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                                       NOISE in BIOCHEMICAL SYSTEMS

Even today a good many distinguished minds seem unable to accept or even to understand that from

a source of noise natural selection could quite unaided have drawn all the music of the biosphere

(Jacques Monod)

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  22. Zikai Xu, Khem Raj Ghusinga, Abhyudai Singh: Noise Analysis in Biochemical Complex Formation. BioRxiv, 2018, 17 pages. DOI 10.1101/310847

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  26. Boada Yadira, Vignoni Alejandro, Pico Jesus: Engineered Control of Genetic Variability Reveals Interplay among Quorum Sensing, Feedback Regulation, and Biochemical Noise. ACS Synthetic Biology, Vol. 6, no. 10, 2017, pp. 1903 – 1912. DOI 10.1021/acssynbio.7b00087

  27. Vo Hong Thanh: Stochastic simulation of biochemical reactions with partial-propensity and rejection-based approaches. Mathematical Biosciences, Vol. 292, 2017, pp. 67 – 75. DOI 10.1016/j.mbs.2017.08.001

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  45. Kobayashi Tetsuya J., Yokota Ryo, Aihara Kazuyuki: Feedback Regulation and Its Efficiency in Biochemical Networks. Journal of Statistical Physics, Vol. 162, no. 5, Special Issue: SI, 2016, pp. 1425 – 1449. DOI 10.1007/s10955-015-1443-2

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  47. Godec Aljaz, Metzler Ralf: Active transport improves the precision of linear long distance molecular signalling. Journal of Physics A: Mathematical and Theoretical, Vol. 49, no. 36, 2016, Article # 364001. DOI 10.1088/1751-8113/49/36/364001

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  49. Hahl Sayuri K., Kremling Andreas: A Comparison of Deterministic and Stochastic Modeling Approaches for Biochemical Reaction Systems: On Fixed Points, Means, and Modes. Frontiers in Genetics, Vol. 7, 2016, Article # 157. DOI 10.3389/fgene.2016.00157

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  51. Enciso German A.: Transient absolute robustness in stochastic biochemical networks. Journal of the Royal Society Interface, Vol. 13, no. 121, 2016, Article # 20160475. DOI 10.1098/rsif.2016.0475

  52. Marchetti Luca, Priami Corrado, Vo Hong Thanh: HRSSA - Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks. Journal of Computational Physics, Vol. 317, 2016, pp. 301 – 317. DOI 10.1016/j.jcp.2016.04.056

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  55. Vo Hong Thanh, Priami Corrado, Zunino Roberto: Accelerating rejection-based simulation of biochemical reactions with bounded acceptance probability. Journal of Chemical Physics, Vol. 144, no. 22, 2016, Article # 224108. DOI 10.1063/1.4953559

  56. Zhang Jiajun, Nie Qing, Zhou Tianshou: A moment-convergence method for stochastic analysis of biochemical reaction networks. Journal of Chemical Physics, Vol. 144, no. 19, 2016, Article # 194109. DOI 10.1063/1.4950767

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  58. Cianci Claudia, Smith Stephen, Grima Ramon: Molecular finite-size effects in stochastic models of equilibrium chemical systems. Journal of Chemical Physics, Vol. 144, no. 8, 2016, Article # 084101. DOI 10.1063/1.4941583

  59. Dixon John, Lindemann Anika, McCoy Jonathan H.: Transient amplification limits noise suppression in biochemical networks. Physical Review E, Vol. 93, no. 1, 2016, Article # 012415. DOI 10.1103/PhysRevE.93.012415

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  61. Smith Stephen, Cianci Claudia, Grima Ramon: Model reduction for stochastic chemical systems with abundant species. Journal of Chemical Physics, Vol. 143, no. 21, 2015, Article # 214105. DOI 10.1063/1.4936394

  62. Milias-Argeitis A., Engblom S., Bauer P., et al.: Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks. Journal of the Royal Society Interface, Vol. 12, no. 113, 2015, Article # 20150831. DOI 10.1098/rsif.2015.0831

  63. Zimmer C., Sahle S., Pahle J.: Exploiting intrinsic fluctuations to identify model parameters. IET Systems Biology, Vol. 9, no. 2, 2015, pp. 64 – 73. DOI 10.1049/iet-syb.2014.0010

  64. Barroo C., De Decker Y., de Bocarme T.V., et al.: Fluctuating Dynamics of Nanoscale Chemical Oscillations: Theory and Experiments. Journal of Physical Chemistry Lett., Vol. 6, no. 12, 2015, pp. 2189 – 2193. DOI 10.1021/acs.jpclett.5b00850

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  67. Polettini M., Wachtel A., Espositoc M.: Dissipation in noisy chemical networks: The role of deficiency. Journal of Chemical Physics, Vol. 143, no. 18, 2015, Article # 184103. DOI 10.1063/1.4935064

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  69. Chen Bor-Sen, Wong Shang-Wen, Li Cheng-Wei: On the Calculation of System Entropy in Nonlinear Stochastic Biological Networks. Entropy, Vol. 17, no. 10, 2015, pp. 6801 – 6833. DOI 10.3390/e17106801

  70. Vo Hong Thanh, Priami Corrado: Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm. Journal of Chemical Physics, Vol. 143, no. 5, 2015, Article # 054104. DOI 10.1063/1.4927916

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  72. Caravagna G., De Sano L., Antoniotti M.: Automatising the analysis of stochastic biochemical time-series. BMC Bioinformatics, Vol. 16, Supplement: 9, 2015, Article # S8. DOI 10.1186/1471-2105-16-S9-S8

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  75. Ruess Jakob, Lygeros John: Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks. ACM Trans on Modeling and Computer Simulation, Vol. 25, no. 2, Special Issue: SI, 2015, Article # 8. DOI 10.1145/2688906

  76. Zimmer Christoph, Sahle Sven, Pahle Juergen: Exploiting intrinsic fluctuations to identify model parameters. IET Systems Biology, Vol. 9, no. 2, 2015, pp. 64 – 73. DOI 10.1049/iet-syb.2014.0010

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  78. Lipinski-Kruszka J., Stewart-Ornstein J., Chevalier M.W., et al.: Using Dynamic Noise Propagation to Infer Causal Regulatory Relationships in Biochemical Networks. ACS Synthetic Biology, Vol. 4, no. 3, 2015, pp. 258 – 264. DOI 10.1021/sb5000059

  79. Oyarzun Diego A., Lugagne Jean-Baptiste, Stan Guy-Bart V.: Noise Propagation in Synthetic Gene Circuits for Metabolic Control. ACS Synthetic Biology, Vol. 4, no. 2, 2015, pp. 116 – 125. DOI 10.1021/sb400126a

  80. Privman Vladimir, Katz Evgeny: Can bio-inspired information processing steps be realized as synthetic biochemical processes? Physica Status Solidi A - Applications and Materials Science, Vol. 212, no. 2, 2015, pp. 219 – 228. DOI 10.1002/pssa.201400131

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  90. Hu Bo, Rappel Wouter-Jan, Levine Herbert: How input noise limits biochemical sensing in ultrasensitive systems. Physical Review E, Vol. 90, no. 3, 2014, Article # 032702. DOI 10.1103/PhysRevE.90.032702

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Links:

http://www.nslij-genetics.org/wli/1fnoise/ (A bibliography on 1/f noise in biosystems)

http://papers.cnl.salk.edu/PDFs/

http://iopscience.iop.org/1742-5468/focus/extra.focus5

 

 


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