Design principles of biochemical oscillators

Cited by (1,001)

Items 201–300 of 1,001

1. Synchronization in Dynamical Networks of Locally Coupled Self-Propelled Oscillators
   Demian Levis, Ignacio Pagonabarraga, Albert Dı́az-Guilera · 2017 · Physical Review X
2. Mammalian synthetic biology for studying the cell
   Melina Mathur, Joy S. Xiang, Christina D. Smolke · 2016 · The Journal of Cell Biology
3. Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis
   Eliza J. R. Peterson, Abrar A Abidi, Mario L. Arrieta‐Ortiz, Boris H. Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, Nitin S. Baliga · 2020 · Cell Reports
4. A non-linear system patterns Rab5 GTPase on the membrane
   A Cezanne, Janelle L. Lauer, A Solomatina, Ivo F. Sbalzarini, Marino Zerial · 2020 · eLife
5. Topological Phase Transition in Coupled Rock-Paper-Scissors Cycles
   Johannes Knebel, Philipp M. Geiger, Erwin Frey · 2020 · Physical Review Letters
6. Bigger, Better, Faster
   Eric C. Greenwald, Jeffrey J. Saucerman · 2011 · Journal of Cardiovascular Pharmacology
7. The 2 micron plasmid: a selfish genetic element with an optimized survival strategy within Saccharomyces cerevisiae
   Syed Meraj Azhar Rizvi, Hemant Kumar Prajapati, Santanu Ghosh · 2017 · Current Genetics
8. The future of radiation-induced abscopal response: beyond conventional radiotherapy approaches
   Slavisa Tubin, Weisi Yan, Waleed Fouad Mourad, Piero Fossati, Mohammad Khurram Khan · 2020 · Future Oncology
9. Wake-sleep cycles are severely disrupted by diseases affecting cytoplasmic homeostasis
   Stephen Beesley, Dae Wook Kim, Matthew R. D'Alessandro, Yuanhu Jin, Kwangjun Lee, Hyunjeong Joo, Yang Young, Robert J. Tomko, John Faulkner, Joshua J. Gamsby et al. · 2020 · Proceedings of the National Academy of Sciences
10. Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle
    Zhen Liu, Pu Yang, Fei Li, Clifford A. Shaffer, Stefan Hoops, John J. Tyson, Yang Cao · 2012 · The Journal of Chemical Physics
11. Oscillation dynamics underlie functional switching of NF-κB for B-cell activation
    Kentaro Inoue, Hisaaki Shinohara, Marcelo Behar, Noriko Yumoto, Gouhei Tanaka, Alexander Hoffmann, Kazuyuki Aihara, Mariko Okada · 2016 · npj Systems Biology and Applications
12. Oscillatory Behaviors in Genetic Regulatory Networks Mediated by MicroRNA With Time Delays and Reaction-Diffusion Terms
    Yuan Zhang, Haihong Liu, Fang Yan, Jin Zhou · 2017 · IEEE Transactions on NanoBioscience
13. Design of Tunable Oscillatory Dynamics in a Synthetic NF-κB Signaling Circuit
    Zhibo Zhang, Qiuyue Wang, Yuxi Ke, Shiyu Liu, Jianqi Ju, Wendell A. Lim, Chao Tang, Ping Wei · 2017 · Cell Systems
14. Photochemical Control over Oscillations in Chemical Reaction Networks
    Aleksandr A. Pogodaev, Albert S. Y. Wong, Wilhelm T. S. Huck · 2017 · Journal of the American Chemical Society
15. Pairing of segmentation clock genes drives robust pattern formation
    Oriana Q. H. Zinani, Kemal Keseroǧlu, Ahmet Ali Ay, Ertuğrul M. Özbudak · 2020 · Nature
16. Phase Resetting in an Asymptotically Phaseless System: On the Phase Response of Limit Cycles Verging on a Heteroclinic Orbit
    Kendrick Matthew Shaw, Youngmin Park, Hillel J. Chiel, Peter J. Thomas · 2012 · SIAM Journal on Applied Dynamical Systems
17. Positive‐feedback loops in cell cycle progression
    Joseph R. Pomerening · 2009 · FEBS Letters
18. Transcriptional Bursting Diversifies the Behaviour of a Toggle Switch: Hybrid Simulation of Stochastic Gene Expression
    Pavol Bokes, John R. King, Andrew T. A. Wood, Matthew Loose · 2013 · Bulletin of Mathematical Biology
19. Autonomous Chemical Oscillator Circuit Based on Bidirectional Chemical‐Microfluidic Coupling
    Georgi Paschew, Jörg Schreiter, Andreas Voigt, Cesare Pini, Joseph Páez Chávez, Merle Allerdißen, Uwe Marschner, Stefan Siegmund, René Schüffny, Frank Jülicher et al. · 2016 · Advanced Materials Technologies
20. Circadian processes in the RNA life cycle
    Manon Torres, Denis Becquet, Jean‐Louis Franc, Anne‐Marie François‐Bellan · 2018 · Wiley Interdisciplinary Reviews - RNA
21. Evolving Robust Gene Regulatory Networks
    Nasimul Noman, Taku Monjo, Pablo Moscato, Hitoshi Iba · 2015 · PLoS ONE
22. Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures
    Ildefonso M. De la Fuente · 2010 · International Journal of Molecular Sciences
23. Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks
    Shuohao Liao, Tomáš Vejchodský, Radek Erban A · 2015 · Journal of The Royal Society Interface
24. Genetic oscillators in development
    Koichiro Uriu · 2016 · Development Growth & Differentiation
25. Dynamic properties of noise and Her6 levels are optimized by miR‐9, allowing the decoding of the Her6 oscillator
    Ximena Soto, Veronica Biga, Jochen Kursawe, Robert Lea, Parnian Doostdar, Riba Thomas, Nancy Papalopulu · 2020 · The EMBO Journal
26. Bifurcation threshold of the delayed van der Pol oscillator under stochastic modulation
    Mathieu Gaudreault, François Drolet, Jorge Viñals · 2012 · Physical Review E
27. Design Principles of Phosphorylation-Dependent Timekeeping in Eukaryotic Circadian Clocks
    Koji L. Ode, Hiroki R. Ueda · 2017 · Cold Spring Harbor Perspectives in Biology
28. Voltage-sustained self-oscillation of a nano-mechanical electron shuttle
    D. R. Koenig, Eva Maria Weig · 2012 · Applied Physics Letters
29. Reliability of Transcriptional Cycles and the Yeast Cell-Cycle Oscillator
    Volkan Sevi̇m, Xinwei Gong, Joshua E. S. Socolar · 2010 · PLoS Computational Biology
30. The topology design principles that determine the spatiotemporal dynamics of G-protein cascades
    Mikhail A. Tsyganov, Walter Kölch, Boris Ν. Kholodenko · 2012 · Molecular BioSystems
31. Systems and synthetic biology approaches in understanding biological oscillators
    Zhengda Li, Qiong Yang · 2017 · Quantitative Biology
32. Coupling of growth rate and developmental tempo reduces body size heterogeneity in C. elegans
    Klement Stojanovski, Helge Großhans, Benjamin D. Towbin · 2022 · Nature Communications
33. Tuning Genetic Clocks Employing DNA Binding Sites
    Shridhar Jayanthi, Domitilla Del Vecchio · 2012 · PLoS ONE
34. Signal processing in cellular clocks
    Daniel B. Forger · 2011 · Proceedings of the National Academy of Sciences
35. Noise induced oscillations and coherence resonance in a generic model of the nonisothermal chemical oscillator
    David S. A. Simakov, Juan Pérez‐Mercader · 2013 · Scientific Reports
36. Modelling Physiological and Pharmacological Control on Cell Proliferation to Optimise Cancer Treatments
    Jean Clairambault · 2009 · Mathematical Modelling of Natural Phenomena
37. Inhibition of Ras activity coordinates cell fusion with cell–cell contact during yeast mating
    Laura Merlini, Bita Khalili, Omaya Dudin, Laetitia Michon, Vincent Vincenzetti, Sophie G. Martin · 2018 · The Journal of Cell Biology
38. Systems Biology Approaches and Precision Oral Health: A Circadian Clock Perspective
    Henry A. Adeola, Silvana M. Papagerakis, Pétros Papagerakis · 2019 · Frontiers in Physiology
39. Shape changes and budding of giant vesicles induced by an internal chemical trigger: an interplay between osmosis and pH change
    Gábor Holló, Ylenia Miele, Federico Rossi, István Lagzi · 2021 · Physical Chemistry Chemical Physics
40. Substrate induced generation of transient self-assembled catalytic systems
    Syed Pavel Afrose, Chandranath Ghosh, Dibyendu Das · 2021 · Chemical Science
41. Sigma Factor-Mediated Tuning of Bacterial Cell-Free Synthetic Genetic Oscillators
    Maaruthy Yelleswarapu, Ardjan J. van der Linden, Bob van Sluijs, Pascal A. Pieters, Emilien Dubuc, Tom F. A. de Greef, Wilhelm T. S. Huck · 2018 · ACS Synthetic Biology
42. A Multiphysics Model of In Vitro Transcription Coupling Enzymatic Reaction and Precipitation Formation
    Satoru Akama, Masayuki Yamamura, T. Kigawa · 2012 · Biophysical Journal
43. Self-regulated intelligent systems: where adaptive entities meet chemical oscillators
    Hongwei Zhou, Xiaobin Ding, Zhaohui Zheng, Yuxing Peng · 2013 · Soft Matter
44. Processing Oscillatory Signals by Incoherent Feedforward Loops
    Carolyn Zhang, Ryan Tsoi, Feilun Wu, Lingchong You · 2016 · PLoS Computational Biology
45. Engineering a Functional Small RNA Negative Autoregulation Network with Model-Guided Design
    Chelsea Y. Hu, Melissa K. Takahashi, Yan Zhang, Julius B. Lucks · 2018 · ACS Synthetic Biology
46. Role of radical pairs and feedback in weak radio frequency field effects on biological systems
    Frank Stephenson Barnes, Ben Greenebaum · 2018 · Environmental Research
47. A Systems Biology Roadmap to Decode mTOR Control System in Cancer
    Mohammadreza Dorvash, Mohammad Farahmandnia, Iman Tavassoly · 2019 · Interdisciplinary Sciences Computational Life Sciences
48. On the use of catalysis to bias reaction pathways in out-of-equilibrium systems
    Michelle P. van der Helm, Tuanke de Beun, Rienk Eelkema · 2021 · Chemical Science
49. Classifying the Topology of AHL-Driven Quorum Sensing Circuits in Proteobacterial Genomes
    Zsolt Gelencsér, Kumari Sonal Choudhary, Bruna Gonçalves Coutinho, Sanjarbek Hudaiberdiev, Borisz Galbáts, Vittorio Venturi, Sándor Pongor · 2012 · Sensors
50. Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways
    Eiryo Kawakami, Vivek K Singh, Kazuko Matsubara, Takashi Ishii, Yukiko Matsuoka, Takeshi Hase, Priya Kulkarni, Kenaz Siddiqui, Janhavi Kodilkar, Nitisha Danve et al. · 2016 · npj Systems Biology and Applications
51. Noise Reduction in Complex Biological Switches
    Luca Cardelli, Attila Csikász‐Nagy, Neil Dalchau, Mirco Tribastone, Max Tschaikowski · 2016 · Scientific Reports
52. The plant hormone auxin beats the time for oscillating light-regulated lateral root induction
    Stefan Kircher, Peter Schöpfer · 2018 · Development
53. Phase transition in thermodynamically consistent biochemical oscillators
    Nguyen, B., Seifert, U., Barato, A. · 2018 · Max Planck Digital Library
54. Universal minimal cost of coherent biochemical oscillations
    Lukas Oberreiter, Udo Seifert, Andre C. Barato · 2022 · Physical review. E
55. Centrioles generate a local pulse of Polo/PLK1 activity to initiate mitotic centrosome assembly
    Siu‐Shing Wong, Zachary M. Wilmott, Saroj Saurya, Ines Alvarez‐Rodrigo, Felix Zhou, Kwai‐Yin Chau, Alain Goriely, Jordan W. Raff · 2022 · The EMBO Journal
56. Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools
    Maalavika Pillai, Emilia Hojel, Mohit Kumar Jolly, Yogesh Goyal · 2023 · Nature Computational Science
57. Harmonic Oscillations in Homeostatic Controllers: Dynamics of the p53 Regulatory System
    Ingunn W. Jolma, Xiao Yu Ni, Ludger Rensing, Peter Ruoff · 2010 · Biophysical Journal
58. An Asymptotic Analysis of a 2-D Model of Dynamically Active Compartments Coupled by Bulk Diffusion
    Jia Gou, Michael J. Ward · 2016 · Journal of Nonlinear Science
59. Memory functions reveal structural properties of gene regulatory networks
    Edgar Herrera-Delgado, R. Pérez-Carrasco, J. Briscoe, Peter Sollich · 2017 · PLoS Comput. Biol.
60. A whole-body model for glycogen regulation reveals a critical role for substrate cycling in maintaining blood glucose homeostasis.
    Xu, Ke, Morgan, Kevin T., Todd Gehris, Abby, Elston, Timothy C., Gomez, Shawn M. · 2011 · PLoS Computational Biology
61. Oscillatory serotonin function in depression
    Ronald M. Salomon, Ronald L. Cowan · 2013 · Synapse
62. Temporally resolved direct delivery of second messengers into cells using nanostraws
    Alexander M. Xu, Sally A. Kim, Derek S. Wang, Amin Aalipour, Nicholas A. Melosh · 2016 · Lab on a Chip
63. The molecular basis of metabolic cycles and their relationship to circadian rhythms
    Jane Mellor · 2016 · Nature Structural & Molecular Biology
64. Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise
    Mariana Gómez-Schiavon, Nicolas E. G. Buchler · 2019 · PLoS Computational Biology
65. Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization
    Alexander I. Novichkov, Anton I. Hanopolskyi, Xiaoming Miao, Linda J. W. Shimon, Yael Diskin‐Posner, Sergey N. Semenov · 2021 · Nature Communications
66. Intermittent ERK oscillations downstream of FGF in mouse embryonic stem cells
    Dhruv Raina, Fiorella Fabris, Luis G. Morelli, Christian J. Schröter · 2022 · Development
67. Rhythmicity and waves in the cortex of single cells
    Yang Yang, Min Wu · 2018 · Philosophical Transactions of the Royal Society B Biological Sciences
68. Geometric Control of Frequency Modulation of cAMP Oscillations due to Calcium in Dendritic Spines
    Donya Ohadi, Padmini Rangamani · 2019 · Biophysical Journal
69. Cytokinesis through biochemical–mechanical feedback loops
    Alexandra Surcel, Yee-Seir Kee, Tianzhi Luo, Douglas N. Robinson · 2010 · Seminars in Cell and Developmental Biology
70. Information flow in the presence of cell mixing and signaling delays during embryonic development
    Gabriela Petrungaro, Luis G. Morelli, Koichiro Uriu · 2018 · Seminars in Cell and Developmental Biology
71. A Robust Model for Circadian Redox Oscillations
    Marta del Olmo, Achim Kramer, Hanspeter Herzel · 2019 · International Journal of Molecular Sciences
72. Fabrication of a biomimetic hydrogel actuator with rhythmic deformation driven by a pH oscillator
    Caixia Yang, Fang Su, Yan Liang, Wenyuan Xu, Shan Li, Enxiang Liang, Guoxiang Wang, Ningbo Zhou, Qiong Wan, Xianguo Ma · 2020 · Soft Matter
73. Circadian clock effects on cellular proliferation: Insights from theory and experiments
    Shaon Chakrabarti, Franziska Michor · 2020 · Current Opinion in Cell Biology
74. Nonmodular oscillator and switch based on RNA decay drive regeneration of multimodal gene expression
    Benjamin Nordick, Polly Y. Yu, Guangyuan Liao, Tian Hong · 2022 · Nucleic Acids Research
75. Timing control in regulatory networks by multisite protein modifications
    Carlos Salazar, Anneke Brümmer, Lilia Alberghina, Thomas Höfer · 2010 · Trends in Cell Biology
76. Mechanisms generating bistability and oscillations in microRNA-mediated motifs
    Peipei Zhou, Shuiming Cai, Zengrong Liu, Ruiqi Wang · 2012 · Physical Review E
77. A Systems Engineering Perspective on Homeostasis and Disease
    Yoram Vodovotz B, Gary C. An, Ioannis P. Androulakis · 2013 · Frontiers in Bioengineering and Biotechnology
78. The physics of bacterial decision making
    Eshel Ben‐Jacob, Mingyang Lu, Daniel Schultz, José N. Onuchic · 2014 · Frontiers in Cellular and Infection Microbiology
79. Inositol 1,4,5-trisphosphate receptors and pacemaker rhythms
    Yue‐Kun Ju, Elizabeth A. Woodcock, David G. Allen, Mark B. Cannell · 2012 · Journal of Molecular and Cellular Cardiology
80. Influence of Molecular Structure on the Properties of Out-of-Equilibrium Oscillating Enzymatic Reaction Networks
    Albert S. Y. Wong, Sjoerd G. J. Postma, Ilia N. Vialshin, Sergey N. Semenov, Wilhelm T. S. Huck · 2015 · Journal of the American Chemical Society
81. A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpoint
    Dávid Deritei, Jordan C. Rozum, Erzsébet Ravasz Regan, Réka Albert · 2019 · Scientific Reports
82. Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback
    Thomas George Minchington, Sam Griffiths‐Jones, Nancy Papalopulu · 2020 · Scientific Reports
83. Time-keeping and decision-making in the cell cycle
    John J. Tyson, Béla Novák · 2022 · Interface Focus
84. Universal structures for adaptation in biochemical reaction networks
    Robyn P. Araujo, Lance A. Liotta · 2023 · Nature Communications
85. Approaching the molecular origins of collective dynamics in oscillating cell populations
    Pankaj Mehta, Thomas Gregor · 2010 · Current Opinion in Genetics & Development
86. An Effective Method for Evolving Reaction Networks in Synthetic Biochemical Systems
    Huy Q. Dinh, Nathanaël Aubert-Kato, Nasimul Noman, Teruo Fujii, Yannick Rondelez, Hitoshi Iba · 2015 · IEEE Transactions on Evolutionary Computation
87. Modeling Gene Expression in Time and Space
    Pau Rué, Jordi García‐Ojalvo · 2013 · Annual Review of Biophysics
88. From biological data to oscillator models using SINDy
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89. Materials Inspired by Living Functions
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90. Inheritance of oscillation in chemical reaction networks
    Murad Banaji · 2018 · Applied Mathematics and Computation
91. Force generation by a propagating wave of supramolecular nanofibers
    Ryou Kubota, Masahiro Makuta, Ryo Suzuki, Masatoshi Ichikawa, Motomu Tanaka, Itaru Hamachi · 2020 · Nature Communications
92. Build to understand: synthetic approaches to biology
    Le-Zhi Wang, Fuqing Wu, Kevin Flores, Ying‐Cheng Lai, Xiao Wang · 2015 · Integrative Biology
93. Stochastic thermodynamics of self-oscillations: the electron shuttle
    Christopher W. Wächtler, Philipp Strasberg, Sabine H. L. Klapp, Gernot Schaller, Christopher Jarzynski · 2019 · New Journal of Physics
94. The plasticity of TGF-βsignaling
    Géraldine Cellière, Georgios Fengos, Marianne Hervé, Dagmar Iber · 2011 · BMC Systems Biology
95. Regulation of oscillation dynamics in biochemical systems with dual negative feedback loops
    Lan K. Nguyen · 2012 · Journal of The Royal Society Interface
96. Reciprocal regulation between mRNA and microRNA enables a bistable switch that directs cell fate decisions
    Xiao‐Jun Tian, Hang Zhang, Jingyu Zhang, Jianhua Xing · 2016 · FEBS Letters
97. Network design principle for robust oscillatory behaviors with respect to biological noise
    Lingxia Qiao, Zhibo Zhang, Wei Zhao, Ping Wei, Lei Zhang · 2022 · eLife
98. Phosphate Sink Containing Two-Component Signaling Systems as Tunable Threshold Devices
    Munia Amin, Varun B. Kothamachu, Elisenda Feliu, Birgit E. Scharf, Steven L. Porter, Orkun S. Soyer · 2014 · PLoS Computational Biology
99. Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes
    Nick E. Phillips, Cerys S Manning, Nancy Papalopulu, Magnus Rattray · 2017 · PLoS Computational Biology
100. A spatial physiological model for p53 intracellular dynamics
     Luna Dimitrio, Jean Clairambault, Roberto Natalini D · 2012 · Journal of Theoretical Biology