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margaritis's fluctuations [68 articles]

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  • Colored extrinsic fluctuations and stochastic gene expression
    Mol Syst Biol, Vol. 4 (6 May 2008)
    by Vahid Shahrezaei, Julien F Ollivier, Peter S Swain
    posted to theory stochastic_simulations stochasticity noise fluctuations extrinsic by margaritis on 2008-05-07 11:47:21 as ** along with 2 people Ema jjray
  • Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression
    Science, Vol. 319, No. 5861. (18 January 2008), pp. 339-343.
    by Juan M Pedraza, Johan Paulsson
    posted to bursting fluctuations gene-expression noise stochasticity by margaritis on 2008-01-18 11:07:20 as ***** along with 7 people ddcttrl balicea cjeans heliopais roys sb_journal_club rschulz
  • Fluctuations, pauses and backtracking in DNA transcription
    Biophys. J. (24 August 2007), biophysj.107.105767.
    by Margaritis Voliotis, Netta Cohen, Carmen Molina-Paris, Tanniemola Liverpool
    posted to backtracking fluctuations noise stochasticity transcription by margaritis on 2008-01-09 11:22:22 as ****
  • Dynamical quorum sensing: Population density encoded in cellular dynamics
    Proceedings of the National Academy of Sciences, Vol. 104, No. 47. (20 November 2007), pp. 18377-18381.
    by Silvia De Monte, Francesco D'ovidio, Sune Dano, Preben G Sorensen
    posted to fluctuations population_density quorum_sensing by margaritis on 2007-11-21 11:04:41 as *****
  • Molecular level stochastic model for competence cycles in Bacillus subtilis
    Proceedings of the National Academy of Sciences, Vol. 104, No. 45. (6 November 2007), pp. 17582-17587.
    by Daniel Schultz, Ben, Jose N Onuchic, Peter G Wolynes
    posted to bsubtilis competence fluctuations noise stochasticity by margaritis on 2007-11-07 17:44:50 as *** along with 3 people jjray balabu lshaw
  • Dissecting Timing Variability in Yeast Meiosis
    Cell, Vol. 131, No. 3. (2 November 2007), pp. 544-556.
    by Iftach Nachman, Aviv Regev, Sharad Ramanathan
    posted to experiment fluctuations meiosis noise stochasticity yeast by margaritis on 2007-11-07 17:36:48 as ***** along with 2 people and 1 group dpollard balabu EisenLab
  • Living with noisy genes: how cells function reliably with inherent variability in gene expression.
    Annu Rev Biophys Biomol Struct, Vol. 36 (2007), pp. 413-434.
    by N Maheshri, EK O'Shea
    posted to fluctuations noise review stochasticity by margaritis on 2007-11-01 14:16:52 as ** along with 2 people jjray madhadron
  • Symmetry and Stochastic Gene Regulation
    Physical Review Letters, Vol. 99, No. 10. (2007)
    by Alexandre F Ramos, José EM Hornos
    posted to fluctuations gene-expression noise stochasticity theory by margaritis on 2007-10-05 12:40:56 as ***
  • Synchrony Dynamics During Initiation, Failure, and Rescue of the Segmentation Clock
    Science, Vol. 317, No. 5846. (28 September 2007), pp. 1911-1915.
    by Ingmar H Riedel-Kruse, Claudia Muller, Andrew C Oates
    posted to development fluctuations gene-networks noise robustness by margaritis on 2007-10-05 12:19:37 as *** along with 2 people balabu heliopais
  • Nonequilibrium Statistical Mechanics of Dividing Cell Populations
    Physical Review Letters, Vol. 99, No. 13. (2007)
    by Naama Brenner, Yair Shokef
    posted to cell_division fluctuations stochasticity theory by margaritis on 2007-09-28 16:31:45 as **
  • Living with Noisy Genes: How Cells unction Reliably with Inherent Variability in Gene Expression
    Annual Review of Biophysics and Biomolecular Structure, Vol. 36, No. 1., 413.
    by Maheshri
    posted to fluctuations noise review stochasticity by margaritis on 2007-09-07 13:33:15 as ***
  • A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks
    BMC Bioinformatics, Vol. 8 (24 May 2007), 175.
    by Asawari Samant, Babatunde A Ogunnaike, Dionisios G Vlachos
    posted to fluctuations noise stochasticity stochastic_simulations theory by margaritis on 2007-08-31 18:02:40 as ***
  • Combinatorial promoter design for engineering noisy gene expression
    PNAS (24 July 2007), 0608451104.
    by Kevin F Murphy, Gabor Balazsi, James J Collins
    posted to experiment fluctuations gene-expression noise stochasticity yeast by margaritis on 2007-08-01 12:17:17 as ***** along with 1 person jjray
  • Frequency domain analysis of noise in autoregulated gene circuits.
    Proc Natl Acad Sci U S A, Vol. 100, No. 8. (15 April 2003), pp. 4551-4556.
    by ML Simpson, CD Cox, GS Sayler
    posted to fluctuations gene-expression gene-networks noise spectra stochasticity theory by margaritis on 2007-07-13 17:00:59 as read along with 4 people marcio dylanwalker rklancer kfm9876
  • Attenuation of noise in ultrasensitive signaling cascades.
    Biophys J, Vol. 82, No. 6. (June 2002), pp. 2943-2950.
    by M Thattai, A van Oudenaarden
    posted to fluctuations gene-expression noise stochasticity theory by margaritis on 2007-07-13 14:12:10 as read
  • Noise in Gene Expression Determines Cell Fate in Bacillus subtilis.
    Science (14 June 2007)
    by Hédia Maamar, Arjun Raj, David Dubnau
    posted to bsubtilis experiment fluctuations noise stochasticity by margaritis on 2007-07-09 18:06:07 as *** along with 4 people jjray sebastien_vigneau cjeans cabbagezs
  • Stochastic gene expression as a many-body problem
    PNAS, Vol. 100, No. 5. (4 March 2003), pp. 2374-2379.
    by Masaki Sasai, Peter G Wolynes
    posted to fluctuations gene-expression noise stochasticity theory by margaritis on 2007-07-09 11:51:07 as ** along with 2 people ddcttrl malkocb
  • Signal Detection, Modularity, and the Correlation between Extrinsic and Intrinsic Noise in Biochemical Networks
    Physical Review Letters, Vol. 97, No. 6. (2006)
    by Sorin T Nicola, Patrick B Warren, Pieter
    posted to fluctuations gene-expression noise stochasticity theory by margaritis on 2007-07-09 11:48:45 as read
  • Noisy signal amplification in ultrasensitive signal transduction.
    Proc Natl Acad Sci U S A, Vol. 102, No. 2. (11 January 2005), pp. 331-336.
    by T Shibata, K Fujimoto
    posted to fluctuations gene-expression gene-networks noise stochasticity theory by margaritis on 2007-07-09 11:46:44 as read along with 3 people rklancer imouthesmp lingchong
  • Programmed population control by cell-cell communication and regulated killing.
    Nature, Vol. 428, No. 6985. (22 April 2004), pp. 868-871.
    by L You, RS Cox, R Weiss, FH Arnold
    posted to experiment fluctuations gene-expression gene-networks noise robustness stochasticity by margaritis on 2007-06-14 16:11:07 as ** along with 5 people rklancer tuck johncumbers dbikard discreteonyxorb
  • Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity.
    Cell, Vol. 122, No. 2. (29 July 2005), pp. 169-182.
    by LS Weinberger, JC Burnett, JE Toettcher, AP Arkin, DV Schaffer
    posted to experiment fluctuations gene-expression hiv noise stochasticity by margaritis on 2007-06-14 16:03:45 as ** along with 3 people rklancer lingchong balabu
  • Diffusion of transcription factors can drastically enhance the noise in gene expression.
    Biophys J, Vol. 91, No. 12. (15 December 2006), pp. 4350-4367.
    by JS van Zon, MJ Morelli, S Tănase-Nicola, PR ten Wolde
    posted to bursting fluctuations gene-expression noise simulations stochasticity theory by margaritis on 2007-06-11 11:23:37 as ** along with 3 people ddcttrl jjray balabu
  • Transient Dynamics of Genetic Regulatory Networks
    Biophys. J., Vol. 92, No. 10. (15 May 2007), pp. 3501-3512.
    by Matthew R Bennett, Dmitri Volfson, Lev Tsimring, Jeff Hasty
    posted to fluctuations gene-expression noise stochasticity theory by margaritis on 2007-06-11 11:17:17 as ** along with 3 people lshaw ibschwartz dylan77
  • Effective Temperature in Stochastic Kinetics and Gene Networks
    Biophys. J., Vol. 91, No. 1. (1 July 2006), pp. 84-94.
    by Ting Lu, Jeff Hasty, Peter G Wolynes
    posted to fluctuations gene-expression noise stochasticity theory by margaritis on 2007-06-11 11:16:43 as read along with 2 people ddcttrl kupopo
  • Eukaryotic Transcription: What Does It Mean for a Gene to Be 'on'?
    Current Biology, Vol. 16, No. 10. (23 May 2006), pp. R371-R373.
    by Ido Golding, Edward C Cox
    posted to bursting fluctuations noise stochasticity transcription by margaritis on 2007-05-06 17:42:32 as read along with 1 person and 1 group cmm FAB-lab
  • Noisy information processing through transcriptional regulation.
    Proc Natl Acad Sci U S A (9 April 2007)
    by Eric Libby, Theodore J J Perkins, Peter S S Swain
    posted to fluctuations information-theory noise stochasticity theory by margaritis on 2007-05-01 18:28:56 as ** along with 2 people jjray shigepong
  • Deterministic characterization of stochastic genetic circuits
    PNAS, Vol. 104, No. 18. (1 May 2007), pp. 7402-7407.
    by Matthew Scott, Terence Hwa, Brian Ingalls
    posted to fluctuations noise stochasticity theory by margaritis on 2007-05-01 18:21:12 as ** along with 2 people jjray balabu
  • Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.
    Biophys J, Vol. 81, No. 6. (December 2001), pp. 3116-3136.
    by TB Kepler, TC Elston
    posted to fluctuations noise stochasticity theory by margaritis on 2007-05-01 16:44:54 as *** along with 2 people monod jjray
  • Noise in a minimal regulatory network: plasmid copy number control.
    Q Rev Biophys, Vol. 34, No. 1. (February 2001), pp. 1-59.
    by J Paulsson, M Ehrenberg
    posted to fluctuations noise by margaritis on 2007-03-28 13:30:17 as **
  • An excitable gene regulatory circuit induces transient cellular differentiation
    Nature, Vol. 440, No. 7083., pp. 545-550.
    by Gã¼rol M Sã¼el, Jordi Garcia-Ojalvo, Louisa M Liberman, Michael B Elowitz
    posted to bsubtilis excitability fluctuations noise stochasticity by margaritis on 2007-03-26 12:15:42 as read along with 10 people and 1 group rklancer jjray alexg madhadron balabu nickluscombe comb dbikard mhucka paurue EBI-regulation
  • Tunability and Noise Dependence in Differentiation Dynamics
    Science, Vol. 315, No. 5819. (23 March 2007), pp. 1716-1719.
    by Gurol M Suel, Rajan P Kulkarni, Jonathan Dworkin, Jordi Garcia-Ojalvo, Michael B Elowitz
    posted to bsubtilis excitability fluctuations noise stochasticity by margaritis on 2007-03-26 11:55:59 as read along with 3 people and 2 groups jjray dbikard zwang Centre de Recherches Interdisciplinaires SynBioSys
  • Promoter Crosstalk Effects on Gene Expression
    Journal of Molecular Biology, Vol. 365, No. 4. (26 January 2007), pp. 911-920.
    by Mathias Hampf, Manfred Gossen
    posted to fluctuations noise promoter stochasticity by margaritis on 2007-03-08 21:03:13 as read along with 1 person jjray
  • Transcriptional Pulsing of a Developmental Gene
    Current Biology, Vol. 16, No. 10. (23 May 2006), pp. 1018-1025.
    by Jonathan R Chubb, Tatjana Trcek, Shailesh M Shenoy, Robert H Singer
    posted to bursting fluctuations gene-expression noise promoter stochasticity transcription by margaritis on 2007-03-08 21:00:34 as read along with 3 people and 1 group jjray emilyhare qfwills EisenLab
  • Regulated cell-to-cell variation in a cell-fate decision system.
    Nature, Vol. 437, No. 7059. (Sep 2005), pp. 699-706.
    by Colman A Lerner, A Gordon, E Serra, T Chin, O Resnekov, D Endy, CG Pesce, R Brent
    posted to fluctuations gene-expression noise stochasticity yeast by margaritis on 2007-03-08 20:47:47 as ** along with 1 person madhadron
  • Cell population heterogeneity during growth of Bacillus subtilis.
    Genes Dev, Vol. 19, No. 24. (15 December 2005), pp. 3083-3094.
    by DB Kearns, R Losick
    posted to bsubtilis fluctuations noise stochasticity by margaritis on 2007-03-08 20:46:12 as read along with 2 people madhadron mhucka
  • Stochastic gene expression: from single molecules to the proteome.
    Curr Opin Genet Dev (19 February 2007)
    by Benjamin B B Kaufmann, Alexander van Oudenaarden
    posted to fluctuations gene-expression noise review stochasticity by margaritis on 2007-03-08 20:34:36 as read along with 3 people brianb jjray madhadron
  • Stochastic mRNA Synthesis in Mammalian Cells
    PLoS Biology, Vol. 4, No. 10. (1 October 2006), e309.
    by Arjun Raj, Charles S Peskin, Daniel Tranchina, Diana Y Vargas, Sanjay Tyagi
    posted to bursting fluctuations noise stochasticity by margaritis on 2007-03-06 18:33:02 as read along with 7 people jjray nirfriedman madhadron balabu cottrell qfwills johncumbers
  • Random timing in signaling cascades
    Mol Syst Biol, Vol. 3 (13 February 2007)
    by Juan M Pedraza, Johan Paulsson
    posted to fluctuations noise stochasticity views by margaritis on 2007-02-13 16:22:20 as read
  • Filtering transcriptional noise during development: concepts and mechanisms
    Nature Reviews Genetics, Vol. 7, No. 1., pp. 34-44.
    by Alfonso M Arias, Penelope Hayward
    posted to fluctuations mrna noise review stochasticity by margaritis on 2007-01-15 11:21:41 as read along with 2 people and 1 group emilyhare dbikard EisenLab
  • Probing Gene Expression in Live Cells, One Protein Molecule at a Time
    Science, Vol. 311, No. 5767. (17 March 2006), pp. 1600-1603.
    by Ji Yu, Jie Xiao, Xiaojia Ren, Kaiqin Lao, Sunney X Xie
    posted to bursting experiment fluctuations gene-expression noise stochasticity by margaritis on 2007-01-10 14:09:10 as read along with 4 people dayjm balabu jiyu skoch3
  • Origins of extrinsic variability in eukaryotic gene expression
    Nature (21 December 2005)
    by Dmitri Volfson, Jennifer Marciniak, William J Blake, Natalie Ostroff, Lev S Tsimring, Jeff Hasty
    posted to yeast stochasticity noise gene-expression fluctuations experiment by margaritis on 2007-01-10 13:55:47 as read along with 6 people and 1 group jyuh bayesian dpollard balabu timflutre cjeans EisenLab
  • Intrinsic and extrinsic contributions to stochasticity in gene expression.
    Proc Natl Acad Sci U S A, Vol. 99, No. 20. (1 October 2002), pp. 12795-12800.
    by PS Swain, MB Elowitz, ED Siggia
    posted to theory stochasticity noise gene-expression fluctuations by margaritis on 2007-01-10 13:52:43 as read along with 5 people jjray JKelly555 madhadron balabu timflutre
  • Gene regulation at the single-cell level.
    Science, Vol. 307, No. 5717. (25 March 2005), pp. 1962-1965.
    by N Rosenfeld, JW Young, U Alon, PS Swain, MB Elowitz
    posted to stochasticity single-cell noise gene-expression fluctuations experiment by margaritis on 2007-01-10 13:48:44 as read along with 13 people rklancer snuppepuppan kentsis Toze bayesian balicea JKelly555 balabu comb mhucka timflutre csgillespie vladimirov
  • Stochastic gene expression in fluctuating environments.
    Genetics, Vol. 167, No. 1. (May 2004), pp. 523-530.
    by M Thattai, A van Oudenaarden
    posted to stochasticity noise gene-expression fluctuations by margaritis on 2007-01-10 13:39:46 as read along with 6 people rklancer jjray balabu dbikard mhucka timflutre
  • Contributions of low molecule number and chromosomal positioning to stochastic gene expression
    Nature Genetics, Vol. 37, No. 9. (07 August 2005), pp. 937-944.
    by Attila Becskei, Benjamin B Kaufmann, Alexander van Oudenaarden
    posted to stochasticity noise gene-expression fluctuations experiment by margaritis on 2007-01-10 13:37:17 as read along with 2 people rklancer cjeans
  • Predicting stochastic gene expression dynamics in single cells.
    Proc Natl Acad Sci U S A, Vol. 103, No. 19. (9 May 2006), pp. 7304-7309.
    by JT Mettetal, D Muzzey, JM Pedraza, EM Ozbudak, A van Oudenaarden
    posted to theory noise gene-expression fluctuations by margaritis on 2007-01-10 13:33:52 as read along with 5 people ddcttrl madhadron jiyu proulx dbikard
  • Regulation of noise in the expression of a single gene.
    Nat Genet, Vol. 31, No. 1. (May 2002), pp. 69-73.
    by EM Ozbudak, M Thattai, I Kurtser, AD Grossman, A van Oudenaarden
    posted to stochasticity noise gene-expression fluctuations experiment by margaritis on 2007-01-10 13:31:20 as read along with 8 people dylanwalker jiny rklancer rahmilale dbikard mhucka kfm9876 vladimirov
  • Intrinsic noise in gene regulatory networks.
    Proc Natl Acad Sci U S A, Vol. 98, No. 15. (17 July 2001), pp. 8614-8619.
    by M Thattai, A van Oudenaarden
    posted to stochasticity noise gene-expression fluctuations experiment by margaritis on 2007-01-10 13:30:13 as read along with 3 people jjray bayesian timflutre
  • Noise Propagation in Gene Networks
    Science, Vol. 307, No. 5717. (25 March 2005), pp. 1965-1969.
    by Juan M Pedraza, Alexander van Oudenaarden
    posted to stochasticity noise gene-networks gene-expression fluctuations experiment by margaritis on 2007-01-10 13:26:35 as read along with 12 people dylanwalker brianb jiny suizan rklancer snuppepuppan JKelly555 samal madhadron jiyu mhucka timflutre
  • Noise in Gene Expression: Origins, Consequences, and Control
    Science, Vol. 309, No. 5743. (23 September 2005), pp. 2010-2013.
    by Jonathan M Raser, Erin K O'Shea
    posted to stochasticity review noise gene-expression fluctuations by margaritis on 2007-01-10 13:24:05 as read along with 11 people and 2 groups kagibbs dylanwalker shikin rklancer monod dayjm xico nirfriedman koller mhucka suizan GeneGo WetBiology
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