Design principles of biochemical oscillators

Cited by (1,000)

Items 901–1,000 of 1,000

1. Circuit design for static genetic memory
   Chun‐Liang Lin, Yu‐Jia Hu, Weixian Li · 2017 · The Journal of Engineering
2. Asymmetry between Activators and Deactivators in Functional Protein Networks
   Ammar Tareen, Ned S. Wingreen, Ranjan Mukhopadhyay · 2020 · Scientific Reports
3. A Traffic Network Congestion Diffusion Model Based on Gene Regulation Mechanism
   Xiangwei Wu, Ning Huang, Kan Xu · 2019 · Lecture notes in electrical engineering
4. Mathematical Models for Gene Regulatory Network Dynamics
   Jinzhi Lei · 2021 · Lecture notes on mathematical modelling in the life sciences
5. A thermodynamic description for physiological transmembrane transport
   Marco Arieli Herrera-Valdez · 2018 · F1000Research
6. Deciphering the impact of pulsatile input in the population-level synchrony of the Hes1 oscillators
   Amitava Giri, Sandip Kar · 2023 · Journal of Chemical Sciences
7. Comparison of Multi-Node Networks on Biological Properties
   Haipeng Lin, Jing Han · 2023 · Chinese Control Conference (CCC)
8. Optimization of synthetic oscillatory biological networks through Reinforcement Learning
   Leonardo Giannantoni, Alessandro Savino, Stefano Di Carlo · 2023 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
9. Biological Rhythms Generated by a Single Activator-Repressor Loop with Inhomogeneity and Diffusion
   Pablo Rojas, Oreste Piro, Martı́n E. Garcia · 2024 · Physical Review Letters
10. Ion current oscillation of polyelectrolyte modified micropipettes
    Tianyi Xiong, Wenjie Ma, Ping Yu · 2024 · Faraday Discussions
11. Functional control of network dynamical systems: An information theoretic approach
    Moirangthem Sailash Singh, Ramkrishna Pasumarthy, Umesh Vaidya, Steffen K. Leonhardt · 2024 · Information Sciences
12. Quantifying the environment's temperature effect on gene expression: Lyapunov exponent and multifractal dimension approach
    Fatemeh Nemati, Sohrab Behnia · 2025 · Chinese Journal of Physics
13. Dynamic localization of chemotaxis proteins in Bacillus subtilis
    Kang Wu · 2010 · Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)
14. RMOD: A Tool for Regulatory Motif Detection in Signaling Network
    Jin‐Ki Kim, Gwan‐Su Yi · 2013 · PLoS ONE
15. Analysis of Biological Smooth Oscillators Inspired by the Relay Control Tuning Method
    Yan Zhang, Jian Chen, Guang Li · 2014 · IFAC Proceedings Volumes
16. Systems approaches in molecular and cell biology: making sense out of data and providing meaning to models
    Olaf Wolkenhauer A, Angelyn R. Lao, Stig William Omholt, Harald A. Martens · 2009 · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE
17. Concurrent systems and time synchronization
    Mark Burgin, Annette Grathoff · 2018 · International Journal of General Systems
18. Attenuation of Pulse Disturbances in Biomolecular Oscillators
    Soumyadip Banerjee, Venkat Bokka, Shaunak Sen · 2018 · IFAC-PapersOnLine
19. Analysis of a Minimal Gene Regulatory Network for Cell Differentiation
    Irene Zorzan, Simone Del Favero, Barbara Di Camillo, Luca Schenato B · 2018 · IEEE Control Systems Letters
20. Genotype Components as Predictors of Phenotype in Model Gene Regulatory Networks
    SEYMOUR J. GARTE, A. Albert · 2019 · Acta Biotheoretica
21. Network medicine-travelling with the insulin receptor: Encounter of the second type
    Martial Boutchueng-Djidjou, Robert L. Faure · 2019 · EClinicalMedicine
22. Robustness of a biomolecular oscillator to pulse perturbations
    Soumyadip Banerjee, Shaunak Sen · 2020 · IET Systems Biology
23. Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation
    Jiayin Hong, Julius Palme, Bo Hua, Michael Springer · 2021 · PLoS Computational Biology
24. Application of synthetic biology in living functional materials
    Xi Zhang, Pengcheng Li, Jiandong Huang, Zhuojun Dai · 2020 · Chinese Science Bulletin (Chinese Version)
25. Computational modeling of chromosome re-replication in mutant strains of fission yeast
    Béla Novák, John J. Tyson · 2021 · Molecular Biology of the Cell
26. Insights from Mathematical Modeling/Simulations of the In Vitro KaiABC Clock
    Mark O. Byrne · 2021 · Springer eBooks
27. Robust in-phase synchronization in repressor-based coupled gene oscillators
    A B M Shamim Ul Hasan, Supravat Dey, Hiroyuki Kurata, Abhyudai Singh · 2021 · IFAC-PapersOnLine
28. Towards organism-level systems biology by next-generation genetics and whole-organ cell profiling
    Yoichi Minami, Yufei Yuan, Hiroki R. Ueda · 2021 · Biophysical Reviews
29. Dynamical behaviors of quorum sensing network mediated by combinatorial perturbation
    Menghan Chen, Haihong Liu, Ruiqi Wang · 2022 · Mathematical Biosciences & Engineering
30. Dynamical analysis of a delayed p53 oscillator model with p53-Mdm2 positive feedback
    Hongli Yang, Ruimin Huo, Nan Liu, Liangui Yang · 2022 · Results in Physics
31. A General Procedure for Accurate Parameter Estimation in Dynamic Systems Using New Estimation Errors
    Masahiko Nakatsui, Alexandre Sedoglavic, François Lemaire, François Boulier, Aslı Ürgüplü, Katsuihisa Horimoto · 2012 · Lecture notes in computer science
32. Theoretical and Experimental Investigation of Switch-Like Responses Arising from Multisite Protein Phosphorylation.
    Varedi Kolaei, Seyedeh Marjan Varedi Kolaei · 2011
33. Minimum protein oscillator based on multisite phosphorylation/dephosphorylation
    S. Marjan Varedi K., PETER J. WOOLF, Xiaoxia Nina Lin · 2011 · IET Systems Biology
34. Parameter estimation and bifurcation analysis of stochastic models of gene regulatory networks: tensor-structured methods
    Shuohao Liao, Tomáš Vejchodský, Radek Erban A · 2014 · arXiv (Cornell University)
35. Stochastic oscillations induced by intrinsic fluctuations in a self-repressing gene: a deterministic approach
    Jingkui Wang, Marc Lefranc, Quentin Thommen · 2012 · arXiv (Cornell University)
36. A Negative Feedback Regulates The Flow Of Signal Through Akt/mTORC1/S6K1 Pathway
    Poulami Dutta, Vimalathithan Devaraj, Biplab Bose · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
37. Feedback Models in Biological Physics
    Alexander Golden · 2018 · Deep Blue (University of Michigan)
38. Moment Closure Stability Analysis of Stochastic Reaction Networks with Oscillatory Dynamics
    Pedro Henrique Constantino, Yiannis N. Kaznessis · 2019 · arXiv (Cornell University)
39. A New Ultradian Rhythm Linked to Protein Degradation and Synthesis in Mammalian Cells
    L. Ghenim, Cedric P. Allier, Patricia Obeïd, Lionel Hervé, Jean-Yves Fortin, Maxim Y. Balakirev, Xavier Gidrol · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
40. Theory of genetic oscillations with external noisy regulation
    José Negrete, Iván M. Lengyel, Laurel A. Rohde, Ravi A. Desai, Andrew C. Oates, Frank Jülicher · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
41. Mathematical Analysis of Robustness of Oscillations in Models of the Mammalian Circadian Clock
    Benjamin Heidebrecht, Jing Chen, John J. Tyson · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
42. Modelling temperature dependence in the Arabidopsis thaliana circadian clock
    Avello Fernández, Paula Andrea · 2019 · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)
43. From Clocks to Synchrony: The Design of Bioinspired Self‐Regulation in Chemical Systems
    Annette Fiona Taylor · 2021 · Wiley eBooks
44. Noise facilitates entrainment of a population of uncoupled limit cycle oscillators
    Vojtěch Kumpošt, Lennart Hilbert, Ralf Mikut · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
45. Correction: The Yin and Yang of Yeast Transcription: Elements of a Global Feedback System between Metabolism and Chromatin
    Rainer Machné, Douglas B. Murray · 2012 · PLoS ONE
46. Minimal Catalytic Assemblies Can Oscillate Utilizing Feedback Loops
    Antara Reja, Sumit Kumar Pal, Subhajit Bal, Dibyendu Das · 2022 · Research Square
47. Functional consequences of clock components interacting with decoy sites in a genetic oscillator
    Zhanhao Zhang, Supravat Dey, Abhyudai Singh · 2022
48. Extended Curtin-Hammett principle: Origin of pathway selection in reversible reaction networks under kinetic control
    Satoshi Takahashi, Hirofumi Sato, Shûichi Hiraoka · 2023 · ChemRxiv
49. Identification of genes with oscillatory expression in glioblastoma – The paradigm of SOX2
    Richard Zhiming Fu, Oliver Cottrell, Luisa Cutillo, Andrew Rowntree, Zsolt E. Zador, Heiko Wurdak, Nancy Papalopulu, Elli Marinopoulou · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
50. 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, Archana G. Chavan, Supratim Dey, Yunxian Xiao, Lu Hong et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
51. Multiple Notch ligands in the synchronization of the segmentation clock
    Marcos Wappner, Koichiro Uriu, Andrew C. Oates, Luis G. Morelli · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
52. Design of a biomolecular adaptive controller to restore sustained periodic behavior
    Frank Britto Bisso, Subham Dey, Guy-Bart V. Stan, Christian Cuba Samaniego · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
53. Corrections in single-cell migration path in vivo are controlled by pulses in polar Rac1 activation
    Dennis Hoffmann, Tal Agranov, Lucas Kühl, Laura Ermlich, Michal Reichman‐Fried, Benjamin D. Simons, Nir S. Gov, Erez Raz · 2025 · Current Biology
54. Tissue-wide Erk oscillations set the pace of zebrafish notochord segmentation
    Priyom Adhyapok, James Norman, Michel Bagnat, Stefano Di Talia · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
55. Non-muscle Myosin II acts as a negative feedback mediator to control cell contraction dynamics
    Carolin Gierse, Jennifer Hanemann, Leif Dehmelt · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
56. An Efficient Adjoint-Free Melnikov–Lyapunov Diagnostic for Transition Detection in Slow–Fast Chemical Reaction Networks
    Sri Venkata Durga Sudarsan Madhyannapu, Pradheep Kumar S. · 2026 · SSRN Electronic Journal
57. Estudo espectroscópico in situ e espectrométrico on line da eletro-oxidação oscilatória de álcoois simples sobre platina
    Emerson Paulinho Boscheto · 2013
58. Mathematical modelling of the core regulatory feedback mechanisms of p53 protein that decide cell fate
    Ket Hing Chong · 2014 · Lincoln University Research Archive (Lincoln University)
59. The cyanobacterial circadian clock
    Brettschneider, Christian · 2011 · edoc Publication server (Humboldt University of Berlin)
60. Negative Feedback and Competition in the Yeast Polarity Establishment Circuit
    Chi‐Fang Wu · 2013 · DukeSpace (Duke University)
61. Network architectural conditions for prominent and robust stochastic oscillations
    Jaewook Joo, Jinmyung Choi · 2011 · arXiv (Cornell University)
62. Identification of network motifs capable of frequency-tunable and robust oscillation
    Matthew Bailey, Jaewook Joo · 2011 · arXiv (Cornell University)
63. A theoretical investigation of protein recruitment during the DNA damage response and of the dynamics of DNA replication
    Daniel Löb · 2013 · Technischen Universität Darmstadt
64. Computational methods to predict and enhance decision-making with biomedical data.
    Behnaz Abdollahi · 2015
65. Physical Models of Cell Polarity
    Tyler Drake · 2013
66. Metabolische Oszillationen in Hefe
    Willi Gottstein · 2015 · edoc Publication server (Humboldt University of Berlin)
67. Are Quasi-Steady-State Approximated Models Suitable for Quantifying Intrinsic Noise Accurately?
    Dola Sengupta, Sandip Kar · 2015 · PLoS ONE
68. Theoretical effects of monotonically changing and fluctuating temperature on oscillating biological systems
    Micha Peleg, Maria Grazia Corradini · 2010 · Ecological Complexity
69. Delay-managed tradeoff in the molecular dynamics of the segmentation clock
    Henglin Song, Zhanjiang Yuan, Tianshou Zhou · 2013 · Molecular BioSystems
70. Functional tunability of biological circuits from tinkers
    Changhong Shi, Tianshou Zhou · 2012 · IEEE International Conference on Systems Biology
71. Controlling neural clustering using delayed inputs*
    Gábor Orosz, Jeff Moehlis · 2009 · IFAC Proceedings Volumes
72. Stochastic simulation methods for biochemical systems with multi-state and multi-scale features
    Yang Cao, Zhen Liu · 2012 · VTechWorks (Virginia Tech)
73. Dynamic effects of extrinsic noise in a simple oscillatory gene network with delayed negative-feedback regulation: an electronic modeling approach
    Moisés Santillán · 2015 · bioRxiv (Cold Spring Harbor Laboratory)
74. SURVEY AND SUMMARY A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence
    Deepak Balasubramanian, Lisa M. Schneper, Hansi Kumari, Kalai Mathee · 2012
75. Heart rate variability and rhythmic influences in human endotoxemia
    Jeremy D. Scheff · 2013
76. Metabolische Oszillationen in Hefe
    Lebenswissenschaftlichen Fakultät · 2014
77. strategies, perspectives and challenges Reverse engineering and identification in systems biology:
    Alejandro F. Villaverde, Julio R. Banga · 2014
78. Design principles of noise-induced oscillation in biochemical reaction networks: II. coupled positive and negative feedback loops
    Jaewook Joo, Chauhan, Sanjeev · 2014 · arXiv (Cornell University)
79. Computational Properties of Cell Regulatory Pathways Through Petri Nets
    Paolo Dini · 2016 · Emergence, complexity and computation
80. Stability and Neimark-Sacker bifurcation analysis for a discrete genetic network
    Feng Liu, Xiang Gen Yin, Longsheng Wei, Fenglan Sun, Hua O. Wang · 2016 · Chinese Control Conference (CCC)
81. Optimal Design of Robust Synthetic Biological Oscillators
    Chia Hua Chuang Chun Liang Lin · 2015 · Current Synthetic and Systems Biology
82. Spatiotemporal Dynamics of Gradient Sensing and Polarization in Yeast
    Meng Jin · 2019 · Carolina Digital Repository (University of North Carolina at Chapel Hill)
83. Computational Tools for Chemical Toxicity Testing and Risk Assessment Under the Framework of Adverse Outcome Pathways
    Moiz M. Mumtaz, P. Ruiz, Q. Zhang · 2017 · Royal Society of Chemistry eBooks
84. Mathematical models of cell polarization
    Xu, Bin · 2018 · J. Willard Marriott Library
85. The Role of Genotype in the Predictability of Dynamical Behavior in Complex Model Gene Regulatory Networks
    SEYMOUR J. GARTE, Albert A · 2017 · Journal of Theoretical and Computational Science
86. On the Relation between Chemical Oscillations and Self-Replication
    Erwan Bigan, Pierre Plateau · 2017 · Artificial Life
87. Controlling insulin resistance through modulation of interplay between mediators of cellular senescence: A mathematical study
    Chakit Arora · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
88. QUALITATIVE ANALYSIS OF DELAYED-CONCENTRATION IN OREGONATOR-BASED CHEMICAL OSCILLATORS
    Hakkı Ulaş Ünal · 2018 · Anadolu University Journal of Science and Technology-A Applied Sciences and Engineering
89. Topological Structure and Biological Function of Gene Network Regulated by MicroRNA
    Zengrong Liu, Jianwei Shen, Shuiming Cai, Fang Yan · 2018 · Springer eBooks
90. Computational Models of Cell Cycle Transitions
    Rosa D. Hernansaiz-Ballesteros, Kirsten Jenkins, Attila Csikász‐Nagy · 2018 · Methods in molecular biology
91. Entrainment memories: What does stable mean?
    Manfred Gödel · 2018 · PsyCh Journal
92. Systems studies on spatiotemporal dynamics of kinase signaling
    Ambhighainath Ganesan · 2014
93. Investigating Nonlinear Enzyme Kinetics as an Internal Control System for Nanoreactor Drug Release
    Stephen J. Jones · 2018 · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)
94. Dynamics of Scaffold Protein Tethered Signal Transduction
    Eric C. Greenwald · 2015
95. Robust and flexible response of Ostreococcus tauri circadian clock to light/dark cycles of varying photoperiod
    Quentin Thommen, Benjamin Pfeuty, Florence Corellou, François‐Yves Bouget, Marc Lefranc · 2011 · arXiv (Cornell University)
96. Quantifying the Dynamics of Coupled Networks of Switches and Oscillators
    Matthew R. Francis, Elana Judith Fertig · 2012 · Lecture notes in computer science
97. Reaction Networks, Oscillatory Motifs and Parameter Estimation in Biochemical Systems
    Igor Schreiber, František Muzika, Jan Červený · 2019 · Lecture notes in computer science
98. Localized Spatial Emergent Behaviour in Bacterial Cells via Band-Detect Network Motif
    Irene Zorzan · 2019 · European Control Conference (ECC)
99. МЕРЕЖЕВА ОСНОВА ФУНКЦІОНУВАННЯ БІОЛОГІЧНИХ ОСЦИЛЯТОРІВ — ТРИГЕРІВ КОЛИВАЛЬНИХ ЛАНЦЮГІВ У КЛІТИНАХ І БЕЗКЛІТИННИХ СИСТЕМАХ. АНАЛІТИЧНИЙ ОГЛЯД
    Ozar P. Mintser, В. М. Заліський, Larysa Yu. Babintseva · 2019 · Medical Informatics and Engineering
100. It’s about time: Analysing an alternative approach for reductionist modelling of linear pathways in systems biology
     Niklas Korsbo, Henrik Jönsson · 2019 · bioRxiv (Cold Spring Harbor Laboratory)