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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)

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  16. Ludger J., Pezeshkian Weria, Ipsen J.H., Shillcock J.C.: Clustering on Membranes: Fluctuations and More. Trends in Cell Biology, Vol. 28, no. 5, 2018, pp. 405 – 415. DOI 10.1016/j.tcb.2018.01.009

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  20. Rupprecht J.-F., Amit Singh Vishen, Shivashankar G.V., Madan Rao, Prost J.: Maximal fluctuations of confined actomyosin gels: dynamics of the cell nucleus. Physical Review Lett., Vol. 120, 2018, Article # 098001. DOI 10.1103/PhysRevLett.120.098001

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  22. Li Hongying, Yao Chengli: The influence of internal noise on the detection of hormonal signal with the existence of external noise in a cell system. Applied Mathematics and Computation, Vol. 314, 2017, pp. 1 – 6. DOI 10.1016/j.amc.2017.06.021

  23. Faure A.J., Schmiedel J.M., Lehner B.: Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells. Cell Systems, Vol. 5, no. 5, 2017, pp. 471 – 484. DOI 10.1016/j.cels.2017.10.003

  24. 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

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  27. Almeira N., Risau-Gusman S.: Role of transcriptional bursts in cellular oscillations. Journal of Theoretical Biology, Vol. 426, 2017, pp. 49 – 56. DOI 10.1016/j.jtbi.2017.05.029

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  31. Chang Amy Y., Marshall Wallace F.: Organelles - understanding noise and heterogeneity in cell biology at an intermediate scale. Journal of Cell Science, Vol. 130, no. 5, 2017, pp. 819 – 826. DOI 10.1242/jcs.181024

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  35. Maike M.K. Hansen, Ravi V. Desai, Michael L. Simpson, Leor S. Weinberger: Cytoplasmic import and processing of mRNA amplify transcriptional bursts accounting for the majority of cellular noise. BioRxiv, 2017. DOI 10.1101/222901

  36. Colin R., Rosazza C., Vaknin A., Sourjik V.: Multiple sources of slow activity fluctuations in a bacterial chemosensory network. eLife, Vol. 6, 2017, Article # e26796. DOI 10.7554/eLife.26796

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  38. Bernitt Erik, Döbereiner Hans-Günther: Spatiotemporal Patterns of Noise-Driven Confined Actin Waves in Living Cells. Physical Review Lett., Vol. 118, no. 4, Article # 048102, 2017. DOI 10.1103/PhysRevLett.118.048102

  39. Evans Arthur A., Basanta Bhaduri, Popescu Gabriel, Levine A.J.: Geometric localization of thermal fluctuations in red blood cells. PNAS, Vol. 114, no. 11, 2017, pp. 2865 – 2870. DOI 10.1073/pnas.1613204114

  40. Ping Liu, Ruijie Song, Gregory L. Elison, Weilin Peng, Murat Acar: Noise reduction as an emergent property of single-cell aging. Nature Communications, Vol. 8, 2017, Article # 680. DOI 10.1038/s41467-017-00752-9

  41. Bizzarri M., Masiello M.G., Cucina A., Pensotti A.: Gravity constraint in cell phenotypic determination. Organisms – Journal of Biological Sciences, Vol. 1, no. 2, 2017, pp. 61 – 68. DOI 10.13133/2532-5876_2.8

  42. Fang-Yi Chu, Haley Shannon C., Zidovska Alexandra: On the origin of shape fluctuations of the cell nucleus. PNAS, Vol. 114, no. 39, 2017, pp. 10338 – 10343. DOI 10.1073/pnas.1702226114

  43. Arakelyan V.B., Danko V.P., Grigoryan R.P.: Influence of the External Noise Intensity on the Kinetics of Ligands Binding to Receptors. Journal of Contemporary Physics (Armenian Academy of Sciences), Vol. 52, no. 1, 2017, pp 70 –75. DOI 10.3103/S106833721701011X

  44. Naud Richard, Payeur Alexandre, Longtin André: Noise Gated by Dendrosomatic Interactions Increases Information Transmission. Physical Review X, Vol. 7, no. 3, 2017, Article # 031045. DOI 10.1103/PhysRevX.7.031045

  45. Arikta Biswas, Amal Alex, Bidisha Sinha: Mapping Cell Membrane Fluctuations Reveals Their Active Regulation and Transient Heterogeneities. Biophysical Journal, Vol. 113, no. 8, 2017, pp. 1768 – 1781. DOI 10.1016/j.bpj.2017.08.041

  46. Vasallo B.G., Galán-Prado F., Mateos J., González T., et al.: Stochastic model for action potential simulation including ion shot noise. Journal of Computational Electronics, Vol. 16, no. 2, 2017, pp 419 – 430. DOI 10.1007/s10825-017-0967-x

  47. García-Morales Vladimir, Manzanares José A., Mafe Salvador: Weakly coupled map lattice models for multicellular patterning and collective normalization of abnormal single-cell states. Physical Review E, Vol. 95, no. 4, 2017, Article # 042324. DOI 10.1103/PhysRevE.95.042324

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  51. Modi S., Vargas-Garcia C.A., Ghusinga K.R., Singh A.: Analysis of Noise Mechanisms in Cell-Size Control. Biophysical Journal, Vol. 112, no. 11, 2017, pp. 2408 – 2418. DOI 10.1016/j.bpj.2017.04.050

  52. 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

  53. 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

  54. 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

  55. Soltani M., Vargas-Garcia C.A., Antunes D., Singh A.: Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes. PLOS Computational Biology, Vol. 12, no. 8, 2016, Article # e1004972. DOI 10.1371/journal.pcbi.1004972

  56. Vargas-Garcia C.A., Soltani M., Singh A.: Conditions for Cell Size Homeostasis: A Stochastic Hybrid System Approach. IEEE Life Sciences Lett., Vol. 2, no. 4, 2016, pp. 47 – 50. DOI 10.1109/LLS.2016.2646383

  57. 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

  58. 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

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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.

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  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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

  73. 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

  74. 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

  75. 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

  76. 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

  77. 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

  78. 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

  79. 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

  80. 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

  81. 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

  82. 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

  83. 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

  84. 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

  85. 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

  86. 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

  87. 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

  88. 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

  89. 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

  90. 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

  91. 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

  92. 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

  93. 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

  94. 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

  95. 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

  96. 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

  97. 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

  98. 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

  99. 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

  100. 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

  101. 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

  102. 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

  103. 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

  104. 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

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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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