Design principles of biochemical oscillators

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Items 101–200 of 1,000

1. Mechanochemical Principles of Spatial and Temporal Patterns in Cells and Tissues
   Anaïs Bailles, Emily W. Gehrels, Thomas Lecuit · 2022 · Annual Review of Cell and Developmental Biology
2. Fine-tuning of AMPK–ULK1–mTORC1 regulatory triangle is crucial for autophagy oscillation
   Marianna Holczer, Bence Hajdú, Tamás Lőrincz, András Szarka, Gábor Bánhegyi, Orsolya Kapuy · 2020 · Scientific Reports
3. Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems
   Souvik Ghosh, Mathieu G. Baltussen, Nikita M. Ivanov, Rianne Haije, ‪Miglė Jakštaitė, Tao Zhou, Wilhelm T. S. Huck · 2024 · Chemical Reviews
4. Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis
   2019
5. Insulin signalling elicits hunger-induced feeding in Drosophila
   Sreesha R. Sudhakar, Himani Pathak, Niyas Rehman, Jervis Fernandes, Smitha Vishnu, Jishy Varghese · 2019 · Developmental Biology
6. Genetically targeted single-channel optical recording reveals multiple Orai1 gating states and oscillations in calcium influx
   Joseph L. Dynes, Anna Amcheslavsky, Michael D. Cahalan · 2015 · Proceedings of the National Academy of Sciences
7. Misuse of the Michaelis–Menten rate law for protein interaction networks and its remedy
   Jae Kyoung Kim, John J. Tyson · 2020 · PLoS Computational Biology
8. Vesicle-to-Micelle Oscillations and Spatial Patterns
   István Lagzi, Dawei Wang, Bartłomiej Kowalczyk, Bartosz A. Grzybowski · 2010 · Langmuir
9. Adaptive Posttranslational Control in Cellular Stress Response Pathways and Its Relationship to Toxicity Testing and Safety Assessment
   Qiang Zhang, Sudin Bhattacharya, Jingbo Pi, Rebecca A. Clewell, Paul Lawford Carmichael, Melvin E. Andersen · 2015 · Toxicological Sciences
10. Protein sequestration versus Hill‐type repression in circadian clock models
    Jae Kyoung Kim · 2016 · IET Systems Biology
11. Dynamics and control of the ERK signaling pathway: Sensitivity, bistability, and oscillations
    Yaman Arkun, Mohammadreza Yasemi · 2018 · PLoS ONE
12. Molecular Signaling Network Motifs Provide a Mechanistic Basis for Cellular Threshold Responses
    Qiang Zhang, Sudin Bhattacharya, Rory B. Conolly, Harvey J. Clewell III M.A., Norbert E. Kaminski, Melvin E. Andersen · 2014 · Environmental Health Perspectives
13. A modular positive feedback-based gene amplifier
    Goutam J Nistala, Kang Wu, Christopher V. Rao, Kaustubh D. Bhalerao · 2010 · Journal of Biological Engineering
14. Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation
    Lingxia Qiao, Wei Zhao, Chao Tang, Qing Hua Nie, Lei Zhang · 2019 · Cell Systems
15. Bridging the gap between in vitro and in vivo: Dose and schedule predictions for the ATR inhibitor AZD6738
    Stephen Checkley, Linda MacCallum, James W.T. Yates, Paul Jasper, Haobin Luo, John Tolsma, Claus Bendtsen · 2015 · Scientific Reports
16. A sequestration feedback determines dynamics and temperature entrainment of the KaiABC circadian clock
    Christian Brettschneider, Rebecca Rose, Stefanie Hertel, Ilka Maria IM Axmann, Albert J. R. Heck, Markus Kollmann · 2010 · Molecular Systems Biology
17. A comprehensive molecular interaction map of the budding yeast cell cycle
    Kazunari Kaizu, Samik Ghosh, Yukiko Matsuoka, Hisao Moriya, Yuki Shimizu‐Yoshida, Hiroaki Kitano · 2010 · Molecular Systems Biology
18. A Dynamical Paradigm for Molecular Cell Biology
    John J. Tyson, Béla Novák · 2020 · Trends in Cell Biology
19. Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays
    Yoko Suzuki, Mingyang Lu, Eshel Ben‐Jacob, José N. Onuchic · 2016 · Scientific Reports
20. Differential interactions between Notch and ID factors control neurogenesis by modulating Hes factor autoregulation
    Marcelo Boareto, Dagmar Iber, Verdon Taylor · 2017 · Development
21. Developmental mechanisms underlying variable, invariant and plastic phenotypes
    Katie Abley, James C W Locke, Ottoline Leyser · 2016 · Annals of Botany
22. Viewpoint: Homeostasis as Inspiration—Toward Interactive Materials
    Michael Markus Lerch, Alison Grinthal, Joanna Aizenberg · 2020 · Advanced Materials
23. Computational modeling of mammalian signaling networks
    Jacob Hughey, Timothy K. Lee, Markus W. Covert · 2009 · WIREs Systems Biology and Medicine
24. Controlling biological networks by time-delayed signals
    Gábor Orosz, Jeff Moehlis, Richard M. Murray · 2009 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
25. UNC-6 (netrin) stabilizes oscillatory clustering of the UNC-40 (DCC) receptor to orient polarity
    Zheng Wang, Lara M. Linden, Kaleb M. Naegeli, Joshua W. Ziel, Qiuyi Chi, Elliott J. Hagedorn, Natasha Saint Savage, David R. Sherwood · 2014 · The Journal of Cell Biology
26. pH Wave-Front Propagation in the Urea-Urease Reaction
    Magdalena M. Wrobel, Tamás Bánsági, Stephen K. Scott, Annette Fiona Taylor, Chris Bounds, Arturo Carranza, John A. Pojman · 2012 · Biophysical Journal
27. Frequency and amplitude control of cortical oscillations by phosphoinositide waves
    Ding Xiong, Shengping Xiao, Su Guo, Qingsong Lin, Fubito Nakatsu, Min Wu · 2016 · Nature Chemical Biology
28. The Goodwin Oscillator and its Legacy
    Didier Gonze, Peter Ruoff · 2020 · Acta Biotheoretica
29. microRNA input into a neural ultradian oscillator controls emergence and timing of alternative cell states
    Marc Goodfellow, Nick E. Phillips, Cerys S Manning, Tobias Galla, Nancy Papalopulu · 2014 · Nature Communications
30. Intrathyroidal feedforward and feedback network regulating thyroid hormone synthesis and secretion
    Jing, Li, Zhang, Qiang · 2022 · Frontiers in Endocrinology
31. Computational Systems Biology and Dose-Response Modeling in Relation to New Directions in Toxicity Testing
    Qiang Zhang, Sudin Bhattacharya, Melvin E. Andersen, Rory B. Conolly · 2010 · Journal of Toxicology and Environmental Health Part B
32. Mathematical modeling of an oscillating gene circuit to unravel the circadian clock network of Arabidopsis thaliana
    Nora Bujdoso, Seth J Davis · 2013 · Frontiers in Plant Science
33. A Design Principle for a Posttranslational Biochemical Oscillator
    Craig C. Jolley, Koji L. Ode, Hiroki R. Ueda · 2012 · Cell Reports
34. Coherence of biochemical oscillations is bounded by driving force and network topology
    Andre C. Barato, Udo Seifert · 2017 · Physical review. E
35. A Statistical Approach Reveals Designs for the Most Robust Stochastic Gene Oscillators
    Mae Louise Woods, Miriam Leon, Rubén Perez‐Carrasco, Chris P. Barnes · 2016 · ACS Synthetic Biology
36. Oscillations in Cdc14 release and sequestration reveal a circuit underlying mitotic exit
    Romilde Manzoni, Francesca Montani, Clara Visintin, Fabrice Caudron, Andrea Ciliberto, Rosella Visintin · 2010 · The Journal of Cell Biology
37. Adapting machine-learning algorithms to design gene circuits
    Tom W. Hiscock · 2019 · BMC Bioinformatics
38. Chaotic Motifs in Gene Regulatory Networks
    Zhaoyang Zhang, Weiming Ye, Yu Qian, Zhigang Zheng, Xuhui Huang, Gang Hu · 2012 · PLoS ONE
39. Cell Cycle Control by a Minimal Cdk Network
    Claude Gérard, John J. Tyson, Damien Y. M. Coudreuse, Béla Novák · 2015 · PLoS Computational Biology
40. A synthetic–natural hybrid oscillator in human cells
    Jared E. Toettcher, Caroline S. Mock, Eric Batchelor, Alexander Loewer, Galit Lahav · 2010 · Proceedings of the National Academy of Sciences
41. Pattern formation on membranes and its role in bacterial cell division
    Simon Kretschmer, Petra Schwille · 2016 · Current Opinion in Cell Biology
42. Bistable emergence of oscillations in growing Bacillus subtilis biofilms
    Rosa Martinez-Corral, Jintao Liu, Gürol M. Süel, Jordi García‐Ojalvo · 2018 · Proceedings of the National Academy of Sciences
43. CRISPR-based gene expression control for synthetic gene circuits
    Javier Santos‐Moreno, Yolanda Schaerli · 2020 · Biochemical Society Transactions
44. A catalytically active oscillator made from small organic molecules
    Matthijs ter Harmsel, Oliver R. Maguire, Sofiya A. Runikhina, Albert S. Y. Wong, Wilhelm T. S. Huck, Syuzanna R. Harutyunyan · 2023 · Nature
45. Reentrainment of the circadian pacemaker during jet lag: East-west asymmetry and the effects of north-south travel
    Casey O. Diekman, Amitabha Bose · 2017 · Journal of Theoretical Biology
46. Elements of biological oscillations in time and space
    Yangxiaolu Cao, Allison J. Lopatkin, Lingchong You · 2016 · Nature Structural & Molecular Biology
47. Light‐Fueled Nonequilibrium and Adaptable Hydrogels for Highly Tunable Autonomous Self‐Oscillating Functions
    Xuehan Yang, Wencheng Shi, Zhe Chen, Mengqi Du, Shiyan Xiao, Shaoxing Qu, Chuang Li · 2023 · Advanced Functional Materials
48. Cytokine combination therapy prediction for bone remodeling in tissue engineering based on the intracellular signaling pathway
    Xiaoqiang Sun, Jing Su, Jiguang Bao, Tao Peng, Le Zhang, Yuanyuan Zhang, Yunzhi Yang, Xiaobo Zhou · 2012 · Biomaterials
49. The molecular clockwork of a protein‐based circadian oscillator
    Joseph S. Markson, Erin K. O’Shea · 2009 · FEBS Letters
50. Metabolic Feedback Circuits Provide Rapid Control of Metabolite Dynamics
    Di Liu, Fuzhong Zhang · 2018 · ACS Synthetic Biology
51. Circadian rhythms and the HPA axis: A systems view
    Androulakis, Ioannis P. · 2021 · WIREs Mechanisms of Disease
52. Mechanisms That Enhance Sustainability of p53 Pulses
    Jae Kyoung Kim, Trachette Levon Jackson · 2013 · PLoS ONE
53. Chemical communication and dynamics of droplet emulsions in networks of Belousov–Zhabotinsky micro-oscillators produced by microfluidics
    Kristian Torbensen, Federico Rossi, Sandra Ristori, Ali Abou‐Hassan · 2017 · Lab on a Chip
54. Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases
    Somponnat Sampattavanich, Bernhard Steiert, Bernhard A. Kramer, Benjamin M. Gyori, John G. Albeck, Peter Karl Sorger · 2018 · Cell Systems
55. Chaotic activation of developmental signalling pathways drives idiopathic pulmonary fibrosis
    Antoine Froidure, Emmeline Marchal‐Duval, Méline Homps-Legrand, Mada Ghanem, A. Justet, Bruno Crestani, Arnaud Mailleux · 2020 · European Respiratory Review
56. A structural classification of candidate oscillatory and multistationary biochemical systems
    Blanchini, Franco, Franco, Elisa, Giordano, Giulia · 2014 · Bulletin of Mathematical Biology
57. Artificial Evolution of Graphene Oxide Chemzyme with Enantioselectivity and Near‐Infrared Photothermal Effect for Cascade Biocatalysis Reactions
    Can Xu, Chuanqi Zhao, Meng Cathy Li, Li Jun Wu, Jinsong Ren, Xiaogang Qu · 2014 · Small
58. Stability of Wake-Sleep Cycles Requires Robust Degradation of the PERIOD Protein
    Matthew R. D'Alessandro, Stephen Beesley, Jae Kyoung Kim, Zachary Jones, Rongmin Chen, Julie Wi, Kathleen E. Kyle, Daniel L. Vera, Michele Pagano, Richard S. Nowakowski et al. · 2017 · Current Biology
59. Finding gene network topologies for given biological function with recurrent neural network
    Jingxiang Shen, Feng Liu, Yuhai Tu, Chao Tang · 2021 · Nature Communications
60. Dynamic signal encoding—From cells to organisms
    Katharina F. Sonnen, Alexander Aulehla · 2014 · Seminars in Cell and Developmental Biology
61. Adjoint Method Provides Phase Response Functions for Delay-Induced Oscillations
    Kiyoshi Kotani, Ikuhiro Yamaguchi, Yutaro Ogawa, Yasuhiko Jimbo, Hiroya Nakao, Bard Ermentrout · 2012 · Physical Review Letters
62. Mechanochemical feedback underlies coexistence of qualitatively distinct cell polarity patterns within diverse cell populations
    JinSeok Park, William R. Holmes, Sung Hoon Lee, Hong Nam Kim, Deok‐Ho Kim, Moon Kyu Kwak, Chiaochun Joanne Wang, Leah Edelstein-keshet A, Andre Levchenko · 2017 · Proceedings of the National Academy of Sciences
63. Modeling the dynamic behavior of biochemical regulatory networks
    John J. Tyson, Teeraphan Laomettachit, Pavel Kraikivski · 2018 · Journal of Theoretical Biology
64. The systems biology of mitochondrial fission and fusion and implications for disease and aging
    Chauhan, Anuradha, Vera, Julio, Wolkenhauer, Olaf · 2014 · Biogerontology
65. Oxidation–Reduction Cycles of Peroxiredoxin Proteins and Nontranscriptional Aspects of Timekeeping
    Nathaniel P. Hoyle, John Stuart O'Neill · 2014 · Biochemistry
66. A tunable artificial circadian clock in clock-defective mice
    Matthew R. D'Alessandro, Stephen Beesley, Jae Kyoung Kim, Rongmin Chen, Estela Abich, Wayne Y Cheng, Paul Yi, Joseph S. Takahashi, Choogon Lee · 2015 · Nature Communications
67. A mathematical model coupling polarity signaling to cell adhesion explains diverse cell migration patterns
    William R. Holmes, JinSeok Park, Andre Levchenko, Leah Edelstein-keshet A · 2017 · PLoS Computational Biology
68. 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
69. Signatures of nonlinearity in single cell noise-induced oscillations
    Philipp Thomas, Arthur V. Straube, Jens Timmer, Christian C. Fleck, Ramon Grima · 2013 · Journal of Theoretical Biology
70. Phase transition in thermodynamically consistent biochemical oscillators
    Basile Nguyen, Udo Seifert, Andre C. Barato · 2018 · The Journal of Chemical Physics
71. Computing with biological switches and clocks
    Neil Dalchau, Gregory Szép, Rosa D. Hernansaiz-Ballesteros, Chris P. Barnes, Luca Cardelli, Andrew Phillips, Attila Csikász‐Nagy · 2018 · Natural Computing
72. Temporal control of the integrated stress response by a stochastic molecular switch
    Klein, Philipp, Kallenberger, Stefan M., Roth, Hanna, Roth, Karsten, Ly-Hartig, Thi Bach Nga, Magg, Vera, Aleš, Janez, Talemi, Soheil Rastgou, Qiang, Yu, Wolf, Steffen et al. · 2022 · Science Advances
73. Time-series clustering of gene expression in irradiated and bystander fibroblasts: an application of FBPA clustering
    Shanaz A. Ghandhi, Anshu Sinha, Marianthi Markatou, Sally A. Amundson · 2011 · BMC Genomics
74. Robust Adaptation and Homeostasis by Autocatalysis
    Tormod Drengstig, Xiao Yu Ni, Kristian Thorsen, Ingunn W. Jolma, Peter Ruoff · 2012 · The Journal of Physical Chemistry B
75. Computing with Competition in Biochemical Networks
    Anthony J. Genot, Teruo Fujii, Yannick Rondelez · 2012 · Physical Review Letters
76. Grip on complexity in chemical reaction networks
    Albert S. Y. Wong, Wilhelm T. S. Huck · 2017 · Beilstein Journal of Organic Chemistry
77. p53 dynamics orchestrates with binding affinity to target genes for cell fate decision
    Mengqiu Wu, Hui Ye, Zhiyuan Tang, Chang Shao, Gaoyuan Lu, Baoqiang Chen, Yuyu Yang, Guangji Wang, Haiping Hao · 2017 · Cell Death and Disease
78. An Autonomous Oscillation Times and Executes Centriole Biogenesis
    Mustafa G. Aydogan, Thomas L. Steinacker, Mohammad Mofatteh, Zachary M. Wilmott, Felix Zhou, Lisa Gartenmann, Alan Wainman, Saroj Saurya, Zsofia A. Novak, Siu‐Shing Wong et al. · 2020 · Cell
79. Systems Modeling of Anti-apoptotic Pathways in Prostate Cancer: Psychological Stress Triggers a Synergism Pattern Switch in Drug Combination Therapy
    Xiaoqiang Sun, Jiguang Bao, Kyle C. Nelson, King C. Li, George Kulik, Xiaobo Zhou · 2013 · PLoS Computational Biology
80. Association between glucose metabolism, the circadian cycle and hypoxia: Evaluation of the NPAS2 and Rev-Erb-α protein serum levels in obstructive sleep apnea patients – a pilot study
    Filip Franciszek Karuga, Julia Jaromirska, Marcin Sochal, Piotr Białasiewicz, Agata Gabryelska · 2024 · Dental and Medical Problems
81. How to Turn a Genetic Circuit into a Synthetic Tunable Oscillator, or a Bistable Switch
    Lucia Marucci, David A. W. Barton, Irene Cantone, Maria Aurelia Ricci, Maria Pia Cosma, Stefania Santini, Diego di Bernardo, Mario di Bernardo · 2009 · PLoS ONE
82. Bistability and Oscillations in Gene Regulation Mediated by Small Noncoding RNAs
    Dengyu Liu, Xiao Chang, Zengrong Liu, Luonan Chen, Ruiqi Wang · 2011 · PLoS ONE
83. Oscillatory control of signalling molecules
    Pawel Paszek, Dean Andrew Jackson, Michael White · 2010 · Current Opinion in Genetics & Development
84. Tight Coupling of Metabolic Oscillations and Intracellular Water Dynamics in Saccharomyces cerevisiae
    Henrik Seir Thoke, Asger Tobiesen, Jonathan Richard Brewer, Per Lyngs Hansen, Roberto Pablo Stock, Lars Folke Olsen, Luís A. Bagatolli · 2015 · PLoS ONE
85. Molecular Mechanisms that Regulate the Coupled Period of the Mammalian Circadian Clock
    Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett, Krešimir Josić́ · 2014 · Biophysical Journal
86. Dynamic proteomics in modeling of the living cell. Protein-protein interactions
    Alexander A. Terentiev, Nurbubu T. Moldogazieva, К. В. Шайтан · 2009 · Biochemistry (Moscow)
87. Regulation of Gene Expression and Signaling Pathway Activity in Mammalian Cells by Automated Microfluidics Feedback Control
    Lorena Postiglione, Sara Napolitano, Elisa Pedone, Daniel L. Rocca, Francesco Aulicino, Marco Santorelli, Barbara Tumaini, Lucia Marucci, Diego di Bernardo · 2018 · ACS Synthetic Biology
88. Cell type–dependent bimodal p53 activation engenders a dynamic mechanism of chemoresistance
    Ruizhen Yang, Bo Yuan Huang, Yanting Zhu, Yang Li, Feng Liu, Jue Shi · 2018 · Science Advances
89. Modeling circadian clocks: From equations to oscillations
    Didier Gonze · 2011 · Open Life Sciences
90. Physical Oncology: A Bench-to-Bedside Quantitative and Predictive Approach
    Hermann B. Frieboes, Mark A. J. Chaplain, Alastair Mark Thompson, Elaine L. Bearer, John S. Lowengrub, Vittorio Cristini C · 2011 · Cancer Research
91. MicroRNA-Mediated Positive Feedback Loop and Optimized Bistable Switch in a Cancer Network Involving miR-17-92
    Yichen Li, Yumin Li, Hui Zhang, Yong Chen · 2011 · PLoS ONE
92. Inphase and Antiphase Synchronization in a Delay-Coupled System With Applications to a Delay-Coupled FitzHugh–Nagumo System
    Yongli Song, Jian Xu · 2012 · IEEE Transactions on Neural Networks and Learning Systems
93. Robust Entrainment of Circadian Oscillators Requires Specific Phase Response Curves
    Benjamin Pfeuty, Quentin Thommen, Marc Lefranc · 2011 · Biophysical Journal
94. MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells
    Richard Moore, Hsu Kiang Ooi, Taek Kang, Leonidas G. Bleris, Lan Ma · 2015 · PLoS Computational Biology
95. Regulation of Cdc42 for polarized growth in budding yeast
    Kristi E. Miller, Pil Jung Kang, Hay-Oak Park · 2020 · Microbial Cell
96. The Goodwin model revisited: Hopf bifurcation, limit-cycle, and periodic entrainment
    Aurore Woller, Didier Gonze, Thomas Erneux · 2014 · Physical Biology
97. Priming and positioning of lateral roots in Arabidopsis. An approach for an integrating concept
    Stefan Kircher, Peter Schöpfer · 2015 · Journal of Experimental Botany
98. Adaptation with transcriptional regulation
    Wenjia Shi, Wenzhe Ma, Liyang Xiong, Mingyue Zhang, Chao Tang · 2017 · Scientific Reports
99. Incoherent Inputs Enhance the Robustness of Biological Oscillators
    Zhengda Li, Shixuan Liu, Qiong Yang · 2017 · Cell Systems
100. Towards a physical understanding of developmental patterning
     José Negrete, Andrew C. Oates · 2021 · Nature Reviews Genetics