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                                                   NOISE in CELLS

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)

  1. Hung Yao-Chen, Lin Chai-Yu: Modeling intrinsic noise in random Boolean networks. Physica A - Statistical Mechanics and its Applications, Vol. 395, 2014, pp. 121 – 127. DOI 10.1016/j.physa.2013.10.049

  2. Brennecke P. A., Simon Kim, Jong Kyoung, Kolodziejczyk A. A, Zhang Xiuwei, Proserpio V., Baying B., Benes V., Teichmann S. A, Marioni J.C.: Accounting for technical noise in single-cell RNA-seq experiments. Nature Methods, Vol. 11, no. 2, 2014, pp. 210 – 210. DOI 10.1038/nmeth0214-210b

  3. Horbacz K.: Continuous random dynamical systems. Journal of Mathematical Analysis and Applic., Vol. 408, no. 2, 2013, pp. 623 – 637. DOI 10.1016/j.jmaa.2013.06.050

  4. Yuan Zhu, Xiao-Fei Zhang, Dao-Qing Dai, Meng-Yun Wu: Identifying Spurious Interactions and Predicting Missing Interactions in the Protein-Protein Interaction Networks via a Generative Network Model. IEEE/ACM Trans on Computational Biology and Bioinformatics, Vol. 10, no. 1, 2013, pp. 219 – 225. DOI 10.1109/TCBB.2012.164

  5. dos Santos R.V., da Silva L.M.: The noise and the KISS in the cancer stem cells niche. Journal of Theoretical Biology, Vol. 335, 2013, pp. 79 – 87. DOI 10.1016/j.jtbi.2013.06.025

  6. Thomas P., Straube A. V., Timmer J., Fleck C., Grima R.: Signatures of nonlinearity in single cell noise-induced oscillations. Journal of Theoretical Biology, Vol. 335, 2013, pp. 222 – 234. DOI 10.1016/j.jtbi.2013.06.021

  7. Sadati M., Qazvini N.T., Krishnan R., Park Chan Young, Fredberg J.J.: Collective migration and cell jamming. Differentiation, Vol. 86, no. 3, Special no. SI, 2013, pp. 121 – 125. DOI 10.1016/j.diff.2013.02.005

  8. Wang Bing, Yin Zhixiang: Effects of colored noise and noise delay on a calcium oscillation system. Physica A - Statistical Mechanics and its Applications, Vol. 392, no. 19, 2013, pp. 4203 – 4209. DOI 10.1016/j.physa.2013.05.016

  9. Gonze D.: Modeling the effect of cell division on genetic oscillators. Journal of Theoretical Biology, Vol. 325, 2013, pp. 22 – 33. DOI 10.1016/j.jtbi.2013.02.001

  10. Flegg M. B., Ruediger S., Erban R.: Diffusive spatio-temporal noise in a first-passage time model for intracellular calcium release. Journal of Chemical Physics, Vol. 138, no. 15, 2013, Article # 154103. DOI 10.1063/1.4796417

  11. Junker J. P., van Oudenaarden A.: When Noisy Neighbors Are a Blessing: Analysis of Gene Expression Noise Identifies Coregulated Genes. Molecular Cell, Vol. 45, no. 4, 2012, pp. 437 – 438. DOI 10.1016/j.molcel.2012.02.002

  12. Sargsyan K., Safta C., Debusschere B., Najm H.: Multiparameter Spectral Representation of Noise-Induced Competence in Bacillus Subtilis. IEEE/ACM Trans on Computational Biology and Bioinformatics, Vol. 9, no. 6, 2012, pp.1709 – 1723. DOI 10.1109/TCBB.2012.107

  13. Greese B., Bensch K., Wester R., Ronneberger O., Timmer J., Hülskamp M., Fleck C.: Influence of cell-to-cell variability on spatial pattern formation. IET Systems Biology, Vol. 6, no. 4, 2012, pp 143 – 153. DOI 10.1049/iet-syb.2011.0050

  14. Medvedev G.S., Zhuravytska S.: Shaping bursting by electrical coupling and noise. Biological Cybernetics, Vol. 106, no. 2, 2012, pp. 67 – 88. DOI 10.1007/s00422-012-0481-y

  15. Liu Zhen, Pu Yang, Li Fei, Shaffer C.A. , Hoops S., Tyson J.J. , Cao Yang: Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle. Journal of Chemical Physics, Vol. 136, no. 3, 2012, Article # 034105. DOI 10.1063/1.3677190

  16. Chan Ming-Cheng, Spieth P.M., Quinn K., Parotto M., Zhang Haibo, Slutsky A.S.: Circadian rhythms: From basic mechanisms to the intensive care unit. Critical Care Medicine, Vol. 40, no. 1, 2012, pp. 246 – 253. DOI 10.1097/CCM.0b013e31822f0abe

  17. Snijder B., Sacher R., Raemoe P., et al.: Single-cell analysis of population context advances RNAi screening at multiple levels. Molecular Systems Biology,  Vol. 8, 2012, Article # 579. DOI 10.1038/msb.2012.9

  18. Hongyuan Zhu, Tianqi Chen, Xue Lei, Wei Tian, Youfang Cao, Ping Ao: Understand the noise of CI expression in phage λ lysogen. Chinese Control Conference (CCC), 2012, pp.7432 – 7436.

  19. Ito Y., Kawachi S., Uchida K.: Robustness analysis and optimization of circadian clocks fluctuated by intrinsic noise. 8th Asian Control Conference (ASCC), 2011, pp. 506 – 511. URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5899123&isnumber=5899042

  20. H. Koeppl, M. Hafner, A. Ganguly, A. Mehrotra : Deterministic characterization of phase noise in biomolecular oscillators. Phys. Biol., Vol. 8, no 5, 2011, pp 055008 (16 pages) DOI 10.1088/1478-3975/8/5/055008

  21. Rosenstein J., Sorgenfrei S., Shepard K. L. : Noise and bandwidth performance of single-molecule biosensors. IEEE Custom Integrated Circuits Conf (CICC) — 2011, pp. 1 – 7. DOI 10.1109/CICC.2011.6055375

  22. R. Schiller, A. Horvath : Generalized Johnson-Nyquist noise: white noise of temperature and pressure at the nanoscale. Physical Chemistry Chemical Physics, Vol. 13, 2011, pp 9281 – 9284. DOI10.1039/C0CP01482F

  23. Hongying Li, Jianhong Bi, Yu Shen : Propagation and enhancement of the noise-induced signal in a coupled cell system. Applied Mathematical Modelling, Vol. 35, no. 6, 2011, pp 2682 – 2687. DOI 10.1016/j.apm.2010.11.063

  24. Kobayashi T.J.: Bayesian information decoding by a cell. 21st Int. Conf. on Noise and Fluctuations (ICNF), 12-16 June 2011, pp 490 – 492. DOI 10.1109/ICNF.2011.5994377

  25. Dandach S.H., Khammash M.: Stochastic strategies for survival: Bacterial competence in Bacillus Subtilis. American Control Conference (ACC), 2011, pp. 2296 – 2301. URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5991255&isnumber=5989965

  26. Nguyen L.K., Kulasiri D.: Distinct noise-controlling roles of multiple negative feedback mechanisms in a prokaryotic operon system. IET Systems Biology, Vol. 5, no. 2, 2011, pp. 145 – 156. DOI 10.1049/iet-syb.2010.0020

  27. Yamada T., Ou J., Furusawa C., Hirasawa T., Yomo T., Shimizu H.: Relationship between noise characteristics in protein expressions and regulatory structures of amino acid biosynthesis pathways. IET Systems Biology, Vol. 4, no 1, 2010, pp 82 – 89. DOI 10.1049/iet-syb.2008.0158

  28. Zhang Yanbin, Wang Junwei, Kong Wanzeng, Zhang Jianhai, Yang Kun: Constructive effects of noise on cell signaling in bistable map kinase cascades. 29th Chinese Control Conf. (CCC), 2010, pp. 5147 – 5152. URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5573433&isnumber=5571954

  29. Zhang Jiajun, Zhou Tianshou: Noise-induced rhythm and synchronization across an ensemble of stochastic genetic oscillators. Chinese Control Conference (CCC), 2008, pp. 409 – 413. DOI 10.1109/CHICC.2008.4605310

  30. J. A. Ubersax, J. E. Ferrell: A noisy 'Start' to the cell cycle. Molecular Systems Biology, Vol 2, 2006, msb4100056-E1-msb4100056-E2 DOI 10.1038/msb4100056

  31. Hong Qian: Reducing Intrinsic Biochemical Noise in Cells and Its Thermodynamic Limit. Journal of Molecular Biology, Vol. 362, no. 3, 2006, pp 387 – 392. doi:10.1016/j.jmb.2006.07.068

  32. S. S. Andrews, A. P. Arkin: Simulating cell biology. Current Biology, Vol. 16, no. 14, 2006, pp R523 – R527. http://www.smoldyn.org/andrews/papers/Andrews_Arkin_2006.pdf

  33. D. Gonze, A. Goldbeter: Circadian rhythms and molecular noise. Chaos, Vol. 16, no 2, 2006, pp 026110, (11 pages). DOI 10.1063/1.2211767

  34. M. Bier: How to evaluate the electric noise in a cell membrane? Acta Physica Polonica B, Vol. 37, no. 5, 2006, pp 1409 – 1424.

  35. A. Kurakin: Self-organization versus Watchmaker: stochastic dynamics of cellular organization. Biol. Chem., Vol. 386, March 2005, pp 247 – 254, DOI 10.1515/BC.2005.030

  36. Heinrichs A.: Systems biology: The variable cell. Nature Reviews Molecular Cell Biology, Vol 6, 2005, pp 822. DOI 10.1038/nrm1768

  37. F. J. Isaacs, J. J. Collins: Plug-and-play with RNA. Nature Biotechnology, Vol. 23, no. 3, March 2005, pp 306 – 307. DOI 10.1038/nbt0305-306

  38. F. J. Isaacs, W. J. Blake, J. J. Collins: Signal processing in a single cell. Science, Vol. 307, no 5717, 25 March 2005, pp 1886 – 1888. DOI 10.1126/science.1110797

  39. C. V. Rao, D. M. Wolf, A. P. Arkin: Control, exploitation and tolerance of intracellular noise. Nature, Vol. 420, 14 November 2002, pp 231 – 237. DOI 10.1038/nature01258 http://eao.igc.gulbenkian.pt/ti/4u/PDBEBBiochemicalKinetics/Nature-2002-420-231.pdf

  40. A. Goldbeter: Computational approaches to cellular rhythms. Nature, Vol 420, no 6912, 2002, pp 238 – 245. DOI 10.1038/nature01259

  41. M. Takano, T. Takahashi, K. Nagayama: Helix-Coil Transition and 1/f Fluctuation in a Polypeptide. Phys. Rev. Lett. Vol. 80, no. 25, 22 June 1998, pp 5691 – 5694. DOI 10.1103/PhysRevLett.80.5691

Links:

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

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

http://en.wikipedia.org/wiki/Cellular_noise


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