Design principles of biochemical oscillators

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.

Monod, J., Wyman, J., & Changeux, J. (1965) · Journal of Molecular Biology · doi:10.1016/s0022-2836(65)80285-6 · Cited by 7,681

A synthetic oscillatory network of transcriptional regulators

Elowitz, M., & Leibler, S. (2000) · Nature · doi:10.1038/35002125 · Cited by 4,812

Oscillation and Chaos in Physiological Control Systems

Mackey, M. C., & Glass, L. (1977) · Science · doi:10.1126/science.267326 · Cited by 4,184

A theory of biological pattern formation

Gierer, A., & Meinhardt, H. (1972) · Kybernetik · doi:10.1007/bf00289234 · Cited by 3,158

Molecular Bases for Circadian Clocks

Dunlap, J. C. (1999) · Cell · doi:10.1016/s0092-8674(00)80566-8 · Cited by 2,900

The IκB-NF-κB Signaling Module: Temporal Control and Selective Gene Activation

Hoffmann, A., Levchenko, A., Scott, M. L., & Baltimore, D. (2002) · Science · doi:10.1126/science.1071914 · Cited by 1,890

Cyclin: A protein specified by maternal mRNA in sea urchin eggs that is destroyed at each cleavage division

Evans, T., Rosenthal, E. T., Youngblom, J., Distel, D. L., & Hunt, T. (1983) · Cell · doi:10.1016/0092-8674(83)90420-8 · Cited by 1,516

Cell-signalling dynamics in time and space

Kholodenko, B. N. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1838 · Cited by 1,347

An amplified sensitivity arising from covalent modification in biological systems.

Goldbeter, A., & Koshland, D. E. (1981) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.78.11.6840 · Cited by 1,209

Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression

Nelson, D. E., Ihekwaba, A. E. C., Elliott, M., Johnson, J. R., Gibney, C. A., Foreman, B. E., Nelson, G., See, V., Horton, C. A., Spiller, D. G., et al. (2004) · Science · doi:10.1126/science.1099962 · Cited by 1,186

Noisy Delay Denoises Biochemical Oscillators

Song, Y. M., Campbell, S., Shiau, L., Kim, J. K., & Ott, W. (2024) · Physical Review Letters · doi:10.1103/physrevlett.132.078402 · Cited by 13

Effects of acute tryptophan depletion on raphé functional connectivity in depression

Weinstein, J. J., Rogers, B. P., Taylor, W. D., Boyd, B. D., Cowan, R. L., Shelton, K. M., & Salomon, R. M. (2015) · Psychiatry Research Neuroimaging · doi:10.1016/j.pscychresns.2015.08.015 · Cited by 15

Synthetic biology of cell signaling

Hansen, J., & Benenson, Y. (2015) · Natural Computing · doi:10.1007/s11047-015-9526-1 · Cited by 12

Discrete breathers in an array of self-excited oscillators: Exact solutions and stability

Shiroky, I. B., & Gendelman, O. (2016) · Chaos An Interdisciplinary Journal of Nonlinear Science · doi:10.1063/1.4965985 · Cited by 13

Active hydrodynamics of synchronization and ordering in moving oscillators

Banerjee, T., & Basu, A. (2017) · Physical review. E · doi:10.1103/physreve.96.022201 · Cited by 13

Mathematical modeling of the relocation of the divalent metal transporter DMT1 in the intestinal iron absorption process

Cegarra, L., Rodriguez, A. C., Gerdtzen, Z. P., Núñez, M. T., & Salgado, J. C. (2019) · PLoS ONE · doi:10.1371/journal.pone.0218123 · Cited by 13

Theory of time delayed genetic oscillations with external noisy regulation

Negrete, J., Lengyel, I. M., Rohde, L. A., Desai, R. A., Oates, A. C., & Jülicher, F. (2021) · New Journal of Physics · doi:10.1088/1367-2630/abd80b · Cited by 13

Stochastic models for single‐cell data: Current challenges and the way forward

Hsu, I. S., & Moses, A. M. (2021) · FEBS Journal · doi:10.1111/febs.15760 · Cited by 13

Encoding and Decoding of p53 Dynamics in Cellular Response to Stresses

Wang, P., Wang, H., Gao, X., Zhu, H.-X., Zhang, X., Liu, F., & Wang, W. (2023) · Cells · doi:10.3390/cells12030490 · Cited by 13

Methods for and results from the study of design principles in molecular systems

Salvadó, B., Karathia, H., Usié, A., Vilaprinyó, E., Omholt, S. W., Albert Sorribas, B., & Alves, R. (2011) · Mathematical Biosciences · doi:10.1016/j.mbs.2011.02.005 · Cited by 13

Strong feedback limit of the Goodwin circadian oscillator

Woller, A., Gonze, D., & Erneux, T. (2013) · Physical Review E · doi:10.1103/physreve.87.032722 · Cited by 13

AN ATLAS OF ROBUST, STABLE, HIGH-DIMENSIONAL LIMIT CYCLES

Wilds, R., & Glass, L. (2009) · International Journal of Bifurcation and Chaos · doi:10.1142/s0218127409025225 · Cited by 13

Hopf Bifurcation and Delay-Induced Turing Instability in a Diffusive lac Operon Model

Cao, X., Song, Y., & Tonghua Zhang, A. (2016) · International Journal of Bifurcation and Chaos · doi:10.1142/s0218127416501674 · Cited by 13

Delay models for the early embryonic cell cycle oscillator

Rombouts, J., Vandervelde, A., & Gelens, L. (2018) · PLoS ONE · doi:10.1371/journal.pone.0194769 · Cited by 13

Magnesium efflux from Drosophila Kenyon cells is critical for normal and diet-enhanced long-term memory

Wu, Y., Funato, Y., Meschi, E., Jovanoski, K. D., Miki, H., & Waddell, S. (2020) · eLife · doi:10.7554/elife.61339 · Cited by 13

Mouse Hair Cycle Expression Dynamics Modeled as Coupled Mesenchymal and Epithelial Oscillators

Tasseff, R. A., Bheda-Malge, A., DiColandrea, T., Bascom, C. C., Isfort, R. J., & Gelinas, R. E. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003914 · Cited by 13

Parameter optimization by using differential elimination: a general approach for introducing constraints into objective functions

Nakatsui, M., Horimoto, K., Okamoto, M., Tokumoto, Y. M., & Miyake, J. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-s2-s9 · Cited by 13

Design patterns of biological cells

Andrews, S. S., Wiley, H. S., & Sauro, H. M. (2024) · BioEssays · doi:10.1002/bies.202300188 · Cited by 15

Selenium catalysis enables negative feedback organic oscillators

Li, X., Fomitskaya, P., Smaliak, V. A., Smith, B. S., Скорб, Е. В., & Semenov, S. N. (2024) · Nature Communications · doi:10.1038/s41467-024-47714-6 · Cited by 13

Mechanochemical dynamics of collective cells and hierarchical topological defects in multicellular lumens

Yu, P., Li, Y., Fang, W. P., Feng, X., & Li, B. (2024) · Science Advances · doi:10.1126/sciadv.adn0172 · Cited by 12

Exact Power Spectrum in a Minimal Hybrid Model of Stochastic Gene Expression Oscillations

Jia, C., Qian, H., & Zhang, M. Q. (2024) · SIAM Journal on Applied Mathematics · doi:10.1137/23m1560914 · Cited by 14

Explanation and Organizing Principles in Systems Biology

Breidenmoser, T., & Olaf Wolkenhauer, A. (2015) · History, philosophy and theory of the life sciences · doi:10.1007/978-94-017-9822-8_11 · Cited by 12

Spatiotemporal coordinated hierarchical properties of cellular protrusion revealed by multiscale analysis

Miyoshi, H., & ADACHI, T. (2012) · Integrative Biology · doi:10.1039/c2ib20013a · Cited by 12

One Thousand and One Oscillators at the Pollen Tube Tip: The Quest for a Central Pacemaker Revisited

Damineli, D. S. C., Portes, M. T., & Feijó, J. A. (2017) · Springer eBooks · doi:10.1007/978-3-319-56645-0_15 · Cited by 12

Oscillatory Dynamics of p53 Genetic Network Induced by Feedback Loops and Time Delays

Wang, C., Liu, H., & Zhou, J. (2019) · IEEE Transactions on NanoBioscience · doi:10.1109/tnb.2019.2924079 · Cited by 12

Self-assembly–based posttranslational protein oscillators

Kimchi, O., Goodrich, C. P., Courbet, A., Curatolo, A. I., Woodall, N. B., Baker, D. A., & Brenner, M. P. (2020) · Science Advances · doi:10.1126/sciadv.abc1939 · Cited by 12

Controlling Chaos in Van Der Pol Dynamics Using Signal-Encoded Deep Learning

Zhai, H., & Sands, T. A. (2022) · Mathematics · doi:10.3390/math10030453 · Cited by 16

Motor properties from persistence: a linear molecular walker lacking spatial and temporal asymmetry

Zuckermann, M. J., Angstmann, C. N., Schmitt, R. K., Blab, G. A., Bromley, E. H. C., Forde, N. R., Linke, H., & Curmi, P. M. G. (2015) · New Journal of Physics · doi:10.1088/1367-2630/17/5/055017 · Cited by 11

Design of a molecular clock with RNA-mediated regulation

Blanchini, F., Samaniego, C. C., Franco, E., & Giordano, G. (2014) · IEEE Conference on Decision and Control (CDC) · doi:10.1109/cdc.2014.7040109 · Cited by 12

Molecular noise induces concentration oscillations in chemical systems with stable node steady states

Toner, D. L. K., & Grima, R. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4788979 · Cited by 12

The role of mRNA and protein stability in the function of coupled positive and negative feedback systems in eukaryotic cells

Bendtsen, K. M., Jensen, M. H., Krishna, S., & Semsey, S. (2015) · Scientific Reports · doi:10.1038/srep13910 · Cited by 12

The quest for the central players governing pollen tube growth and guidance

Hayashi, M., & Palmgren, M. B. (2020) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiaa092 · Cited by 12

A Symmetric Dual Feedback System Provides a Robust and Entrainable Oscillator

Maeda, K., & Kurata, H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030489 · Cited by 12

Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing

Chakravarti, D., Cho, J. H., Weinberg, B. H., Wong, N. M. L., & Wong, W. W. (2016) · Integrative Biology · doi:10.1039/c5ib00325c · Cited by 13

The Hepato-Hypothalamic-Pituitary-Adrenal-Renal Axis: Mathematical Modeling of Cortisol’s Production, Metabolism, and Seasonal Variation

Pierre, K. K., Schlesinger, N., & Androulakis, I. P. (2017) · Journal of Biological Rhythms · doi:10.1177/0748730417729929 · Cited by 12

Identification of genes with oscillatory expression in glioblastoma: the paradigm of SOX2

Fu, R. Z., Cottrell, O., Cutillo, L., Rowntree, A., Zador, Z. E., Wurdak, H., Papalopulu, N., & Marinopoulou, E. (2024) · Scientific Reports · doi:10.1038/s41598-024-51340-z · Cited by 13

Synthetic gene circuit evolution: Insights and opportunities at the mid-scale

Helenek, C., Krzysztoń, R., Petreczky, J., Wan, Y., Cabral, M., Coraci, D., & Balázsi, G. (2024) · Cell chemical biology · doi:10.1016/j.chembiol.2024.05.018 · Cited by 13

Arp2/3-dependent endocytosis ensures Cdc42 oscillations by removing Pak1-mediated negative feedback

Harrell, M. A., Liu, Z., Campbell, B. F., Chinsen, O., Hong, T., & Das, M. E. (2024) · The Journal of Cell Biology · doi:10.1083/jcb.202311139 · Cited by 10

Feedback driven autonomous cycles of assembly and disassembly from minimal building blocks

Reja, A., Jha, S., Sreejan, A., Pal, S., Bal, S., Gadgil, C. J., & Das, D. (2024) · Nature Communications · doi:10.1038/s41467-024-54197-y · Cited by 12

Exploring nonlinear phenomena in animal vocalizations through oscillator theory

del Olmo, M., Schmal, C., & Herzel, H. (2025) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2024.0015 · Cited by 11

Self-Amplifying Pulsatile Protein Dynamics without Positive Feedback

Martinez-Corral, R., Raimúndez, E., Lin, Y., Elowitz, M. B., & García‐Ojalvo, J. (2018) · Cell Systems · doi:10.1016/j.cels.2018.08.012 · Cited by 11

Mechanisms of hemoglobin cycling in anemia patients treated with erythropoiesis-stimulating agents

Jörg, D. J., Fuertinger, D. H., & Kotanko, P. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010850 · Cited by 11

Transient pulse formation in jasmonate signaling pathway

Banerjee, S., & Bose, I. (2010) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.12.037 · Cited by 11

Quasi-multiparameter sensitivity measure for robustness analysis of complex biochemical networks

Maeda, K., & Kurata, H. (2010) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.12.012 · Cited by 11

To senesce or not to senesce: how primary human fibroblasts decide their cell fate after DNA damage

Kollárovič, G., Studencka‐Turski, M., Ivanova, L., Lauenstein, C., Heinze, K., Lapytsko, A., Talemi, S. R., Figueiredo, A. S., & Schaber, J. (2016) · Aging · doi:10.18632/aging.100883 · Cited by 11

Nonlinearity arising from noncooperative transcription factor binding enhances negative feedback and promotes genetic oscillations

Lengyel, I. M., Soroldoni, D., Oates, A. C., & Morelli, L. G. (2014) · Papers in Physics · doi:10.4279/pip.060012 · Cited by 11

Dynamic Environments as a Tool to Preserve Desired Output in a Chemical Reaction Network

Maguire, O. R., Wong, A. S. Y., Baltussen, M. G., van Duppen, P., Pogodaev, A. A., & Huck, W. T. S. (2019) · Chemistry - A European Journal · doi:10.1002/chem.201904725 · Cited by 12

An Introduction to Circadian Endocrine Physiology: Implications for Exercise and Sports Performance

Postolache, T. T., Gulati, A., Okusaga, O. O., & Stiller, J. W. (2020) · Contemporary Endocrinology · doi:10.1007/978-3-030-33376-8_20 · Cited by 13

Model-based investigation of the transcriptional activity of p53 and its feedback loop regulation via 14-3-3σ

Vera, J., Nikolov, S. G., Lai, X., Singh, A., & Olaf Wolkenhauer, A. (2011) · IET Systems Biology · doi:10.1049/iet-syb.2010.0080 · Cited by 11

Information Routing Driven by Background Chatter in a Signaling Network

Domedel-Puig, N., Rué, P., Pons, A. J., & García‐Ojalvo, J. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002297 · Cited by 12

Functional characteristics of additional positive feedback in genetic circuits

Wang, P., Zhang, Y., Lü, J., & Yu, X. (2014) · Nonlinear Dynamics · doi:10.1007/s11071-014-1673-x · Cited by 11

The IQGAP-related protein DGAP1 mediates signaling to the actin cytoskeleton as an effector and a sequestrator of Rac1 GTPases

Filić, V., Marinović, M., Faix, J., & Weber, I. T. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1606-3 · Cited by 10

Computational Systems Biology

Palaniappan, S. K., Yachie‐Kinoshita, A., & Ghosh, S. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20287-2 · Cited by 12

Inferring kinetic parameters of oscillatory gene regulation from single cell time-series data

Burton, J., Manning, C. S., Rattray, M., Papalopulu, N., & Kursawe, J. (2021) · Journal of The Royal Society Interface · doi:10.1098/rsif.2021.0393 · Cited by 9

Rethinking Robust Adaptation: Characterization of Structural Mechanisms for Biochemical Network Robustness through Topological Invariants

Hirono, Y., Gupta, A., & Khammash, M. (2025) · PRX Life · doi:10.1103/prxlife.3.013017 · Cited by 13

Negative feedback equalizes polarity sites in a multi-budding yeast

Crocker, A. W., Petrucco, C. A., Guan, K., Wirshing, A. C. E., Ekena, J. L., Lew, D. J., Elston, T. C., & Gladfelter, A. S. (2024) · Current Biology · doi:10.1016/j.cub.2025.05.011 · Cited by 10

Generation of oscillating gene regulatory network motifs

van Dorp, M., Lannoo, B., & Carlon, E. (2013) · Physical Review E · doi:10.1103/physreve.88.012722 · Cited by 10

A Fresh Look at Growth Oscillations in Pollen Tubes: Kinematic and Mechanistic Descriptions

Hemelryck, M. V., Bernal, R., Rojas, E., Dumais, J., & Kroeger, J. H. (2017) · Springer eBooks · doi:10.1007/978-3-319-56645-0_14 · Cited by 10

Long negative feedback loop enhances period tunability of biological oscillators

Maeda, K., & Kurata, H. (2017) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2017.12.014 · Cited by 10

Oscillations Governed by the Incoherent Dynamics in Necroptotic Signaling

Xu, F., Yin, Z., Zhu, L., Jin, J., He, Q., Li, X., & Shuai, J. (2021) · Frontiers in Physics · doi:10.3389/fphy.2021.726638 · Cited by 10

Spatiotemporal Patterning Enabled by Gene Regulatory Networks

Roy, U., Singh, D., Vincent, N., Haritas, C. K., & Jolly, M. K. (2023) · ACS Omega · doi:10.1021/acsomega.2c04581 · Cited by 13

Diurnal gene oscillations modulated by RNA metabolism in tomato

Zhang, Y., Xu, P., Xue, W., Zhu, W., & Yu, X. (2023) · The Plant Journal · doi:10.1111/tpj.16400 · Cited by 10

A robust ultrasensitive transcriptional switch in noisy cellular environments

Jeong, E. M., & Kim, J. K. (2024) · npj Systems Biology and Applications · doi:10.1038/s41540-024-00356-2 · Cited by 10

Dynamics of SIN Asymmetry Establishment

Bajpai, A., Feoktistova, A., Chen, J., McCollum, D., Sato, M., Salas, R. E. C., Gould, K. L., & Csikász‐Nagy, A. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003147 · Cited by 10

Frequency Spectrum of Transepithelial Potential Difference Reveals Transport-Related Oscillations

Montalbetti, N., & Fischbarg, J. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2009.05.063 · Cited by 10

Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle

Lin, Y., Li, Y., Crosson, S., Dinner, A. R., & Scherer, N. F. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002778 · Cited by 10

Robustness of synthetic oscillators in growing and dividing cells

Paijmans, J., Lubensky, D. K., & ten Wolde, P. R. (2017) · Physical review. E · doi:10.1103/physreve.95.052403 · Cited by 11

Progress in programming spatiotemporal patterns and machine-assembly in cell-free protein expression systems

Tayar, A. M., Daube, S. S., & Bar‐Ziv, R. (2017) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2017.05.005 · Cited by 10

Amplitude-phase description of stochastic neural oscillators across the Hopf bifurcation

Powanwe, A. S., & Longtin, A. (2021) · Physical Review Research · doi:10.1103/physrevresearch.3.033040 · Cited by 10

Chaos and Its Degradation-Promoting-Based Control in an Antithetic Integral Feedback Circuit

Zand, A. M., Tavazoei, M. S., & Kuznetsov, N. V. (2021) · IEEE Control Systems Letters · doi:10.1109/lcsys.2021.3129320 · Cited by 10

Cell cycle oscillations driven by two interlinked bistable switches

Parra‐Rivas, P., Ruiz-Reynés, D., & Gelens, L. (2023) · Molecular Biology of the Cell · doi:10.1091/mbc.e22-11-0527 · Cited by 10

Efficient, Formal, Material, and Final Causes in Biology and Technology

Ellis, G. (2023) · Entropy · doi:10.3390/e25091301 · Cited by 10

A Sparse Update Method for Solving Underdetermined Systems of Nonlinear Equations Applied to the Manipulation of Biological Signaling Pathways

Kuegler, P. B. (2012) · SIAM Journal on Applied Mathematics · doi:10.1137/110834780 · Cited by 9

A design principle underlying the paradoxical roles of E3 ubiquitin ligases

Lee, D., Kim, M., & Cho, K. (2014) · Scientific Reports · doi:10.1038/srep05573 · Cited by 10

From physics to pharmacology?

Allen, R. J., & Elston, T. C. (2010) · Reports on Progress in Physics · doi:10.1088/0034-4885/74/1/016601 · Cited by 11

Light-driven artificial neuron models based on photoswitchable systems

Gentili, P. L., Bartolomei, B., & Micheau, J. C. (2020) · Dyes and Pigments · doi:10.1016/j.dyepig.2020.109086 · Cited by 10

Exploring cores and skeletons in oscillatory gene regulatory networks by a functional weight approach

Zhang, Z., Li, Z., Hu, G., & Zheng, Z. (2014) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/105/18003 · Cited by 10

A Partial Tumor Irradiation Approach for Complex Bulky Disease

Tubin, S. (2024) · Seminars in Radiation Oncology · doi:10.1016/j.semradonc.2024.04.005 · Cited by 9

Choreographing Oscillatory Hydrodynamics with DNA-Coated Gold Nanoparticles

Rao, A., Iglesias, A. S., & Grzelczak, M. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.4c06868 · Cited by 9

Cell Cycle Complexity: Exploring the Structure of Persistent Subsystems in 414 Models

Peter, S., Arokiaraj, A. J., & Ibrahim, B. (2024) · Biomedicines · doi:10.3390/biomedicines12102334 · Cited by 9

Mechanistic origins of temperature scaling in the early embryonic cell cycle

Rombouts, J., Tavella, F., Vandervelde, A., Phong, C., Ferrell, J. E., Yang, Q., & Gelens, L. (2025) · Nature Communications · doi:10.1038/s41467-025-62918-0 · Cited by 9

Similarities of Modulation by Temperature and by Electric Field

Vincze, G., & Szász, A. (2018) · Open Journal of Biophysics · doi:10.4236/ojbiphy.2018.83008 · Cited by 9

The role of feedback mechanisms in biological network models—A tutorial

Radde, N. E. (2011) · Asian Journal of Control · doi:10.1002/asjc.376 · Cited by 9

Optimizing periodicity and polymodality in noise-induced genetic oscillators

Rué, P., Süel, G. M., & García‐Ojalvo, J. (2011) · Physical Review E · doi:10.1103/physreve.83.061904 · Cited by 9

Modeling ncRNA-Mediated Circuits in Cell Fate Decision

Tian, X., Ferro, M. V., & Goetz, H. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-8982-9_16 · Cited by 9

Multistability, quasiperiodicity and chaos in a self-oscillating ring dynamical system with three degrees of freedom based on the van der Pol generator

Astakhov, S., Astakhov, O. V., Fadeeva, N. S., & Astakhov, V. V. (2021) · Chaos Solitons & Fractals · doi:10.1016/j.chaos.2021.110978 · Cited by 9

Dual roles of SIRT1 in the BAX switch through the P53 module: A mathematical modeling study

Liu, N., Yang, H., & Yang, L. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.09.033 · Cited by 9

Mathematical Modeling in Circadian Rhythmicity

del Olmo, M., Grabe, S., & Herzel, H. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-2249-0_4 · Cited by 8

Building a Synthetic Transcriptional Oscillator

Schwarz‐Schilling, M., Kim, J., Samaniego, C. C., Weitz, M., Franco, E., & Simmel, F. C. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2957-3_10 · Cited by 9

Mathematical modeling reveals a critical role for cyclin D1 dynamics in phenotype switching during glioma differentiation

Sun, X., Zheng, X., Zhang, J., Zhou, T., Yan, G., & Zhu, W. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.07.014 · Cited by 10

Cdc42 Oscillations in Yeasts

Bendezú, F. O., & Martin, S. G. (2012) · Science Signaling · doi:10.1126/scisignal.2003630 · Cited by 9

Collective Oscillation Period of Inter-Coupled Biological Negative Cyclic Feedback Oscillators

Wang, Y., Hori, Y., Hara, S., & Doyle, F. J. (2014) · IEEE Transactions on Automatic Control · doi:10.1109/tac.2014.2342072 · Cited by 9

Gene expression model (in)validation by Fourier analysis

Konopka, T., & Rooman, M. J. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-123 · Cited by 9

Bifurcation analysis and chaotic behavior of a discrete-time delayed genetic oscillator model

Liu, F., Yin, X. G., Sun, F., Wang, X., & Wang, H. O. (2017) · Advances in Difference Equations · doi:10.1186/s13662-016-1053-6 · Cited by 9

The effect of integral control in oscillatory and chaotic reaction kinetic networks

Thorsen, K., Drengstig, T., & Ruoff, P. (2019) · Physica D Nonlinear Phenomena · doi:10.1016/j.physd.2019.01.002 · Cited by 9

A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks

Uriu, K., & Tei, H. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006787 · Cited by 9

Travelling waves in somitogenesis: Collective cellular properties emerge from time-delayed juxtacrine oscillation coupling

Tomka, T., Iber, D., & Boareto, M. (2018) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2018.04.004 · Cited by 8

Modelling co-translational dimerization for programmable nonlinearity in synthetic biology

Stoof, R., & Goñi‐Moreno, Á. (2020) · Journal of The Royal Society Interface · doi:10.1098/rsif.2020.0561 · Cited by 9

Modeling of dynamic systems with Petri nets and fuzzy logic

Windhager, L. (2013) · doi:10.5282/edoc.15655 · Cited by 9

Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises

Ranganath, V. A., & Maity, I. (2024) · Angewandte Chemie · doi:10.1002/ange.202318134 · Cited by 8

Biochemical oscillations in delayed negative cyclic feedback: Existence and profiles

Hori, Y., Takada, M., & Hara, S. (2013) · Automatica · doi:10.1016/j.automatica.2013.04.020 · Cited by 34

Elements of biological oscillations in time and space

Cao, Y., Lopatkin, A. J., & You, L. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3320 · Cited by 56

Homogeneous Time Constants Promote Oscillations in Negative Feedback Loops

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