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For: Toettcher JE, Mock C, Batchelor E, Loewer A, Lahav G. A synthetic-natural hybrid oscillator in human cells. Proc Natl Acad Sci U S A 2010;107:17047-52. [PMID: 20837528 DOI: 10.1073/pnas.1005615107] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Chew YH, Marucci L. Mechanistic Model-Driven Biodesign in Mammalian Synthetic Biology. Methods Mol Biol 2024;2774:71-84. [PMID: 38441759 DOI: 10.1007/978-1-0716-3718-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
2
Hoces D, Miguens Blanco J, Hernández-López RA. A synthetic biology approach to engineering circuits in immune cells. Immunol Rev 2023;320:120-137. [PMID: 37464881 DOI: 10.1111/imr.13244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 07/20/2023]
3
A synthetic gene circuit for imaging-free detection of signaling pulses. Cell Syst 2022;13:131-142.e13. [PMID: 34739875 PMCID: PMC8857027 DOI: 10.1016/j.cels.2021.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/20/2021] [Accepted: 10/14/2021] [Indexed: 12/24/2022]
4
Mathematical Modelling of p53 Signalling during DNA Damage Response: A Survey. Int J Mol Sci 2021;22:ijms221910590. [PMID: 34638930 PMCID: PMC8508851 DOI: 10.3390/ijms221910590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/14/2021] [Accepted: 09/26/2021] [Indexed: 02/05/2023]  Open
5
Krzysztoń R, Wan Y, Petreczky J, Balázsi G. Gene-circuit therapy on the horizon: synthetic biology tools for engineered therapeutics. Acta Biochim Pol 2021;68:377-383. [PMID: 34460209 PMCID: PMC8590856 DOI: 10.18388/abp.2020_5744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/19/2021] [Indexed: 01/17/2023]
6
Zhang Y, Liu H, Li Z, Miao Z, Zhou J. Oscillatory Dynamics of p53-Mdm2 Circuit in Response to DNA Damage Caused by Ionizing Radiation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:1703-1713. [PMID: 30762566 DOI: 10.1109/tcbb.2019.2899574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
7
Harton MD, Koh WS, Bunker AD, Singh A, Batchelor E. p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions. Mol Syst Biol 2019;15:e8685. [PMID: 31556489 PMCID: PMC6761572 DOI: 10.15252/msb.20188685] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 01/02/2023]  Open
8
Xie M, Fussenegger M. Designing cell function: assembly of synthetic gene circuits for cell biology applications. Nat Rev Mol Cell Biol 2019;19:507-525. [PMID: 29858606 DOI: 10.1038/s41580-018-0024-z] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
9
Li Z, Liu S, Yang Q. Incoherent Inputs Enhance the Robustness of Biological Oscillators. Cell Syst 2019;5:72-81.e4. [PMID: 28750200 DOI: 10.1016/j.cels.2017.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/30/2017] [Accepted: 06/22/2017] [Indexed: 11/25/2022]
10
Andres J, Blomeier T, Zurbriggen MD. Synthetic Switches and Regulatory Circuits in Plants. PLANT PHYSIOLOGY 2019;179:862-884. [PMID: 30692218 PMCID: PMC6393786 DOI: 10.1104/pp.18.01362] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/18/2019] [Indexed: 05/20/2023]
11
Tomazou M, Barahona M, Polizzi KM, Stan GB. Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation. Cell Syst 2018;6:508-520.e5. [PMID: 29680377 DOI: 10.1016/j.cels.2018.03.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/14/2017] [Accepted: 03/19/2018] [Indexed: 01/27/2023]
12
Systems and synthetic biology approaches in understanding biological oscillators. QUANTITATIVE BIOLOGY 2017;6:1-14. [PMID: 29881643 DOI: 10.1007/s40484-017-0120-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
13
Mönke G, Cristiano E, Finzel A, Friedrich D, Herzel H, Falcke M, Loewer A. Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells. Sci Rep 2017;7:46571. [PMID: 28417973 PMCID: PMC5394551 DOI: 10.1038/srep46571] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/17/2017] [Indexed: 01/07/2023]  Open
14
Batchelor E, Loewer A. Recent progress and open challenges in modeling p53 dynamics in single cells. ACTA ACUST UNITED AC 2017;3:54-59. [PMID: 29062976 DOI: 10.1016/j.coisb.2017.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
15
Mathur M, Xiang JS, Smolke CD. Mammalian synthetic biology for studying the cell. J Cell Biol 2016;216:73-82. [PMID: 27932576 PMCID: PMC5223614 DOI: 10.1083/jcb.201611002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/25/2022]  Open
16
Porter JR, Fisher BE, Batchelor E. p53 Pulses Diversify Target Gene Expression Dynamics in an mRNA Half-Life-Dependent Manner and Delineate Co-regulated Target Gene Subnetworks. Cell Syst 2016;2:272-82. [PMID: 27135539 DOI: 10.1016/j.cels.2016.03.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 12/01/2015] [Accepted: 02/29/2016] [Indexed: 01/22/2023]
17
Castillo-Hair SM, Villota ER, Coronado AM. Design principles for robust oscillatory behavior. SYSTEMS AND SYNTHETIC BIOLOGY 2015;9:125-33. [PMID: 26279706 DOI: 10.1007/s11693-015-9178-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 07/29/2015] [Accepted: 07/31/2015] [Indexed: 11/29/2022]
18
Porter JR, Batchelor E. Using computational modeling and experimental synthetic perturbations to probe biological circuits. Methods Mol Biol 2015;1244:259-76. [PMID: 25487101 PMCID: PMC6311997 DOI: 10.1007/978-1-4939-1878-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
19
Zhang P, Brusic V. Mathematical modeling for novel cancer drug discovery and development. Expert Opin Drug Discov 2014;9:1133-50. [PMID: 25062617 DOI: 10.1517/17460441.2014.941351] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
20
Margaliot M, Sontag ED, Tuller T. Entrainment to periodic initiation and transition rates in a computational model for gene translation. PLoS One 2014;9:e96039. [PMID: 24800863 PMCID: PMC4011696 DOI: 10.1371/journal.pone.0096039] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 04/02/2014] [Indexed: 01/09/2023]  Open
21
Kim JK, Jackson TL. Mechanisms that enhance sustainability of p53 pulses. PLoS One 2013;8:e65242. [PMID: 23755198 PMCID: PMC3670918 DOI: 10.1371/journal.pone.0065242] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/26/2013] [Indexed: 02/07/2023]  Open
22
Chen S, Harrigan P, Heineike B, Stewart-Ornstein J, El-Samad H. Building robust functionality in synthetic circuits using engineered feedback regulation. Curr Opin Biotechnol 2013;24:790-6. [PMID: 23566378 DOI: 10.1016/j.copbio.2013.02.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 02/11/2013] [Accepted: 02/25/2013] [Indexed: 01/02/2023]
23
Qi H, Blanchard A, Lu T. Engineered genetic information processing circuits. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013;5:273-87. [DOI: 10.1002/wsbm.1216] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
24
Herman D, Thomas CM, Stekel DJ. Adaptation for protein synthesis efficiency in a naturally occurring self-regulating operon. PLoS One 2012. [PMID: 23185406 PMCID: PMC3502259 DOI: 10.1371/journal.pone.0049678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
25
Analyzing and engineering cell signaling modules with synthetic biology. Curr Opin Biotechnol 2012;23:785-90. [DOI: 10.1016/j.copbio.2012.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 12/20/2022]
26
Synthetic signaling networks for therapeutic applications. Curr Opin Biotechnol 2012;23:773-9. [DOI: 10.1016/j.copbio.2012.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/03/2012] [Accepted: 01/08/2012] [Indexed: 01/02/2023]
27
Goldbeter A, Gérard C, Gonze D, Leloup JC, Dupont G. Systems biology of cellular rhythms. FEBS Lett 2012;586:2955-65. [PMID: 22841722 DOI: 10.1016/j.febslet.2012.07.041] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 07/17/2012] [Accepted: 07/17/2012] [Indexed: 12/22/2022]
28
Ganesan A, Zhang J. How cells process information: quantification of spatiotemporal signaling dynamics. Protein Sci 2012;21:918-28. [PMID: 22573643 DOI: 10.1002/pro.2089] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 04/23/2012] [Indexed: 02/03/2023]
29
Modeling of hysteresis in gene regulatory networks. Bull Math Biol 2012;74:1727-53. [PMID: 22588784 DOI: 10.1007/s11538-012-9733-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 04/30/2012] [Indexed: 12/26/2022]
30
Ausländer S, Wieland M, Fussenegger M. Smart medication through combination of synthetic biology and cell microencapsulation. Metab Eng 2012;14:252-60. [DOI: 10.1016/j.ymben.2011.06.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/11/2011] [Accepted: 06/09/2011] [Indexed: 01/05/2023]
31
Karlsson M, Weber W. Therapeutic synthetic gene networks. Curr Opin Biotechnol 2012;23:703-11. [PMID: 22305476 DOI: 10.1016/j.copbio.2012.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 01/09/2012] [Accepted: 01/09/2012] [Indexed: 10/14/2022]
32
Botezatu L, Sievers S, Gama-Norton L, Schucht R, Hauser H, Wirth D. Genetic aspects of cell line development from a synthetic biology perspective. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012;127:251-284. [PMID: 22068842 DOI: 10.1007/10_2011_117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
33
Ganesan A, Levchenko A. Principles of model building: an experimentation-aided approach to development of models for signaling networks. Methods Cell Biol 2012;110:1-17. [PMID: 22482943 DOI: 10.1016/b978-0-12-388403-9.00001-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
34
Weber W, Fussenegger M. Emerging biomedical applications of synthetic biology. Nat Rev Genet 2011;13:21-35. [PMID: 22124480 PMCID: PMC7097403 DOI: 10.1038/nrg3094] [Citation(s) in RCA: 262] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
35
Miró-Bueno JM, Rodríguez-Patón A. A simple negative interaction in the positive transcriptional feedback of a single gene is sufficient to produce reliable oscillations. PLoS One 2011;6:e27414. [PMID: 22205920 PMCID: PMC3244268 DOI: 10.1371/journal.pone.0027414] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/17/2011] [Indexed: 11/19/2022]  Open
36
Nandagopal N, Elowitz MB. Synthetic biology: integrated gene circuits. Science 2011;333:1244-8. [PMID: 21885772 DOI: 10.1126/science.1207084] [Citation(s) in RCA: 219] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
37
Weber W, Fussenegger M. Molecular diversity—the toolbox for synthetic gene switches and networks. Curr Opin Chem Biol 2011;15:414-20. [PMID: 21470897 DOI: 10.1016/j.cbpa.2011.03.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 03/15/2011] [Indexed: 01/16/2023]
38
Studying adaptation and homeostatic behaviors of kinetic networks by using MATLAB. Methods Mol Biol 2011;734:153-72. [PMID: 21468989 DOI: 10.1007/978-1-61779-086-7_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
39
Aubel D, Fussenegger M. Watch the clock-engineering biological systems to be on time. Curr Opin Genet Dev 2010;20:634-43. [PMID: 20934319 DOI: 10.1016/j.gde.2010.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 08/02/2010] [Accepted: 09/15/2010] [Indexed: 11/20/2022]
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