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For: Lu T, Shen T, Bennett MR, Wolynes PG, Hasty J. Phenotypic variability of growing cellular populations. Proc Natl Acad Sci U S A 2007;104:18982-7. [PMID: 18025471 PMCID: PMC2141894 DOI: 10.1073/pnas.0706115104] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Indexed: 01/09/2023]  Open
Number Cited by Other Article(s)
1
Liao C, Priyanka P, Lai YH, Rao CV, Lu T. How Does Escherichia coli Allocate Proteome? ACS Synth Biol 2024;13:2718-2732. [PMID: 39120961 PMCID: PMC11415281 DOI: 10.1021/acssynbio.3c00537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
2
Miotto M, Rosito M, Paoluzzi M, de Turris V, Folli V, Leonetti M, Ruocco G, Rosa A, Gosti G. Collective behavior and self-organization in neural rosette morphogenesis. Front Cell Dev Biol 2023;11:1134091. [PMID: 37635866 PMCID: PMC10448396 DOI: 10.3389/fcell.2023.1134091] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/26/2023] [Indexed: 08/29/2023]  Open
3
Nagarajan K, Ni C, Lu T. Agent-Based Modeling of Microbial Communities. ACS Synth Biol 2022;11:3564-3574. [PMID: 36315012 PMCID: PMC10129392 DOI: 10.1021/acssynbio.2c00411] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
4
Terebus A, Manuchehrfar F, Cao Y, Liang J. Exact Probability Landscapes of Stochastic Phenotype Switching in Feed-Forward Loops: Phase Diagrams of Multimodality. Front Genet 2021;12:645640. [PMID: 34306004 PMCID: PMC8297706 DOI: 10.3389/fgene.2021.645640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/26/2021] [Indexed: 11/13/2022]  Open
5
Circuit-Host Coupling Induces Multifaceted Behavioral Modulations of a Gene Switch. Biophys J 2019;114:737-746. [PMID: 29414718 DOI: 10.1016/j.bpj.2017.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/12/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022]  Open
6
Liao C, Blanchard AE, Lu T. An integrative circuit–host modelling framework for predicting synthetic gene network behaviours. Nat Microbiol 2017;2:1658-1666. [DOI: 10.1038/s41564-017-0022-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 08/04/2017] [Indexed: 11/09/2022]
7
Rate-limiting steps in transcription dictate sensitivity to variability in cellular components. Sci Rep 2017;7:10588. [PMID: 28878283 PMCID: PMC5587725 DOI: 10.1038/s41598-017-11257-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/21/2017] [Indexed: 12/28/2022]  Open
8
An Ecological Understanding of Quorum Sensing-Controlled Bacteriocin Synthesis. Cell Mol Bioeng 2016. [DOI: 10.1007/s12195-016-0447-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]  Open
9
Mao J, Lu T. Population-Dynamic Modeling of Bacterial Horizontal Gene Transfer by Natural Transformation. Biophys J 2016;110:258-68. [PMID: 26745428 PMCID: PMC4806214 DOI: 10.1016/j.bpj.2015.11.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 11/07/2015] [Accepted: 11/24/2015] [Indexed: 11/18/2022]  Open
10
Stochastic sensitivity analysis and kernel inference via distributional data. Biophys J 2015;107:1247-1255. [PMID: 25185560 DOI: 10.1016/j.bpj.2014.07.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/08/2014] [Accepted: 07/15/2014] [Indexed: 12/18/2022]  Open
11
Mao J, Blanchard AE, Lu T. Slow and steady wins the race: a bacterial exploitative competition strategy in fluctuating environments. ACS Synth Biol 2015;4:240-8. [PMID: 24635143 DOI: 10.1021/sb4002008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
12
Jia C, Qian M, Kang Y, Jiang D. Modeling stochastic phenotype switching and bet-hedging in bacteria: stochastic nonlinear dynamics and critical state identification. QUANTITATIVE BIOLOGY 2015. [DOI: 10.1007/s40484-014-0035-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
13
Kong W, Celik V, Liao C, Hua Q, Lu T. Programming the group behaviors of bacterial communities with synthetic cellular communication. BIORESOUR BIOPROCESS 2014. [DOI: 10.1186/s40643-014-0024-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
14
Zhou D, Wang Y, Wu B. A multi-phenotypic cancer model with cell plasticity. J Theor Biol 2014;357:35-45. [PMID: 24819463 DOI: 10.1016/j.jtbi.2014.04.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/27/2014] [Accepted: 04/30/2014] [Indexed: 01/08/2023]
15
Blanchard AE, Celik V, Lu T. Extinction, coexistence, and localized patterns of a bacterial population with contact-dependent inhibition. BMC SYSTEMS BIOLOGY 2014;8:23. [PMID: 24576330 PMCID: PMC3942258 DOI: 10.1186/1752-0509-8-23] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/25/2014] [Indexed: 12/20/2022]
16
Monteoliva D, McCarthy CB, Diambra L. Noise minimisation in gene expression switches. PLoS One 2014;8:e84020. [PMID: 24376783 PMCID: PMC3871557 DOI: 10.1371/journal.pone.0084020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/14/2013] [Indexed: 11/19/2022]  Open
17
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: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
18
Elhanati Y, Brenner N. Metabolic variability in micro-populations. PLoS One 2012;7:e52105. [PMID: 23300596 PMCID: PMC3531411 DOI: 10.1371/journal.pone.0052105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 11/09/2012] [Indexed: 01/27/2023]  Open
19
Beal J, Lu T, Weiss R. Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS One 2011;6:e22490. [PMID: 21850228 PMCID: PMC3151252 DOI: 10.1371/journal.pone.0022490] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 06/22/2011] [Indexed: 01/27/2023]  Open
20
Ramos AF, Innocentini GCP, Hornos JEM. Exact time-dependent solutions for a self-regulating gene. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011;83:062902. [PMID: 21797428 DOI: 10.1103/physreve.83.062902] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Indexed: 05/31/2023]
21
Weber M, Buceta J. Noise regulation by quorum sensing in low mRNA copy number systems. BMC SYSTEMS BIOLOGY 2011;5:11. [PMID: 21251314 PMCID: PMC3037314 DOI: 10.1186/1752-0509-5-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 01/20/2011] [Indexed: 01/27/2023]
22
Dong D, Shao X, Deng N, Zhang Z. Gene expression variations are predictive for stochastic noise. Nucleic Acids Res 2010;39:403-13. [PMID: 20860999 PMCID: PMC3025572 DOI: 10.1093/nar/gkq844] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
23
Ramos A, Innocentini G, Forger F, Hornos J. Symmetry in biology: from genetic code to stochastic gene regulation. IET Syst Biol 2010;4:311-29. [DOI: 10.1049/iet-syb.2010.0058] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
24
Wang P, Robert L, Pelletier J, Dang WL, Taddei F, Wright A, Jun S. Robust growth of Escherichia coli. Curr Biol 2010;20:1099-103. [PMID: 20537537 PMCID: PMC2902570 DOI: 10.1016/j.cub.2010.04.045] [Citation(s) in RCA: 647] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/18/2010] [Accepted: 04/19/2010] [Indexed: 10/19/2022]
25
Tanaka N, Papoian GA. Reverse-engineering of biochemical reaction networks from spatio-temporal correlations of fluorescence fluctuations. J Theor Biol 2010;264:490-500. [DOI: 10.1016/j.jtbi.2010.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Revised: 01/31/2010] [Accepted: 02/12/2010] [Indexed: 10/19/2022]
26
Murphy KF, Adams RM, Wang X, Balázsi G, Collins JJ. Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res 2010;38:2712-26. [PMID: 20211838 PMCID: PMC2860118 DOI: 10.1093/nar/gkq091] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
27
Pechmann S, Vendruscolo M. Derivation of a solubility condition for proteins from an analysis of the competition between folding and aggregation. MOLECULAR BIOSYSTEMS 2010;6:2490-7. [DOI: 10.1039/c005160h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
28
Yin S, Wang P, Deng W, Zheng H, Hu L, Hurst LD, Kong X. Dosage compensation on the active X chromosome minimizes transcriptional noise of X-linked genes in mammals. Genome Biol 2009;10:R74. [PMID: 19594925 PMCID: PMC2728528 DOI: 10.1186/gb-2009-10-7-r74] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 06/13/2009] [Accepted: 07/13/2009] [Indexed: 01/14/2023]  Open
29
Gefen O, Balaban NQ. The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress. FEMS Microbiol Rev 2009;33:704-17. [PMID: 19207742 DOI: 10.1111/j.1574-6976.2008.00156.x] [Citation(s) in RCA: 232] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
30
French O, Hopcraft K, Jakeman E, Shepherd T. Intrinsic and measured statistics of discrete stochastic populations. Proc Math Phys Eng Sci 2008. [DOI: 10.1098/rspa.2008.0110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
31
Regulatory control and the costs and benefits of biochemical noise. PLoS Comput Biol 2008;4:e1000125. [PMID: 18716677 PMCID: PMC2518519 DOI: 10.1371/journal.pcbi.1000125] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 06/12/2008] [Indexed: 11/19/2022]  Open
32
Lu T, Ferry M, Weiss R, Hasty J. A molecular noise generator. Phys Biol 2008;5:036006. [PMID: 18698117 DOI: 10.1088/1478-3975/5/3/036006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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