Detection and Localization in Fluidic-Medium Molecular Communication
    Ladan Khaloopour, Mahtab Mirmohseni, Masoumeh Nasiri‐Kenari · 2021 · IEEE Sensors Journal
68. The Pollen Tube Oscillator: Integrating Biophysics and Biochemistry into Cellular Growth and Morphogenesis
    Maria Teresa Portes, Daniel Santa Cruz Damineli, Nuno Moreno, Renato Colaço, Sílvia Costa, José Alberto Feijó · 2015 · Springer eBooks
69. The role of APC/C inhibitor Emi2/XErp1 in oscillatory dynamics of early embryonic cell cycles
    Palakkad Krishnan Unni Vinod, Xin Zhou, Tongli Zhang, Thomas U. Mayer, Béla Novák · 2013 · Biophysical Chemistry
70. Allosteric regulation of pyruvate kinase from Mycobacterium tuberculosis by metabolites
    Jan Snášel, Iva Pichová · 2018 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
71. Practical steps to digital organism models, from laboratory model species to ‘Crops in silico
    Andrew John Millar, Uriel Urquiza‐García, Peter L. Freeman, Alastair C. Hume, Gordon D. Plotkin, Oxana Sorokina, Argyris Zardilis, T. Zieliński · 2018 · Journal of Experimental Botany
72. How to make an oscillator
    Bas J. H. M. Rosier, Tom F. A. de Greef · 2015 · eLife
73. Network switches and their role in circadian clocks
    Marta del Olmo, Stefan Legewie, Michael Brunner, Thomas Höfer, Achim Kramer, Nils Blüthgen, Hanspeter Herzel · 2024 · Journal of Biological Chemistry
74. Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes
    Rogier Braakman, Brandon M. Satinsky, Tyler J. O’Keefe, Krista Longnecker, Shane Hogle, Jamie W. Becker, Robert C. Li, Keven D. Dooley, Aldo A. Arellano, Melissa C. Kido Soule et al. · 2025 · Science Advances
75. In vivo, in vitro, and in silico studies suggest a conserved immune module that regulates malaria parasite transmission from mammals to mosquitoes
    Ian Price, Bard Ermentrout, Rubén Zamora, Bo Wang, Nabil Azhar, Qi Mi, Gregory M. Constantine, James R. Faeder, Shirley Luckhart, Yoram Vodovotz B · 2013 · Journal of Theoretical Biology
76. Circadian clock and oral cancer (Review)
    Minou Nirvani, Cuong Khuu, Tor Paaske Utheim, Lars Peter Sand, Amer Sehic · 2017 · Molecular and Clinical Oncology
77. A minimal “push–pull” bistability model explains oscillations between quiescent and proliferative cell states
    Sandeep Krishna, Sunil Laxman · 2018 · Molecular Biology of the Cell
78. Enhancement of chemical oscillations by self-generated convective flows
    Oleg E. Shklyaev, Victor V. Yashin, Samuel Isaac Stupp, Anna C. Balazs · 2020 · Communications Physics
79. Diffusive coupling of two well-mixed compartments elucidates elementary principles of protein-based pattern formation
    Fridtjof Brauns, Jacob Halatek, Erwin Frey · 2021 · Physical Review Research
80. Stochastic pH Oscillations in a Model of the Urea–Urease Reaction Confined to Lipid Vesicles
    Arthur V. Straube, Stefanie Winkelmann, Christof Schütte, Felix Höfling · 2021 · The Journal of Physical Chemistry Letters
81. Spatially coordinated collective phosphorylation filters spatiotemporal noises for precise circadian timekeeping
    Seok Joo Chae, Dae Wook Kim, Seunggyu Lee, Jae Kyoung Kim · 2023 · iScience
82. Design principles for robust oscillatory behavior
    Sebastian M. Castillo-Hair, Elizabeth Villota, Alberto M. Coronado · 2015 · Systems and Synthetic Biology
83. Escape process and stochastic resonance under noise intensity fluctuation
    Yoshihiko Hasegawa, Masanori Arita · 2011 · Physics Letters A
84. A study on stability and medical implications for a complex delay model for CML with cell competition and treatment
    Ileana Rodica Rădulescu, Doina Cândea, A. Halanay · 2014 · Journal of Theoretical Biology
85. Does the Potential for Chaos Constrain the Embryonic Cell-Cycle Oscillator?
    R. Scott McIsaac, Kerwyn Casey Huang, Anirvan M. Sengupta, Ned S. Wingreen · 2011 · PLoS Computational Biology
86. To grow is not enough: impact of noise on cell environmental response and fitness
    Nash D. Rochman, Fangwei Si, Sean X. Sun · 2016 · Integrative Biology
87. Pattern Formation in the Bromate–Sulfite–Ferrocyanide Reaction
    István Molnár, István Szalai · 2015 · The Journal of Physical Chemistry A
88. A PDE-DDE Model for Cell Polarization in Fission Yeast
    Bin Xu, Paul C. Bressloff · 2016 · SIAM Journal on Applied Mathematics
89. Entrainment of a Bacterial Synthetic Gene Oscillator through Proteolytic Queueing
    Nicholas C. Butzin, Philip Hochendoner, Curtis T. Ogle, William Mather · 2016 · ACS Synthetic Biology
90. Analysis of network motifs in cellular regulation: Structural similarities, input–output relations and signal integration
    Ronny Straube · 2017 · Biosystems
91. Phenotype-centric modeling for elucidation of biological design principles
    Miguel Á. Valderrama-Gómez, Rebecca E. Parales, Michael A. Savageau · 2018 · Journal of Theoretical Biology
92. Subharmonic oscillations in stochastic systems under periodic driving
    Lukas Oberreiter, Udo Seifert, Andre C. Barato · 2019 · Physical review. E
93. Controlling Nuclear NF-κB Dynamics by β-TrCP—Insights from a Computational Model
    Uwe Benary, Jana Wolf · 2019 · Biomedicines
94. Time and space in segmentation
    Erik Clark · 2021 · Interface Focus
95. Systems-level feedback in cell-cycle control
    Béla Novák, Palakkad Krishnan Unni Vinod, Paula Freire, Orsolya Kapuy · 2010 · Biochemical Society Transactions
96. Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation
    Andreea Munteanu, Marco Constante, Mark Isalan, Ricard V. Solé · 2010 · BMC Systems Biology
97. Prokaryotic Circadian Systems: Cyanobacteria and Beyond
    Mingxu Fang, Carrie L. Partch, Andy LiWang, Susan S. Golden · 2025 · Annual Review of Microbiology
98. Resonating neurons stabilize heterogeneous grid-cell networks
    Divyansh Mittal, Rishikesh Narayanan · 2021 · eLife
99. Common multi-day rhythms in smartphone behavior
    Enea Ceolini, Arko Ghosh · 2023 · npj Digital Medicine
100. Pathway bias and emergence of quasi-irreversibility in reversible reaction networks: Extension of Curtin-Hammett principle
     Satoshi Takahashi, Tsukasa Abe, Hirofumi Sato, Shûichi Hiraoka · 2023 · Chem