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                                                    NOISE in GENE EXPRESSION

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. Gomez D., Marathe R., Bierbaum V., Klumpp S.: Modeling stochastic gene expression in growing cells. Journal of theoretical biology, Vol. 348, 2014, pp. 1 – 11. DOI 10.1016/j.jtbi.2014.01.017

  2. Arbel-Goren R., Tal A., Stavans J.: Phenotypic noise: effects of post-transcriptional regulatory processes affecting mRNA. Wiley Interdisciplinary Reviews-RNA, Vol. 5, no. 2, 2014, pp. 197 – 207. DOI 10.1002/wrna.1209

  3. Rieckh G., Tkacik G.: Noise and Information Transmission in Promoters with Multiple Internal States. Biophysical Journal, Vol. 106, no. 5, 2014, pp. 1194 – 1204. DOI 10.1016/j.bpj.2014.01.014

  4. Dey G., Gupta G.D., Ramalingam B., Sathe M., Mayor S., Thattai M.: Exploiting Cell-To-Cell Variability To Detect Cellular Perturbations. PLoS One, Vol. 9, no. 3, 2014, Article # e90540. DOI 10.1371/journal.pone.0090540

  5. Bajikar S.S., Fuchs C., Roller A., Theis F., Janes K. A.: Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles. Proc. of the National Acad. of Sciences of the USA, Vol. 111, no. 5, 2014, pp. E626 – E635. DOI 10.1073/pnas.1311647111

  6. Maity A.K., Bandyopadhyay A., Chaudhury P., Banik S.K.: Role of functionality in two-component signal transduction: A stochastic study. Physical Review E, Vol. 89, no. 3, 2014, Article # 032713. DOI 10.1103/PhysRevE.89.032713

  7. Yvinec R., Zhuge Changjing, Lei Jinzhi, Mackey M.C.: Adiabatic reduction of a model of stochastic gene expression with jump Markov process. Journal of Mathematical Biology, Vol. 68, no. 5, 2014, pp. 1051 – 1070. DOI 10.1007/s00285-013-0661-y

  8. Bhattacharyya B., Kalay Z.: Distribution of population-averaged observables in stochastic gene expression. Physical Review E, Vol. 89, no. 1, 2014, Article # UNSP 012715. DOI 10.1103/PhysRevE.89.012715

  9. Zhang Jiajun, Zhou Tianshou: Promoter-mediated Transcriptional Dynamics. Biophysical Journal, Vol. 106, no. 2, 2014, pp. 479 – 488. DOI 10.1016/j.bpj.2013.12.011

  10. ten Wolde P.R., Mugler A.: Importance of crowding in signaling, genetic, and metabolic networks. Int. Rev. of Cell and Molecular Biology, Vol. 307, 2014, pp. 419 – 442. DOI 10.1016/B978-0-12-800046-5.00012-6

  11. Monteoliva D., McCarthy C.B., Diambra L.: Noise Minimisation in Gene Expression Switches. PLoS One, Vol. 8, no. 12, 2013, Article # e84020. DOI 10.1371/journal.pone.0084020

  12. Boettiger A.N.: Analytic Approaches to Stochastic Gene Expression in Multicellular Systems. Biophysical Journal, Vol. 105, no. 12, 2013, pp. 2629 – 2640. DOI 10.1016/j.bpj.2013.10.033

  13. Sanchez A., Golding I.: Genetic Determinants and Cellular Constraints in Noisy Gene Expression. Science, Vol. 342, no. 6163, 2013, pp. 1188 – 1193. DOI 10.1126/science.1242975

  14. Innocentini G.D.P., Forger M., Ramos A.F., Radulescu O., Hornos J.E.M.: Multimodality and Flexibility of Stochastic Gene Expression. Bulletin of Mathematical Biology, Vol. 75, no. 12, 2013, pp. 2600 – 2630. DOI 10.1007/s11538-013-9909-3

  15. Hansen A.S., O'Shea E.K.: Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression. Molecular Systems Biology, Vol. 9, 2013, Article # 704. DOI 10.1038/msb.2013.56

  16. Thomas P., Matuschek H., Grima R.: How reliable is the linear noise approximation of gene regulatory networks? BMC Genomics, Vol. 14, S4, 2013, Article # S5. DOI 10.1186/1471-2164-14-S4-S5

  17. Maity A.K., Bandyopadhyay A., Chattopadhyay S., Chaudhuri J.R., Metzler R., Chaudhury P., Banik S.K.: Quantification of noise in bifunctionality-induced post-translational modification. Physical Review E, Vol. 88, no. 3, 2013, Article # 032716. DOI 10.1103/PhysRevE.88.032716

  18. Lillacci G., Khammash M.: The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations. Bioinformatics, Vol. 29, no. 18, 2013, pp. 2311 – 2319. DOI 10.1093/bioinformatics/btt380

  19. Little S.C., Tikhonov M., Gregor T.: Precise Developmental Gene Expression Arises from Globally Stochastic Transcriptional Activity. CELL, Vol. 154, no. 4, 2013, pp. 789 – 800. DOI 10.1016/j.cell.2013.07.025

  20. Assaf M., Roberts E., Luthey-Schulten Z., Goldenfeld N.: Extrinsic Noise Driven Phenotype Switching in a Self-Regulating Gene. Physical Review Lett., Vol. 111, no. 5, 2013, Article # 058102. DOI 10.1103/PhysRevLett.111.058102

  21. Vilar J.M.G., Saiz L.: Systems Biophysics of Gene Expression. Biophysical Journal, Vol. 104, no. 12, 2013, pp. 2574 – 2585. DOI 10.1016/j.bpj.2013.04.032

  22. Hebenstreit D.: Are gene loops the cause of transcriptional noise? Trends in Genetics, Vol. 29, no. 6, 2013, pp. 333 – 338. DOI 10.1016/j.tig.2013.04.001

  23. Pendar H., Platini T., Kulkarni R.V.: Exact protein distributions for stochastic models of gene expression using partitioning of Poisson processes. Physical Review E, Vol. 87, no. 4, 2013, Article # 042720. DOI 10.1103/PhysRevE.87.042720

  24. Espinar L., Dies M., Cagatay T., Sueel G.M., Garcia-Ojalvo J.: Circuit-level input integration in bacterial gene regulation. Proc. of the National Acad. of Sciences of the USA, Vol. 110, no. 17, 2013, pp. 7091 – 7096. DOI 10.1073/pnas.1216091110

  25. Nishino Ryota, Sakaue Takahiro, Nakanishi Hiizu: Transcription Fluctuation Effects on Biochemical Oscillations. PLoS One, Vol. 8, no. 4, 2013, Article # e60938. DOI 10.1371/journal.pone.0060938

  26. Carey L.B., van Dijk D., Sloot P.M.A., Kaandorp J.A., Segal E.: Promoter Sequence Determines the Relationship between Expression Level and Noise. PLoS Biology, Vol. 11, no. 4, 2013, Article # e1001528. DOI 10.1371/journal.pbio.1001528

  27. Hormoz S.: Cross Talk and Interference Enhance Information Capacity of a Signaling Pathway. Biophysical Journal, Vol. 104, no. 5, 2013, pp. 1170 – 1180. DOI 10.1016/j.bpj.2013.01.033

  28. Xu Yong, Feng Jing, Li JuanJuan, Zhang Huiqing: Levy noise induced switch in the gene transcriptional regulatory system. Chaos, Vol. 23, no. 1, 2013, Article # 013110. DOI 10.1063/1.4775758

  29. Neuert G., Munsky B., Tan Rui Zhen, Teytelman L., Khammash M., van Oudenaarden A.: Systematic Identification of Signal-Activated Stochastic Gene Regulation. Science, Vol. 339, no. 6119, 2013, pp. 584 – 587. DOI 10.1126/science.1231456

  30. Jaruszewicz J., Zuk P.J., Lipniacki T.: Type of noise defines global attractors in bistable molecular regulatory systems. Journal of Theoretical Biology, Vol. 317, 2013, pp. 140 – 151. DOI 10.1016/j.jtbi.2012.10.004

  31. Yan Ching-Cher Sanders, Hsu Chao-Ping: The fluctuation-dissipation theorem for stochastic kinetics-Implications on genetic regulations. Journal of Chemical Physics, Vol. 139, no. 22, 2013, Article # 224109. DOI 10.1063/1.4837235

  32. Choubey S., Kondev J., Sanchez A.: Regulation of noise in gene expression. Annual Review of Biophysics, Vol. 42, no. 1, 2013, pp. 469 – 491. DOI 10.1146/annurev-biophys-083012-130401

  33. Padovan-Merhar O., Raj A.: Using variability in gene expression as a tool for studying gene regulation. Wiley Interdisciplinary Reviews-Systems Biology and Medicine,  Vol. 5, no. 6, 2013, pp. 751 – 759. DOI 10.1002/wsbm.1243

  34. Flores K.B.: A structured population modeling framework for quantifying and predicting gene expression noise in flow cytometry data. Applied Mathematical Modelling, Vol. 26, no. 7, 2013, pp. 794 – 798. DOI 10.1016/j.aml.2013.03.003

  35. Wu Jincheng, Tzanakakis E.S.: Deconstructing stem cell population heterogeneity: Single-cell analysis and modeling approaches. Biotechnology Advances, Vol. 31, no. 7, SI, 2013, pp. 1047 – 1062. DOI 10.1016/j.biotechadv.2013.09.001

  36. Zhang Hui, Chen Yueling, Chen Yong: Noise Propagation in Gene Regulation Networks Involving Interlinked Positive and Negative Feedback Loops. PLoS One, Vol. 7, no. 12, 2012, Article # e51840. DOI 10.1371/journal.pone.0051840

  37. Venkata D.N., Vidya A., Sagar P., Kumar G., Viswanathan G.A.: Noise Propagation in Two-Step Series MAPK Cascade. PLOS One, Vol. 7, no. 5, 2012, Article # e35958. DOI 10.1371/journal.pone.0035958

  38. R. Salari, D. Wojtowicz, Jie Zheng, D. Levens, Y. Pilpel,T. M. Przytycka: Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression. PLoS Computational Biology, Vol. 8, no. 8, 2012, Article # e1002644. DOI 10.1371/journal.pcbi.1002644

  39. Grima R., Schmidt D., Newman T.J. : Steady-state fluctuations of a genetic feedback loop: an exact solution. Journal of Chemical Physics, Vol. 137, 2012, pp. 035104.  DOI 10.1063/1.4736721

  40. Zhu Hongyuan, Chen Tianqi, Lei Xue, Tian Wei, Cao Youfang, Ao Ping: Understand the noise of CI expression in phage λ lysogen. 31st Chinese Control Conference (CCC), 2012, pp. 7432 – 7436. URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6391256&isnumber=6389889

  41. Yong Zhang, Peng Li, Huang G.M.: Quantifying Dynamic Stability of Genetic Memory Circuits. IEEE/ACM Trans. on Computational Biology and Bioinformatics, Vol. 9, no. 3, 2012, pp. 871 – 884. DOI 10.1109/TCBB.2011.132

  42. Filkov V.: Invited: Identifying mutations from TILLING experiments. IEEE 2nd Int. Conf on Computational Advances in Bio and Medical Sciences (ICCABS), pp.1, 2012 DOI 10.1109/ICCABS.2012.6182620

  43. Kyung H. Kim, H. M. Sauro : Adjusting Phenotypes by Noise Control. PLOS Computational Biology, Vol. 8, no. 1, 2012. DOI 10.1371/journal.pcbi.1002344

  44. Gutierrez P.S., Monteoliva D., Diambra L.: Cooperative Binding of Transcriptional Factors Promotes Bimodal Gene Expression Response. PLoS One, Vol. 7, no. 9, 2012, Article # e44812. DOI 10.1371/journal.pone.0044812

  45. Hai Ling, Zhangqing Zhu, Chunlin Chen: Dynamics of genetic regulatory networks with delays. IEEE Int. Conf. on Networking, Sensing and Control (ICNSC), 2012, pp. 310 – 315. DOI 10.1109/ICNSC.2012.6204936

  46. Nacher J. C, Ryabov V.B.: Nonlinear response of gene expression to chemical perturbations: A noise-detector model and its predictions. BioSystems, 2011. DOI 10.1016/j.biosystems.2011.08.002

  47. Vladimir P. Zhdanov : Periodic perturbation of the bistable kinetics of gene expression. Physica A : Statistical Mecanics and its Applications, 2011, Vol. 390, no. 1, pp. 57 – 64. DOI 10.1016/j.physa2010.03.036

  48. Holloway D.M., Spirov A.V.: Gene expression noise in embryonic spatial patterning: Reliable formation of the head-to-tail axis in the fruit fly. 21st Int. Conf. on Noise and Fluctuations (ICNF), 12-16 June 2011, pp 495 – 498. DOI 10.1109/ICNF.2011.5994379

  49. Singh A. Genetic negative feedback circuits for filtering stochasticity in gene expression. IEEE Conf. on Decision and Control and European Control Conference (CDC-ECC), 2011, pp. 4366 – 4370. DOI 10.1109/CDC.2011.6160746

  50. Singh A.: Negative Feedback Through mRNA Provides the Best Control of Gene-Expression Noise. IEEE Trans on NanoBioscience, Vol. 10, no. 3, 2011, pp. 194 – 200. DOI 10.1109/TNB.2011.2168826

  51. Pan Wei, Wang Zidong, Hu Jun, Gao Huijun: Robust stability of genetic regulatory networks with interval time-varying delays under intrinsic and extrinsic noises. 29th Chinese Control Conference (CCC), 2010, pp. 6245 – 6250. URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5573006&isnumber=5571954

  52. R. Guantes, J. Estrada, J. F. Poyatos: Trade-offs and Noise Tolerance in Signal Detection by Genetic Circuits. PLoS ONE, Vol. 5, no 8, 2010, e12314. doi:10.1371/journal.pone.0012314. http://www.uam.es/personal_pdi/icmnc/rguantes/papers/PLoS1_javi.pdf

  53. Nir Friedman, Long Cai, X. Sunney Xie: Stochasticity in Gene Expression as Observed by Single-molecule Experiments in Live Cells. Israel Journal of Chemistry, Vol. 49, no 3-4, 2010, pp 333 – 342. DOI: 10.1560/IJC.49.3

  54. D. Neems, S. T. Kosak: Turning down the volume on transcriptional noise. Nature Cell Biology, Vol. 12, 2010, pp 929 – 931. DOI 10.1038/ncb1010-929

  55. Eldar A, Elowitz M.B.: Functional roles for noise in genetic circuits. Nature, Vol. 467, no. 7312, 2010, pp. 167 – 173. DOI 10.1038/nature09326

  56. Jia Tao, Kulkarni Rahul V.: Post-Transcriptional Regulation of Noise in Protein Distributions during Gene Expression. Physical Review Lett., Vol. 105, no. 1, 2010,  Article # 018101. DOI: 10.1103/PhysRevLett.105.018101

  57. Jinzhi Lei: Stochasticity in single gene expression with both intrinsic noise and fluctuation in kinetic parameters. Journal of Theoretical Biology, Vol. 256, no 4, 2009, pp 485 – 492. DOI 10.1016/j.jtbi.2008.10.028

  58. Gutierrez P.S., Monteoliva D., Diambra L.: Role of Cooperative Binding on Noise Expression. Physical Review  E, Vol. 80, no. 7, 2009, Article # 011914. DOI 10.1103/PhysRevE.80.011914

  59. A. Singh, J.P. Hespanha: Optimal Feedback Strength for Noise Suppression in Autoregulatory Gene Networks. Biophysical Journal, Vol 96, no 10, 2009, pp 4013 – 4023. DOI 10.1016/j.bpj.2009.02.064

  60. Guoliang Wei, Zidong Wang, James Lam, Karl Fraser, Ganti Prasada Rao, Xiaohui Liu: Robust filtering for stochastic genetic regulatory networks with time-varying delay. Mathematical Biosciences, Vol. 220, no 2, 2009, pp 73 – 80. DOI:10.1016/j.mbs.2009.04.002

  61. Chen Bor-Sen, Yu-Te Chang, Yu-Chao Wang: Robust H-Stabilization Design in Gene Networks Under Stochastic Molecular Noises: Fuzzy-Interpolation Approach. IEEE Trans on Systems, Man, and Cybernetics, Part B: Cybernetics, Vol. 38, no. 1, 2008, pp. 25 – 42. DOI 10.1109/TSMCB.2007.906975

  62. Saiz L., Vilar J.M.G.: Protein-protein/DNA interaction networks: versatile macromolecular structures for the control of gene expression. IET Systems Biology, Vol. 2, no. 5, 2008, pp. 247 – 255. DOI 10.1049/iet-syb:20080091

  63. Ben Lehner: Selection to minimise noise in living systems and its implications for the evolution of gene expression. Molecular Systems Biology, Vol. 4; Article number 170, 2008. DOI 10.1038/msb.2008.11

  64. C. D. Cox, J. M. McCollum, M. S. Allen, R. D. Dar, M. L. Simpson: Using noise to probe and characterize gene circuits. PNAS, 2008. http://www.pnas.org/content/105/31/10809.full.pdf

  65. Zidong Wang, Fuwen Yang, Ho D.W.C., Swift S., Tucker A., Xiaohui Liu: Stochastic Dynamic Modeling of Short Gene Expression Time-Series Data. IEEE Trans on NanoBioscience, Vol. 7, no 1, 2008, pp 44 – 55. DOI 10.1109/TNB.2008.2000149

  66. J. M. Pedraza, J. Paulsson: Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression. Science, Vol. 319, no. 5861, 2008, pp. 339 – 343. DOI 10.1126/science.1144331 http://www.sciencemag.org/content/319/5861/339.abstract#aff-1

  67. J. J. Tabor, T. S. Bayer, Z. B. Simpson, M. Levy, A. D. Ellington: Engineering stochasticity in gene expression. Molecular Biosystems, Vol. 4, no 7, 2008, pp 754 – 761. DOI 10.1039/B801245H http://www.ncbi.nlm.nih.gov/pubmed/18563250

  68. Lestas I., Paulsson J., Ross N.E., Vinnicombe G.: Noise in Gene Regulatory Networks. IEEE Trans on Automatic Control, Vol. 53, special issue, 2008, pp 189 – 200. DOI 10.1109/TAC.2007.911347 

  69. Wang Junwei, Zhou Tianshou: Environmental noise-induced synchronized switching between gene states. 27th Chinese Control Conference, 2008, pp 399 – 403. DOI 10.1109/CHICC.2008.4605179

  70. B.S. Chen, W.S. Wu: Robust filtering circuit design for stochastic gene networks under intrinsic and extrinsic molecular noises. Mathematical Biosciences, Vol. 211, no. 2, 2008, pp. 342 – 355. DOI 10.1016/j.mbs.2007.11.002

  71. B. B. Kaufmann, A. Van Oudenaarden: Stochastic gene expression: from single molecules to the proteome. Current Opinion in Genetics & Development, Vol. 17, no 2, 2007, pp 107 – 112. doi:10.1016/j.gde.2007.02.007

  72. N. N. Batada, L. D. Hurst: Evolution of chromosome organization driven by selection for reduced gene expression noise. Nature Genetics, Vol 39, no 8, 2007, pp 945 – 949. DOI:10.1038/ng2071

  73. K. Kaneko: Evolution of robustness to noise and mutation in gene expression dynamics. PloS ONE, May 2007, no 5 | e434, pp 1 – 8. DOI 10.1371/journal.pone.0000434 http://chaos.c.u-tokyo.ac.jp/papers/bio1/kk2007robust.pdf

  74. N. Maheshri, Erin K. O’Shea: Living with Noisy Genes: How Cells Function Reliably with Inherent Variability in Gene Expression. Annual Review of Biophysics and Biomolecular Structure, Vol. 36, June 2007, pp 413 – 434. DOI: 10.1146/annurev.biophys.36.040306.132705

  75. S. Iyer-Biswas, F. Hayot, C. Jayaprakash: Transcriptional pulsing and consequent stochasticity in gene expression. Arxiv preprint, 2007. http://arxiv.org/PS_cache/arxiv/pdf/0711/0711.1141v1.pdf

  76. A. Bar-Even, J. Paulsson, N. Maheshri, M. Carmi, E. O'Shea, Y. Pilpel, N. Barka: Noise in protein expression scales with natural protein abundance. Nature Genetics, Vol 38, 2006, pp 636 – 643. DOI 10.1038/ng1807

  77. Longo D., J. Hasty: Imaging gene expression: tiny signals make a big noise. Nature Chemical Biology, Vol 2, no 4, 2006, pp 181 – 182. DOI 10.1038/nchembio0406-181

  78. M. Skipper: Synthetic biology: Building up a picture of gene regulation. Nature Reviews Genetics, Vol 7, 2006, pp 242 – 243. DOI 10.1038/nrg1844

  79. J. S. Mattick: The underworld of RNA. Nature Genetics, Vol 38, no 4, 2006, pp 393 – 393. ISSN 1061-4036

  80. C. Adami: Digital genetics: unravelling the genetic basis of evolution. Nature Reviews Genetics Vol. 7, 2006, pp 109 – 118. DOI 10.1038/nrg1771

  81. A. Martinez-Arias, P. Hayward: Filtering transcriptional noise during development: concepts and mechanisms. Nature Reviews Genetics, Vol 7, no 1, 2006, pp 34 – 44. PubMed 16369570

  82. D. W. Austin, M. S. Allen, J. M. McCollum, R. D. Dar, J. R. Wilgus, G. S. Sayler, N. F. Samatova, C. D. Cox, M. L. Simpson: Gene network shaping of inherent noise spectra. Nature, Vol 439, Letter, 2006, pp 608 – 611. DOI 10.1038/nature04194

  83. Baetz K, Kaern M.: Predictable trends in protein noise. Nature Genetics, Vol. 38, no. 6, 2006, pp. 610 – 611. DOI 10.1038/ng0606-610

  84. N. J. Guido, X. Wang, D. Adalsteinsson, D. McMillen, J. Hasty, C. R. Cantor, T. C. Elston, J. J. Collins: A bottom-up approach to gene regulation. Nature, Vol. 439, 16 February 2006, pp 856 – 860. DOI 10.1038/nature04473

  85. B.S. Chen, Y.C. Wang: On the attenuation and amplification of molecular noise in genetic regulatory netwoks. BMC Bioinformatics, Vol. 7, Article # 52, 2006. DOI 10.1186/1471-2105-7-52 http://www.biomedcentral.com/content/pdf/1471-2105-7-52.pdf

  86. M. Scott, B. Ingalls, M. Kaern: Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks. Chaos, Vol. 16, no 2, 2006, pp 026107 (15 pages). DOI 10.1063/1.2211787 http://ctbp.ucsd.edu/pubs/pdf/69.pdf

  87. S. Hooshangi, R. Weiss: The effect of negative feedback on noise propagation in transcriptional gene networks. Chaos, Vol. 16, no 2, 2006, pp 026108 (10 pages). DOI 10.1063/1.2208927

  88. P. S. Swain, A. Longtin: Noise in genetic and neural networks. Chaos, Vol. 16, no 2, 2006, pp 026101 (6 pages). DOI 10.1063/1.2213613 http://mysite.science.uottawa.ca/alongtin/chaos06.pdf

  89. C. D. Cox, J. M. McCollum, D. W. Austin, R. D. Dar, M. L. Simpson: Frequency domain analysis of noise in simple gene circuits. Chaos, Vol. 16, no 2, 2006, pp 026102 (15 pages). DOI 10.1063/1.2204354 http://www.phys.ufl.edu/~hagen/Readings/Chaos_16_026102.pdf

  90. L. S. Tsimring, D. Volfson, J. Hasty: Stochastically driven genetic circuits. Chaos, Vol. 16, no 2, 2006, pp 026103 (12 pages). DOI 10.1063/1.2209571 http://biodynamics.ucsd.edu/publications/chaos2006.pdf

  91. van Zon J.S., Morelli M.J., Tanase-Nicola S., ten Wolde P.R.: Diffusion of transcription factors can drastically enhance the noise in gene expression. Biophysical Journal, Vol. 91, no. 12, 2006, pp. 4350 – 4367. DOI http://dx.doi.org/10.1529/biophysj.106.086157

  92. A. Van Oudenardeen: Stochastic gene expression: from prokaryotes to eukaryotes and from steady-state to out-of-equilibrium. Talk, 2006

  93. Pedraza J.M., van Oudenaarden A.: Noise propagation in gene networks. Science, New Series, Vol. 307, no. 5717, 2005, pp. 1965 – 1969. DOI 10.1126/science.1109090

  94. W. J. Blake, J. J. Collins: And the noise played on: stochastic gene expression and HIV-1 Infection. Cell, Vol. 122, no 2, July 29 2005, pp 147 – 149. DOI 10.1016/j.cell.2005.07.006 http://journals2005.pasteur.ac.ir/CELL/122(2).pdf

  95. M. Kaern, T. C. Elston, W. J. Blake, J. J. Collins: Stochasticity in gene expression: from theories to phenotypes. Nature Reviews/Genetics, Vol. 6, June 2005, pp 451 – 464. DOI 10.1038/nrg1615 http://www.bu.edu/abl/files/stochasticity%20in%20gene.pdf

  96. J. M. Raser, E. K. O'Shea: Noise in gene expression. Origins, consequences and control. Science, Vol. 309, no 5743, 23 September 2005, pp 2010 – 2013. DOI 10.1126/science.1105891

  97. Becskei A., B. B Kaufmann, A. van Oudenaarden: Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nature Genetics, Vol 37, no 9, 2005, pp 937 – 944. DOI 10.1038/ng1616

  98. J. Paulsson: Prime movers of noisy gene expression. Nature Genetics, Vol. 37, no. 9, 2005, pp 925 – 926. DOI 10.1038/ng0905-925

  99. Paulsson J.: Summing up the noise in gene networks. Nature, Vol. 427, 2004, pp. 415 – 418. DOI 10.1038/nature02257

  100. Tao Y.: Intrinsic Noise, Gene Regulation and Steady-State Statistics in a Two-Gene Network. Journal of Theoretical Biology, Vol. 231, no. 4, 2004, pp. 563 – 568. DOI 10.1016/j.jtbi.2004.07.012

  101. J. Mason, P. S. Linsay, J. J. Collins: Evolving complex dynamics in electronic models of genetic networks. Chaos, Vol. 14, no. 3, 2004, pp 707 – 715. DOI http://www.bu.edu/abl/pdf/chaos_mason.pdf

  102. F. J. Isaacs, D. J. Dwyer, C. Ding, D. D. Pervouchine, J. J. Collins: Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology, Vol. 22, no. 7, July 2004, pp 841 – 847. DOI 10.1038/nbt986

  103. H. B. Fraser, A. E. Hirsh, G. Giaever, J. Kumm, M. B. Eisen: Noise minimization in eukaryotic gene expression. PloS Biology, Vol. 2, issue 6, June 2004, pp 0834 – 0838. http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020137#s3

  104. H. F. Nijhout: Stochastic gene expression: dominance, thresholds and boundaries. The Biology of Genetic Dominance, edited by R. A. Veitia, chapt. 8, 2004 Eurekah.com, pp 1 – 15. http://www.biology.duke.edu/nijhout/images/Veitia(Nijhout).pdf

  105. H. Kobayashi, M. Kaern, M. Araki, K. Chung, T. S. Gardner, C. R. Cantor, J. J. Collins: Programmable cells: Interfacing natural and engineered gene networks. PNAS, Vol. 101, no 22, June 1 2004, pp 8414 – 8419. DOI 10.1073/pnas.0402940101 http://www.bu.edu/abl/pdf/pnas_kobayashi.pdf

  106. Korobkova E., Emonet T., Vilar Jose M. G., Shimizu T. S., Cluzel P. : From molecular noise to behavioural variability in a single bacterium. Nature, Vol. 428, 2004, Letters to Editor, pp. 574 – 578. DOI 10.1038/nature02404

  107. El Samad H., Khammash M.: Stochastic stability and its application to the analysis of gene regulatory networks. IEEE Conf. on Decision and Control (CDC), Vol. 3, 2004, pp. 3001 – 3006. DOI 10.1109/CDC.2004.1428924

  108. El-Samad H., Khammash M.: Intrinsic noise rejection in gene networks by regulation of stability. Int. Symp.on Control, Communications and Signal Processing (ISCCSP), 2004, pp. 187 – 190. DOI 10.1109/ISCCSP.2004.1296252

  109. M. Krn,W. J. Blake, J.J. Collins: The engineering of gene regulatory networks. Annual Reviews Biomed. Eng., 2003, pp 179 – 206. DOI 10.1146/annurev.bioeng.5.040202.121553 http://complex.upf.es/~andreea/2006/Bib/Kaern.EngineeringGeneRegulatoryNetworks.Review.pdf

  110. J. M. Lewsky, R. H. Singer: Gene expression and the myth of the average cell. Trends in Cell Biology, Vol. 13, no 1, January 2003, pp 4 – 6. DOI 10.1016/S0962-8924(02)00002-8 http://singerlab.aecom.yu.edu/publications/pdf/SL0301.pdf

  111. W. J. Blake, M. Kaern, C. R. Cantor, J. J. Collins: Noise in eukaryotic gene expression. Nature, Vol. 42, 10 April 2003, pp 633 – 637. DOI 10.1038/nature01546 http://128.197.26.35/cab/CAB%20PDF/Blake%20et%20al%20Nature%20'03.pdf

  112. E. M. Ozbudak, M. Thattai, I. Karstner, A. D. Grossman, A. van Oudenaarden: Regulation of noise in the expression of a single gene. Nature Genetics, Vol. 31, May 2002, pp 69 – 73. DOI 10.1038/ng869 http://www.nature.com/ng/journal/v31/n1/pdf/ng869.pdf

  113. M. B. Elowitz, A. J. Levine, E. D. Siggia, P. S. Swain: Stochastic gene expression in a single cell. Science, Vol. 297, 16 August 2002, pp 1183 – 1186. DOI 10.1126/science.1070919 http://www.google.fr/search?hl=fr&source=hp&q=+Stochastic+gene+expression+in+a+single+cell&aq=f&aqi=&aql=&oq=

  114. V. A. Kuznetsov, G. D. Knott, R. F. Bonner: General statistics of stochastic process of gene expression in eukaryotic cells. Genetics. Vol. 161, July 2002, pp 1321 – 1332. http://www.genetics.org/cgi/content/full/161/3/1321

  115. J. Hasty, D. McMillen, J. J. Collins: Engineered gene circuits. Nature. Vol. 420, 14  Nov. 2002, pp 224 – 230. DOI 10.1038/nature01257 http://chemlabs.nju.edu.cn/pub/Bio_BioChem_BioInfo/Engineered%20gene%20circuits.pdf

  116. Vilar J.M.G., Kueh H.Y., Barkai N., Leibler S.: Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci USA, Vol. 99, no. 9, 2002, pp. 5988 – 5992. DOI 10.1073/pnas.092133899

  117. J. Hasty, F. Isaacs, M. Dolnik, D. McMillen, J. J. Collins: Designer gene networks: Towards fundamental cellular control. Chaos, Vol. 11, no. 1, March 2001, pp 207 – 220. DOI 10.1063/1.1345702

  118. J. Hasty, D. McMillen, F. Isaacs, J. J. Collins: Computational studies of gene regulatory networks: in numero molecular biology. Nature Reviews - Genetics, Vol. 2, April 2001, pp 268 – 279. DOI 10.1038/35066056

  119. M. Thattai, A. van Oudenaarden: Intrinsic noise in gene regulatory networks. PNAS, Vol. 98, no. 15, July 3, 2001, pp 8614 – 8619. DOI 10.1073/pnas.151588598

  120. A. Wagemakers, J. M. Buldu, J. Garcia-Ojalvo, M. A. F. Sanjuan: Des circuits et des gnes. http://www.escet.urjc.es/~fisica/personal/jmbuldu/files/conf_06_wag_cr.pdf

  121. T. S. Gardner, J. J. Collins: Gene regulation: Neutralizing noise in gene networks. Nature, Vol. 405, 1 June 2000, pp 520 – 521. DOI 10.1038/35014708 http://www.bu.edu/abl/files/neutralizing_noise_in.pdf

  122. D. A. Hume: Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood, 1 Oct. 2000, Vol. 96, No. 7, pp 2323 – 2328. http://bloodjournal.hematologylibrary.org/cgi/content/full/96/7/2323

  123. J. Hasty, J. Pradines, M. Dolnik, J. J. Collins: Noise-based switches and amplifiers for gene expression. PNAS, Feb. 29, 2000, Vol. 97, no. 5, pp 2075 – 2080. DOI http://www.pnas.org/content/97/5/2075.full.pdf

  124. T. S. Gardner, C. R. Cantor, J. J. Collins: Construction of a genetic toggle switch in Escherichia coli. Nature, Vol. 403, no 6767, 20 Jan. 2000, pp 339 – 342. DOI 10.1038/35002131

  125. H.H. McAdams, A. Arkin: It's a noisy business! Genetic regulation at the nanomolar scale. TIG, vol. 15, No. 2, February 1999, pp 65 – 69. doi:10.1016/S0168-9525(98)01659-X

  126. H. H. McAdams, A. Arkin: Stochastic mechanisms in gene expression. PNAS, Biochemistry, Vol. 94, February 1997, pp 814 – 819. DOI 10.1073/pnas.94.3.814

 

Links:

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

http://papers.cnl.salk.edu/PDFs/

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

 

 


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