Specificity of Bionoise

Glossary Bio
Acronyms Bio

                                       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)

  1. Chen Jiang-Xing, Zhu Jin-Xing, Zhao Ye-Hua, Sun Wei-Gang, Xu Jiang-Rong,Ying He-Ping: Simulating bistable biochemical systems by means of reactive multiparticle collision dynamics. Communications in Nonlinear Science and Numerical Simulation, Vol. 19, no. 7, 2014, pp. 2505 – 2512. DOI 10.1016/j.cnsns.2013.11.013

  2. Kim Kyung Hyuk, Sauro H.M., Qian Hong: Nonlinear biochemical signal processing via noise propagation. Journal of Chemical Physics, Vol. 139, no. 14, 2013, 23 pages. DOI 10.1063/1.4822103 arXiv:1309.2588

  3. Toner D.L.K., Grima R.: Molecular noise induces concentration oscillations in chemical systems with stable node steady states. Journal of Chemical Physics, Vol. 138, no. 5, 2013, Article # 055101. DOI 10.1063/1.4788979

  4. He Miao, Nie Qing, Zhou Tianshou, Zhang Jiajun: An effective method for computing the noise in biochemical networks. Journal of Chemical Physics, 2013, Vol. 138, no. 8, pp. 084106-1 – 084106-16. DOI 10.1063/1.4792444

  5. Komorowski M., Stumpf M.P.H., Miȩkisz J.: Decomposing noise in biochemical signaling systems highlights the role of protein degradation. Biophysical Journal, Vol. 104, no. 8, 2013, pp. 1783 – 1793. DOI 10.1016/j.bpj.2013.02.027 http://arxiv.org/pdf/1106.1620v1.pdf

  6. Jetka T., Charzynska A., Gambin A, Stumpf M.P.H., Komorowski M.: StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems. Bioinformatics – Oxford, Vol. 30, no. 1, 2013, pp 137 – 138. DOI 10.1093/bioinformatics/btt631 http://sourceforge.net/p/stochdecomp/

  7. Ghosh K., Firman T.: Competition enhances stochasticity in biochemical reactions. Journal of Chemical Physics, Vol. 139, no. 12, 2013, Article # 121915. DOI 10.1063/1.4816527

  8. Telen D., B. Houska, F. Logist, E. Van Derlinden, M. Diehl, J. Van Impe: Optimal experiment design under process noise using Riccati differential equations. Journal of Process Control, Vol. 23, no. 4, 2013, pp. 613 – 629. DOI 10.1016/j.jprocont.2012.11.005

  9. Tostevin F., ten Wolde P.R., Mugler A.: Spatial partitioning improves the reliability of biochemical signaling. PNAS, Vol. 110, no. 15, 2013, pp. 5927 – 5932. DOI 10.1073/pnas.1218301110

  10. Wallace E.W.J., Gillespie D.T., Sanft K.R., Petzold L.R.: Linear noise approximation is valid over limited times for any chemical system that is sufficiently large. IET Systems Biology, Vol. 6, no. 4, 2012, pp. 102 – 115. DOI 0.1049/iet-syb.2011.0038

  11. Thomas P., Matuschek H., Grima R.: Computation of biochemical pathway fluctuations beyond the linear noise approximation using iNA. IEEE Int. Conf. on Bioinformatics and Biomedicine (BIBM), 2012, pp.1 – 5. DOI 10.1109/BIBM.2012.6392668

  12. Thomas P., Matuschek H., Grima R.: Intrinsic Noise Analyzer: a software package for the exploration of stochastic biochemical kinetics using the system-size expansion. PLoS ONE, Vol. 7, no. 6, 2012, pp. e38518. DOI 10.1371/journal.pone.0038518

  13. Thomas P., Straube A.V., Grima R.: The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions. BMC Systems Biology, Vol. 6, no. 39, 2012. DOI 10.1186/1752-0509-6-39

  14. Scott M.: Non-linear corrections to the time-covariance function derived from a multi-state chemical master equation. IET Systems Biology, Vol. 6, no. 4, 2012, pp. 116 – 124. DOI 10.1049/iet-syb.2011.0031

  15. Grima R., Kim J.: Modelling noise in biochemical reaction networks. IET Systems Biology, Vol. 6, no. 4, 2012, pp. 101 DOI 10.1049/iet-syb.2012.0039

  16. Ramaswamy R., Gonzalez-Segredo N., Sbalzarini I.F., Grima R.: Discreteness-induced concentration inversion in mesoscopic chemical systems. Nature Communications, Vol. 3, 2012, pp. 779. DOI 10.1038/ncomms1775

  17. Privman V.: Control of noise in chemical and biochemical information processing. Israel Journal of Chemistry, Vol. 51, no. 1, 2011, pp. 118 – 131. DOI 10.1002/ijch.201000066

  18. Pradyumna S. Singh, Hui-Shan M. Chan, Shuo Kang, S. G. Lemay : Stochastic Amperometric Fluctuations as a Probe for Dynamic Adsorption in Nanofluidic Electrochemical Systems. Journal of the American Chemical Society, Vol. 133, no. 45, 2011, pp. 18289 – 18295. DOI 10.1021/ja2067669

  19. Toettcher J., Castillo A., Tidor B., White J.: Biochemical oscillator sensitivity analysis in the presence of conservation constraints. ACM/EDAC/IEEE Design Automation Conference (DAC), 2011, pp. 806 – 811. URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5981872&isnumber=5981698

  20. Mirsky H.P., Taylor S.R., Harvey R.A., Stelling J., Doyle F.J.: Distribution-based sensitivity metric for highly variable biochemical systems. IET Systems Biology, Vol. 5, no. 1, 2011, pp. 50 – 57. DOI 10.1049/iet-syb.2009.0064

  21. Tembine H., Tempone R., Vilanova P.: Mean field interaction in biochemical reaction networks. Annual Allerton Conf. on Communication, Control, and Computing (Allerton), 2011, pp. 991 – 997. DOI 10.1109/Allerton.2011.6120274

  22. K. Ghosh: Stochastic dynamics of complexation reaction in the limit of small numbers. Journal of Chemical Physics, Vol. 134, no. 19, 2011, 195101. http://dx.doi.org/10.1063/1.3590918

  23. S. Presse, K. Ghosh, K.A. Dill: Modeling Stochastic Dynamics in Biochemical Systems with Feedback using Maximum Caliber. Journal of Physical Chemistry B, Vol. 115, no. 19, 2011, pp. 6202 – 6212. DOI 10.1021/jp111112s

  24. Chen Aimin, Wang Junwei: Signal processing in stochastic biochemical systems with information theory. 30th Chinese Control Conference (CCC), 2011, pp. 5675 – 5679. URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6000964&isnumber=6000362

  25. Vikalo H., Hassibi B., Hassibi A.: Limits of Performance of Quantitative Polymerase Chain Reaction Systems. IEEE Trans on Information Theory, Vol. 56, no. 2, 2010, pp. 688 – 695. DOI 10.1109/TIT.2009.2037088

  26. R. Grima: Intrinsic biochemical noise in crowded intracellular conditions. J. Chem. Phys., Vol. 132, no 18, 2010, pp 185102 – 185102-9. DOI 10.1063/1.3427244

  27. S. Presse, K. Ghosh, R. Phillips, K. A. Dill : Dynamical fluctuations in biochemical reactions and cycles. Physical Review E, Vol. 82, no. 3, 2010, pp. 031905-1 – 031905-6. DOI 10.1103/PhysRevE.82.031905

  28. Chen B.-S., Chen P.-W.: Robust Engineered Circuit Design Principles for Stochastic Biochemical Networks With Parameter Uncertainties and Disturbances. IEEE Trans. on Biomedical Circuits and Systems, Vol. 2, no. 2, 2008, pp. 114 – 132. DOI 10.1109/TBCAS.2008.926728

  29. Ziv E, Nemenman I, Wiggins C.H.: Optimal Signal Processing in Small Stochastic Biochemical Networks. PLoS ONE, Vol. 2, no 10, 2007, e1077. doi:10.1371/journal.pone.0001077 http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0001077

  30. Zahedi S., Navid R., Hassibi A.: Statistical modeling of biochemical detection systems. IEEE Annual Int. Conf Eng. in Medicine and Biology Society (IEMBS), 2004, Vol. 1, pp. 208 – 211. DOI 10.1109/IEMBS.2004.1403128

  31. D. Gonze, J. Halloy, P. Gaspard: Biochemical Clocks and Molecular Noise: Theoretical Study of Robustness Factors. Journal of Chemical Physics, Vol. 116, 2002, pp 10997 – 11010. http://homepages.vub.ac.be/~gaspard/GHG.JCP.02.pdf

  32. H. Herzel, W. Ebeling: Effects of noise and inhomogeneous attractors in biochemical systems. Biomed. Biochem. Acta, Vol. 49, 1990, pp. 941 – 949.

  33. H. Herzel, W. Ebeling, Th. Schulmeister: Nonuniform chaotic dynamics and effects of noise in biochemical systems. Zeitschrift für Naturforschung, Vol. 42, no. 2, 1987, pp. 136 – 142.

  34. H. Herzel, W. Ebeling, L. Schimansky-Geier, E.E. Selkov: The influence of noise on a biochemical oscillator of Volterra type. In Methods and Applications in Connection with Lotka-Volterra Equations in Systems Analysis. Akademie-Verlag, 1985.






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





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