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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. R.S. Yuan, X.M. Zhu, G.W. Wang, S.T. Li, P. Ao: Cancer as robust intrinsic state shaped by evolution: a key issues review. Reports on Progress in Physics, Vol. 80, no. 4, 2017, Article # 042701. http://iopscience.iop.org/article/10.1088/1361-6633/aa538e

  2. Suderman R., Bachman J., Smith A., Sorger P., Deeds E.J.: Fundamental trade-offs between information flow in single cells and cellular populations. PNAS, published online May 2017. DOI 10.1073/pnas.1615660114

  3. Gushinga K.R., Dennehy J.J., Singh A.: First-passage time approach to controlling noise in the timing of intracellular events. PNAS, 2017, Vol. 114, no. 4, pp. 693 – 698. https://doi.org/10.1073/pnas.1609012114

  4. Gushinga K.R., Vargas-Garcia C.A., Singh A.: A mechanistic stochastic framework for regulating bacterial cell division. Scientific Reports, Vol. 6, 2016, Article # 30229. https://dx.doi.org/10.1038%2Fsrep30229

  5. Perez Ipina E., Ponce Dawson S.: Fluctuations, Correlations and the Estimation of Concentrations inside Cells. PLoS One, Vol. 11, no. 3, 2016, Article # e0151132. DOI 10.1371/journal.pone.0151132

  6. Cerulus B., New A.M., Pougach K., Verstrepen K.J.: Noise and Epigenetic Inheritance of Single-Cell Division Times Influence Population Fitness. Current Biology, Vol. 26, no. 9, 2016, pp. 1138 – 1147. http://dx.doi.org/10.1016/j.cub.2016.03.010

  7. Guerrero P., Byrne H.M., Maini P.K., Alarcón T.: From invasion to latency: intracellular noise and cell motility as key controls of the competition between resource-limited cellular populations. J. Mathematical Biology, Vol. 72, no. 1, 2016, pp. 123 – 156. DOI 10.1007/s00285-015-0883-2

  8. Stoeger T., Battich N., Pelkmans L.: Passive Noise Filtering by Cellular Compartmentalization. Cell, Vol. 164, no. 6, 2016, pp. 1151 – 1161. https://doi.org/10.1016/j.cell.2016.02.005

  9. Hsu Chieh, Jaquet V., Maleki F., Becksei A.: Contribution of Bistability and Noise to Cell Fate Transitions Determined by Feedback Opening. J. of Molecular Biology, Vol. 428, no. 20, 2016, pp. 4115 – 4128. https://doi.org/10.1016/j.jmb.2016.07.024

  10. Xiaoshu Chen, Jianzi Zhang: The Genomic Landscape of Position Effects on Protein Expression Level and Noise in Yeast. Cell Systems, Vol. 2, no. 5, 2016, pp. 347 – 354. https://doi.org/10.1016/j.cels.2016.03.009

  11. Vogel R.M.: Single Cell Characterization of Biochemical Noise and Variable Response to Chemical Inhibition. PhD Dissertation, Faculty of the Weill Cornell Graduate School of Medical Sciences, 2016, 122 pages.

  12. Veliz-Cuba A., Gupta C., Bennett M.R., et al.: Effects of cell cycle noise on excitable gene circuits. Physical Biology, Vol. 13, no. 6, 2016, Article # 066007. https://doi.org/10.1088/1478-3975/13/6/066007

  13. Saurabh Kartik Modi, Cesar Augusto Vargas-Garcia, Khem Raj Ghusinga, Abhyudai Singh: Analysis of noise mechanisms in cell size control. BioRxiv, 2016. http://dx.doi.org/10.1101/080465

  14. P.R. ten Wolde: Viewpoint: Putting Bounds on Biochemical Noise. Physics, Vol. 9, no. 12, 2016. https://physics.aps.org/articles/pdf/10.1103/Physics.9.12

  15. Arbel-Goren R., Tal A., Bibudha Parasar, Alvah Dym, Costantino N., Muñoz-García J., Court D.L., Stavans J.: Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli. Nucleic Acids Research, Vol. 44, no. 14, 2016, pp. 6707 – 6720. https://doi.org/10.1093/nar/gkw273

  16. Heltberg M., Kellogg R.A., Sandeep Krishna, Savas Tay, Mogens H. Jensen: Noise Induces Hopping between NF-kB Entrainment Modes. Cell Systems, Vol. 3, no. 6, 2016, pp. 532 – 539. http://dx.doi.org/10.1016/j.cels.2016.11.014

  17. Gupta A., Hepp B., Khammash M.: Noise Induces the Population-Level Entrainment of Incoherent, Uncoupled Intracellular Oscillators. Vol. 3, no. 6, 2016, pp. 521 – 531. http://dx.doi.org/10.1016/j.cels.2016.10.006

  18. Rui He, Rongjing Zhang, Junhua Yuan: Noise-Induced Increase of Sensitivity in Bacterial Chemotaxis. Vol. 111, no. 2, 2016, pp. 430 – 437. https://doi.org/10.1016/j.bpj.2016.06.013

  19. Ciechonska M., Grob A., Isalan M.: From noise to synthetic nucleoli: can synthetic biology achieve new insights? Integrative Biology, Vol. 8, 2016, pp. 383 – 393. DOI 10.1039/C5IB00271K

  20. Lijie Liu, Fanfan Wang, Haiying Lu, et al.: Effects of Noise Exposure on Systemic and Tissue-Level Markers of Glucose Homeostasis and Insulin Resistance in Male Mice. Environmental Health Perspectives, Vol. 124, no. 9, 2016, pp. 1390 – 1398. http://dx.doi.org/10.1289/EHP162

  21. Deniz O., Flores O., Aldea M., Soler-Lopez M., Orozco M.: Nucleosome architecture throughout the cell cycle. Scientific Reports, Vol. 6, 2016, Article # 19729. DOI 10.1038/srep19729

  22. Kazunari Iwamoto, Yuki Shindo, Koichi Takahashi: Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway. PLOS Computational Biology, 2016, 18 pages. DOI 10.1371/journal.pcbi.1005222

  23. Nash Rochman, Fangwei Si, Sean X. Sun: To Grow is Not Enough: Impact of Noise on Cell Environmental Response and Fitness. Integrative Biology, Vol. 8, no. 10, 2016, pp. 1030 – 1039. DOI 10.1039/C6IB00119J

  24. Chepyala S.R., Chen Y.C., Yan C.C., Lu C.Y., Wu Y.C., Hsu C.P.: Noise propagation with interlinked feed-forward pathways. Scientific Reports, Vol. 6, 2016, Article # 23607. DOI 10.1038/srep23607

  25. Guisoni N., Monteoliva D., Diambra L.: Promoters Architecture-Based Mechanism for Noise-Induced Oscillations in a Single-Gene Circuit. PLOS one, Vol. 11, no. 3, 2016, Article # e0151086 (12 pages). DOI 10.1371/journal.pone.0151086

  26. Roberto de la Cruz, P. Guerrero, F. Spill, T. Alarcon: The effects of intrinsic noise on the behaviour of bistable cell regulatory systems under quasi-steady state conditions. The Journal of Chemical Physics, Vol. 143, no. 7, 2015, Article # 074105. http://dx.doi.org/10.1063/1.4928575

  27. Lei X., Tian W., Zhu H., Chen T., Ao P.: Biological Sources of Intrinsic and Extrinsic Noise in cI Expression of Lysogenic Phage Lambda. Scientific Reports, Vol. 5, 2015, Article # 13597. DOI 10.1038/ srep13597

  28. Blaszczyka M., Harmerb N.J., Chirgadzea D.Y., Aschera D.B., Blundel T.L.: Achieving high signal-to-noise in cell regulatory systems: Spatial organization of multiprotein transmembrane assemblies of FGFR and MET receptors. Progress in Biophysics and Molecular Biology, Vol. 118, no. 3, 2015, pp. 103 – 111. https://doi.org/10.1016/j.pbiomolbio.2015.04.007

  29. Rocha P.R.F., Schlett P., Schneider L., Dröge M., Mailänder V., Gomes H.L., Bloma P.W.M., de Leeuw D.M.: Low frequency electric current noise in glioma cell populations. J. of Materials Chemistry B, Vol. 3, no. 25, 2015, pp. 5035 – 5039. DOI 10.1039/C5TB00144G

  30. Sokolik C., Yanxia Liu, Bauer D., et al.: Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise. Cell Systems, Vol. 1, no. 2, 2015, pp. 117 – 129. https://doi.org/10.1016/j.cels.2015.08.001

  31. Assieh Saadatpour, Shujing Lai, Guoji Guo, Guo-Cheng Yuan: Single-Cell Analysis in Cancer Genomics. Trends in Genetics, Vol. 31, no. 10, 2015, pp. 576 – 586. https://doi.org/10.1016/j.tig.2015.07.003

  32. Schaar K., Zöttl A., Stark H.: Detention times of microswimmers close to surfaces: Influence of hydrodynamic interactions and noise. Phys. Rev. Lett., Vol. 115, no. 3, 2015, Article # 038101. https://doi.org/10.1103/PhysRevLett.115.038101

  33. St. John P.C., Doyle F.J. III: Quantifying Stochastic Noise in Cultured Circadian Reporter Cells. PLoS Comput. Biology, Vol. 11, 2015, Article # e1004451, 17 pages. https://doi.org/10.1371/journal.pcbi.1004451

  34. Zoller B., Nicolas D., Molina N., Naef F.: Structure of silent transcription intervals and noise characteristics of mammalian genes. Molecular Systems Biology, Vol. 11, no. 7, 2015, pp. 1 – 15. DOI 10.15252/msb.20156257

  35. Idan Efroni, Pui-Leng Ip, Tal Nawy, Alison Mello, K.D. Birnbaum: Quantification of cell identity from single-cell gene expression profiles. Genome Biology, Vol. 16, no. 9, 2015, 12 pages. DOI 10.1186/s13059-015-0580-x

  36. Oded Sandler, Sivan Pearl Mizrahi, Noga Weiss, Oded Agam, Itamar Simon, N.Q. Balaban: Lineage correlations of single cell division time as a probe of cell-cycle dynamics. Nature, Vol. 519, no. 7544, 2015, pp. 468 – 471. DOI 10.1038/nature14318

  37. Bosia C., Sgrò F., Conti L., Baldassi C., Cavallo F., Di Cunto F., Turco E., Pagnani A., Zecchina R.: Quantitative study of crossregulation, noise and synchronization between microRNA targets in single cells. ArXiv: 1503.06696V1 [q-bio.MN], 2015. DOI 10.1186/s13059-017-1162-x

  38. Pratap R. Patnaik: Indications of Spontaneous Chaos in the Chemotaxis of E. coli under Noise-Induced Parametric Perturbations. Int. Journal of Chemoinformatics and Chemical Engineering, Vol. 4, no. 1, 2015, pp. 52 – 65. DOI 10.4018/IJCCE.2015010104

  39. Baskin T.I.: Ultradian Growth Oscillations in Organs: Physiological Signal or Noise? Rhythms in Plants: Phenomenology, Mechanisms, and Adaptive Significance, E-book Springer Verlag Berlin Heidelberg, 2015, pp. 63 – 76. DOI 10.1007/978-3-540-68071-0_3

  40. Asuka Ota R., Kovary K.M., Akamasa Kudo, Byung Ouk Park, Teruel M.N.: Controlling low rates of cell differentiation through noise and ultrahigh feedback. Science, Vol. 344, no. 6190, 2014, pp. 1384 – 1389. DOI 10.1126/science.1252079

  41. Schulte M.B., Andino R.: Single-Cell Analysis Uncovers Extensive Biological Noise in Poliovirus Replication. Journal of Virology, Vol. 88, no. 11, 2014, pp. 6205 – 6212. http://dx.doi.org/10.1128/JVI.03539-13

  42. Bertolusso R., Bing Tian, Yingxin Zhao, Vergara L., Aqeeb Sabree, Iwanaszko M., Lipniacki T., Brasier A.R., Kimmel M.: Dynamic Cross Talk Model of the Epithelial Innate Immune Response to Double-Stranded RNA Stimulation: Coordinated Dynamics Emerging from Cell-Level Noise. PLOS One, Vol. 9, no. 4, 2014, Article # e93396. https://doi.org/10.1371/journal.pone.0093396

  43. Kiviet D.J., Nghe P., Walker N., Boulineau S., Sunderlikova V., Tans S.J.: Stochasticity of metabolism and growth at the single-cell level. Nature, Vol. 514, no. 7522, 2014, pp. 376 – 379. DOI 10.1038/nature13582

  44. Levchenko A., Nemenman I.: Cellular noise and information transmission. Current Opinion in Biotechnology, Vol. 28, 2014, pp. 156 – 164. https://doi.org/10.1016/j.copbio.2014.05.002

  45. Siyuan Zheng, Hoon Kim, Roel G.W. Verhaak: Silent Mutations Make Some Noise. Cell, Vol. 156, no. 6, 2014, pp. 1129 – 1131. https://doi.org/10.1016/j.cell.2014.02.037

  46. Przemysław Rafał Paździorek: Mathematical Model of Stem Cell Differentiation and Tissue Regeneration with Stochastic Noise. Bulletin of Mathematical Biology, Vol. 76, no. 7, 2014, pp. 1642 – 1669. DOI 10.1007/s11538-014-9971-5

  47. Govern C.C., ten Wolde P.R.: Energy Dissipation and Noise Correlations in Biochemical Sensing. Physical Rev. Lett., Vol. 113, no. 25, 2014, Article # 258102. https://doi.org/10.1103/PhysRevLett.113.258102

  48. Dixit Gauri, Kelley J.B., Houser J.R., Elston T.C., Dohlman H.G.: Cellular Noise Suppression by the Regulator of G Protein Signaling Sst2. Molecular Cell, Vol. 55, no. 1, 2014, pp. 85 – 96. http://dx.doi.org/10.1016/j.molcel.2014.05.019

  49. Schwabe A., Bruggeman F.J.: Contributions of Cell Growth and Biochemical Reactions to Nongenetic Variability of Cells. Biophysical Journal, Vol. 107, no. 2, 2014, pp. 301 – 313. https://doi.org/10.1016/j.bpj.2014.05.004

  50. 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

  51. 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

  52. Toner D.L.K., Grima R.: Molecular noise induces concentration oscillations in chemical systems with stable node steady states. The Journal of Chemical Physics, Vol. 138, 2013, Article # 055101. DOI 10.1063/1.4788979 PMID: 23406149

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  55. 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

  56. 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

  57. 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

  58. 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

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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.

  70. 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

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  72. 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

  73. 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

  74. 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

  75. 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

  76. 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

  77. 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

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  79. Eldar A., Elowitz M.B.: Functional roles for noise in genetic circuits. Nature, Vol. 467, 2010, pp. 167 – 173. DOI 10.1038/ nature09326.

  80. 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

  81. 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

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  85. 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

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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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