Specificity of Bionoise

Glossary Bio
Acronyms Bio

                                                   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. Tsuruyama T.: Information Thermodynamics Derives the Entropy Current of Cell Signal Transduction as a Model of a Binary Coding System. Entropy, 2018, Vol. 20, no. 2, pp. 145 – 153. DOI 10.3390/e20020145

  2. Smith Stephen, Grima Ramon: Single-cell variability in multicellular organisms. Nature Communications, Vol. 9, 2018, Article # 345. DOI 10.1038/s41467-017-02710-x

  3. Sakurai Yuta, Hori Yutaka: Optimization-based synthesis of stochastic biocircuits with statistical specifications. Journal of the Royal Society Interface, Vol. 15, no. 138, 2018, Article # 20170709. DOI 10.1098/rsif.2017.0709

  4. Jingyu Zhang, Xiao-Jun Tian, Yi-Jiun Chen, Weikang Wang, Simon Watkins, Jianhua Xing: Pathway crosstalk enables cells to interpret TGF-β duration. NPJ Systems Biology & Applications, Vol. 4, no. 18, 2018. DOI 10.1038/s41540-018-0060-5

  5. Sardanyes J., Andreu Arderiu, Santiago E.F., et al.: Noise-induced bistability in the quasi-neutral coexistence of viral RNAs under different replication modes. Journal of the Royal Society Interface, Vol. 15, no. 142, 2018, Article # 20180129. DOI 10.1098/rsif.2018.0129

  6. Amir Ariel, Balaban Nathalie Q.: Learning from Noise: How Observing Stochasticity May Aid Microbiology. Trends in Microbiology, Vol. 26, no. 4, 2018, pp. 376 – 385. DOI 10.1016/j.tim.2018.02.003

  7. Po-Yi Ho, Jie Lin, Ariel Amir: Modeling cell size regulation: From single-cell level statistics to molecular mechanisms and population level effects. Annual Review of Biophysics, Vol. 47, 2018, pp. 251 – 271. DOI 10.1146/annurev-biophys-070317-032955.

  8. Mitchell S., Roy Koushik, Zangle T.A., et al.: Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation. PNAS, Vol. 115, no. 12, 2018, pp. E2888 – E2897. DOI 10.1073/pnas.1715639115

  9. Li Ren, Zhou Mingxing, Yue Chunyan, et al.: Multiple single cell screening and DNA MDA amplification chip for oncogenic mutation profiling. LAB on a Chip, Vol. 18, no. 5, 2018, pp. 723 – 734. DOI 10.1039/c7lc00924k

  10. Mayer M., Arrizabalaga O., Lieb F., et al.: Electrophysiological investigation of human embryonic stem cell derived neurospheres using a novel spike detection algorithm. Biosensors & Bioelectronics, Vol. 100, 2018, pp. 462 – 468. DOI 10.1016/j.bios.2017.09.034

  11. Sanyour H., Childs J., Meininger G.A., et al.: Spontaneous oscillation in cell adhesion and stiffness measured using atomic force microscopy. Scientific Reports, Vol. 8, 2018, Article # 2899. DOI 10.1038/s41598-018-21253-9

  12. Fatehi F., Kyrychko S.N., Ross A., et al.: Stochastic Effects in Autoimmune Dynamics. Frontiers in Physiology, Vol. 9, 2018, Article # 45. DOI 10.3389/fphys.2018.00045

  13. Blum C.F., Heramvand N., Khonsari A.S., et al.: Experimental noise cutoff boosts inferability of transcriptional networks in large-scale gene-deletion studies. Nature Communications, Vol. 9, 2018, Article # 133. DOI 10.1038/s41467-017-02489-x

  14. Li Ren, Zhou Mingxing, Li Jine, et al.: Identifying EGFR-Expressed Cells and Detecting EGFR Multi-Mutations at Single-Cell Level by Microfluidic Chip. Nano-Micro Letters, Vol. 10, no. 1, 2018, Article # 16. DOI 10.1007/s40820-017-0168-y

  15. Lück A., Klimmasch L., Großmann P., Germerodt S., Kaleta C.: Computational Investigation of Environment-Noise Interaction in Single-Cell Organisms: The Merit of Expression Stochasticity Depends on the Quality of Environmental Fluctuations. Scientific Reports, Vol. 8, 2018, Article # 333. DOI 10.1038/s41598-017-17441-8

  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

  17. Cardarelli Francesco: Spatiotemporal Fluctuation Analysis of Molecular Diffusion Laws in Live-Cell Membranes. Methods in Molec. Biology, Vol. 1702, 2018, pp. 277 – 290. DOI 10.1007/978-1-4939-7456-6_13

  18. Earnest T.M., Cole J.A., Luthey-Schulten Z.: Simulating biological processes: stochastic physics from whole cells to colonies. Reports on Progress in Physics, Vol. 81, no. 5, 2018, Article # 052601. DOI 10.1088/1361-6633/aaae2c

  19. Monti Michele, Lubensky D.K., Pieter Rein ten Wolde: Optimal entrainment of circadian clocks in the presence of noise. Physical Review E, Vol. 97, no. 3, 2018, Article # 032405. DOI 10.1103/PhysRevE.97.032405

  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

  21. Bose Indrani, Pal Mainak: Criticality in cell differentiation. Journal of Biosciences, Vol. 42, no. 4, 2017, pp. 683 – 693. DOI 10.1007/s12038-017-9721-6

  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

  25. Fan Yongqiang, Evans C.R., Barber K.W., et al.: Heterogeneity of Stop Codon Readthrough in Single Bacterial Cells and Implications for Population Fitness. Molecular Cell, Vol. 67, no. 5, 2017, pp. 826 – 836. DOI 10.1016/j.molcel.2017.07.010

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

  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

  28. Jia Dongya, Jolly Mohit Kumar, Kulkarni Prakash, et al.: Phenotypic Plasticity and Cell Fate Decisions in Cancer: Insights from Dynamical Systems Theory. Cancers, Vol. 9, no. 7, 2017, Article # 70. DOI 10.3390/cancers9070070

  29. Aryaman Juvid, Hoitzing Hanne, Burgstaller Joerg P., et al.: Mitochondrial heterogeneity, metabolic scaling and cell death. Bioessays, Vol. 39, no. 7, 2017, Article # 1700001. DOI 10.1002/bies.201700001

  30. Harton Marie D., Batchelor Eric: Determining the Limitations and Benefits of Noise in Gene Regulation and Signal Transduction through Single Cell, Microscopy-Based Analysis. Journal of Molecular Biology, Vol. 429, no. 8, 2017, pp. 1143 – 1154. DOI 10.1016/j.jmb.2017.03.007

  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

  32. Ziegenhain C., Vieth B., Parekh Swati, et al.: Comparative Analysis of Single-Cell RNA Sequencing Methods. Molecular Cell, Vol. 65, no. 4, 2017, pp. 631 – 643. DOI 10.1016/j.molcel.2017.01.023

  33. Tung Po-Yuan, Blischak John D., Hsiao Chiaowen Joyce, et al.: Batch effects and the effective design of single-cell gene expression studies. Scientific Reports, Vol. 7, 2017, Article # 39921. DOI 10.1038/srep39921

  34. Inna Averbukh, Avishai Gavish, Ben-Zion Shilo, Naama Barkai: Dealing with noise: The challenge of buffering biological variability. Current Opinion in Systems Biology, Vol. 1, 2017, pp. 69 – 74. DOI 10.1016/j.coisb.2016.12.011

  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

  37. Barnhart E.L., Allard J., Lou Sunny S., Theriot J.A., Mogilne A.: Adhesion-Dependent Wave Generation in Crawling Cells. Current Biology, Vol. 27, no. 1, 2017, pp. 27 – 38. DOI 10.1016/j.cub.2016.11.011

  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

  48. Sabass B., Koch M.D., Liu Guannan, Stone H.A., Shaevitz J.W.: Force generation by groups of migrating bacteria. PNAS, 2017. Vol. 114, no. 28, pp. 7266 – 7271. DOI 10.1073/pnas.1621469114

  49. Bartley B.A., Kyung Kim, Medley J. K., Sauro H.M.: Synthetic Biology: Engineering Living Systems from Biophysical Principles. Biophysical Journal, Vol. 112, no. 6, 2017, pp. 1050 – 1058. DOI 10.1016/j.bpj.2017.02.013

  50. Shaffer S.M., Dunagin M.C., Torborg S.R., et al.: Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Nature, Vol. 546, 2017, pp. 431 – 435. DOI 10.1038/nature22794

  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.

  65. 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

  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

  105. 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

  106. 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 PMID: 23831270

  107. 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

  108. 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

  109. 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

  110. 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

  111. 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

  112. 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

  113. 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

  114. 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

  115. 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

  116. 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

  117. 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

  118. 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

  119. 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

  120. 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

  121. 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

  122. 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.

  123. 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

  124. 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

  125. 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

  126. 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

  127. 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

  128. 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

  129. 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

  130. 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

  131. Lestas I., Vinnicombe G., Paulsson J.: Fundamental limits on the suppression of molecular fluctuations. Nature, Vol. 467, 2010, pp. 174 – 178. DOI 10.1038/nature09333.

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

  133. 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

  134. 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

  135. Ping Ao, D. Galas, L. Hood, X.M. Zhu: Cancer as Robust Intrinsic State of Endogenous Molecular-Cellular Network Shaped by Evolution. Medical Hypotheses, Vol. 70, no. 3, 2008, pp. 678 – 684. http://www.sciencedirect.com/science/article/pii/S0306987707004343

  136. 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

  137. Gosak M., Marhl M., Perc M.: Chaos out of internal noise in the collective dynamics of diffusively coupled cells. The European Physical Journal, Vol. B 62, no. 2, 2008, pp. 171 – 177. https://doi.org/10.1140/epjb/e2008-00132-y

  138. Gürol M. Süel, Rajan P. Kulkarni, Jonathan Dworkin, Jordi Garcia-Ojalvo, M.B. Elowitz: Tunability and Noise Dependence in Differentiation Dynamics. Science, Vol. 315, no. 5819, 2007, pp. 1716 – 1719. DOI 10.1126/science.1137455

  139. 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

  140. 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

  141. 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

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

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

  144. 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

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

  146. 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

  147. 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

  148. 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

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

  150. 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


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



Copyright 2010 © UNESCO - All Rights Reserved.