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jjray's library [567 articles]

Recent papers added to jjray's library.
  • How regulatory T cells work
    Nature Reviews Immunology, Vol. 8, No. 7., pp. 523-532.
    by Dario AA Vignali, Lauren W Collison, Creg J Workman
    posted to review regulatory_t_cell immunology by jjray on 2008-07-03 12:55:31 as ** along with 1 person AlfonsoVicenteSuarez
  • Noise in genetic and neural networks.
    Chaos, Vol. 16, No. 2. (June 2006)
    by PS Swain, A Longtin
    posted to noise neural_network mathematical_model gene_network by jjray on 2008-07-01 18:09:49 as ** along with 3 people and 2 groups bayesian cudmore suizan APprecision 801
  • 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 stochastic noise mathematical_model gene_regulation gene_expression by jjray on 2008-07-01 18:08:59 as ** along with 5 people JKelly555 madhadron balabu timflutre margaritis
  • Stochastic gene expression in a single cell.
    Science, Vol. 297, No. 5584. (16 August 2002), pp. 1183-1186.
    by MB Elowitz, AJ Levine, ED Siggia, PS Swain
    posted to stochastic noise gene_regulation gene_expression by jjray on 2008-07-01 18:08:23 as ** along with 14 people and 3 groups dylanwalker tvdbulck balicea jiny wilvc madhadron cottrell mmt litam mhucka timflutre margaritis roland_ewald ptupper UWNICU dIEMoSIRIS MoSi-Rostock
  • 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 noise network mathematical_model gene_regulation by jjray on 2008-07-01 18:07:54 as ** along with 3 people bayesian timflutre margaritis
  • Shaping robust system through evolution
    Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 18, No. 2. (2008)
    by Kunihiko Kaneko
    posted to robustness noise network mathematical_model evolution artificial_evolution by jjray on 2008-07-01 00:06:37 as **
  • A method of estimating the noise level in a chaotic time series
    Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 18, No. 2. (2008)
    by AW Jayawardena, Pengcheng Xu, WK Li
    posted to time_series noise mathematical_model chaos by jjray on 2008-06-30 23:59:02 as **
  • Universal occurrence of the phase-flip bifurcation in time-delay coupled systems
    Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 18, No. 2. (2008)
    by Awadhesh Prasad, Syamal K Dana, Rajat Karnatak, Jürgen Kurths, Bernd Blasius, Ramakrishna Ramaswamy
    posted to mathematical_model ecology dynamical_system delay chaos bifurcation by jjray on 2008-06-30 23:55:49 as **
  • Input reconstruction of chaos sensors
    Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 18, No. 2. (2008)
    by Dongchuan Yu, Fang Liu, Pik Y Lai
    posted to signaling robustness mathematical_model chaos by jjray on 2008-06-30 23:49:25 as **
  • Comparative analyses of bidirectional promoters in vertebrates.
    BMC bioinformatics, Vol. 9 Suppl 6 (2008)
    by MQ Yang, J Taylor, L Elnitski
    posted to promoter phylogeny gene_regulation evolution chromosome_organization by jjray on 2008-06-30 23:20:37 as ** along with 1 person bootsy
  • The mean and noise of stochastic gene transcription
    Journal of Theoretical Biology, Vol. 253, No. 2. (21 July 2008), pp. 271-280.
    by Moxun Tang
    posted to transcription stochastic noise mathematical_model gene_expression by jjray on 2008-06-30 16:19:47 as ** along with 1 person balicea
  • Stochastic coherence in an oscillatory gene circuit model
    Journal of Theoretical Biology, Vol. 253, No. 2. (21 July 2008), pp. 349-354.
    by Robert C Hilborn, Jessie D Erwin
    posted to stochastic oscillation noise feedback adiabatic_elimination by jjray on 2008-06-30 16:13:24 as ** along with 1 person balicea
  • Systematic adiabatic elimination for stochastic processes
    Zeitschrift für Physik B Condensed Matter, Vol. 48, No. 1. (1982), pp. 31-35.
    by Fritz Haake
    posted to stochastic brownian_motion adiabatic_elimination by jjray on 2008-06-30 16:11:29 as **
  • Reversal of learning deficits in a Tsc2(+/-) mouse model of tuberous sclerosis.
    Nature medicine (22 June 2008)
    by Dan Ehninger, Sangyeul Han, Carrie Shilyansky, Yu Zhou, Weidong Li, David J J Kwiatkowski, Vijaya Ramesh, Alcino J J Silva
    posted to tsc rapamycin mouse genetics by jjray on 2008-06-27 17:19:25 as **
  • Evolutionary design principles of modules that control cellular differentiation: consequences for hysteresis and multistationarity
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. 1516-1522.
    by Junil Kim, Tae-Geon Kim, Sung H Jung, Jeong-Rae Kim, Taesung Park, Pat Heslop-Harrison, Kwang-Hyun Cho
    posted to modularity evolution development design_principles artificial_evolution by jjray on 2008-06-27 17:18:11 as **
  • The effect of negative feedback loops on the dynamics of Boolean networks
    Biophys. J. (28 March 2008), biophysj.107.125021.
    by Eduardo Sontag, Alan Veliz-Cuba, Reinhard Laubenbacher, Abdul S Jarrah
    posted to feedback dynamics boolean_network by jjray on 2008-06-26 18:12:12 as ** along with 1 person abduljarrah
  • Uses and abuses of mathematics in biology.
    Science, Vol. 303, No. 5659. (6 February 2004), pp. 790-793.
    by RM May
    posted to opinion mathematical_model mathematical_biology by jjray on 2008-06-26 17:30:35 as ** along with 3 people tral mhucka bayesian
  • Efficient attenuation of stochasticity in gene expression through post-transcriptional control.
    J Mol Biol, Vol. 344, No. 4. (3 December 2004), pp. 965-976.
    by PS Swain
    posted to stochastic noise mathematical_model gene_expression by jjray on 2008-06-25 15:27:57 as ** along with 3 people and 1 group cudmore Jporci kfm9876 APprecision
  • Engineering stochasticity in gene expression.
    Molecular bioSystems, Vol. 4, No. 7. (July 2008), pp. 754-761.
    by JJ Tabor, TS Bayer, ZB Simpson, M Levy, AD Ellington
    posted to synthetic_biology stochastic review gene_expression by jjray on 2008-06-25 15:24:51 as ** along with 1 person austin
  • Inferring the conditional mean
    (19 Oct 2007)
    by Gusztav Morvai, Benjamin Weiss
    posted to time_series stochastic statistical_method by jjray on 2008-06-24 22:34:48 as ** along with 1 person ansobol
  • Dynamics and Design Principles of a Basic Regulatory Architecture Controlling Metabolic Pathways
    PLoS Biology, Vol. 6, No. 6. (1 June 2008), e146.
    by Chen-Shan Chin, Victor Chubukov, Emmitt R Jolly, Joe Derisi, Hao Li
    posted to saccharomyces_cerevisiae metabolism mathematical_model feedback design_principles by jjray on 2008-06-24 19:56:11 as ** along with 4 people zwang marck michaelbarton djkt
  • Community structure in directed networks.
    Physical review letters, Vol. 100, No. 11. (21 March 2008)
    by EA Leicht, ME Newman
    posted to network method graph_theory by jjray on 2008-06-24 17:19:25 as read
  • From the Cover: Modularity and community structure in networks
    PNAS, Vol. 103, No. 23. (6 June 2006), pp. 8577-8582.
    by MEJ Newman
    posted to network_inference network modularity method by jjray on 2008-06-24 17:17:28 as read along with 17 people and 3 groups ellakat carlk aqeel ChaTo jfr yas balicea ddahlem cmm fukken kubyaddi adriandefroment gcalda hannu marcio phreeza Diego_Prada T_lab FAB-lab ThinkTank
  • Shannon Meets Carnot: Mutual Information Via Thermodynamics
    (19 Jun 2008)
    by Ori Shental, Ido Kanter
    posted to thermodynamics information by jjray on 2008-06-24 15:23:32 as ** along with 2 people and 1 group ansobol A_Olympia logics of knowledge
  • Optimal dynamical range of excitable networks at criticality
    Nat Phys, Vol. 2, No. 5. (May 2006), pp. 348-351.
    by Osame Kinouchi, Mauro Copelli
    posted to network dynamic_range criticality by jjray on 2008-06-24 05:55:27 as **
  • Positive feedback in cellular control systems.
    BioEssays : news and reviews in molecular, cellular and developmental biology, Vol. 30, No. 6. (June 2008), pp. 542-555.
    by AY Mitrophanov, EA Groisman
    posted to two-component_system review positive_feedback mathematical_model feedback by jjray on 2008-06-23 22:52:24 as read
  • Mechanism of the PII-activated phosphatase activity of Escherichia coli NRII (NtrB): how the different domains of NRII collaborate to act as a phosphatase.
    Biochemistry, Vol. 42, No. 29. (29 July 2003), pp. 8885-8899.
    by AA Pioszak, AJ Ninfa
    posted to two-component_system quantitative_data phosphorylation bacteria by jjray on 2008-06-23 21:45:32 as read
  • Functional dissection of the dimerization and enzymatic activities of Escherichia coli nitrogen regulator II and their regulation by the PII protein.
    Biochemistry, Vol. 39, No. 44. (7 November 2000), pp. 13433-13449.
    by P Jiang, MR Atkinson, C Srisawat, Q Sun, AJ Ninfa
    posted to two-component_system quantitative_data phosphorylation bacteria by jjray on 2008-06-23 21:45:24 as read
  • Asymmetry in the autophosphorylation of the two-component regulatory system transmitter protein nitrogen regulator II of Escherichia coli.
    Biochemistry, Vol. 39, No. 17. (2 May 2000), pp. 5057-5065.
    by P Jiang, JA Peliska, AJ Ninfa
    posted to two-component_system quantitative_data phosphorylation bacteria by jjray on 2008-06-23 21:44:21 as read
  • Phosphorylation alters the interaction of the response regulator OmpR with its sensor kinase EnvZ.
    The Journal of biological chemistry, Vol. 277, No. 13. (29 March 2002), pp. 11143-11148.
    by K Mattison, LJ Kenney
    posted to two-component_system quantitative_data binding_constant bacteria by jjray on 2008-06-23 20:21:53 as read
  • Central role of the BvgS receiver as a phosphorylated intermediate in a complex two-component phosphorelay.
    The Journal of biological chemistry, Vol. 271, No. 52. (27 December 1996), pp. 33176-33180.
    by MA Uhl, JF Miller
    posted to two-component_system quantitative_data phosphorylation kinetics bacteria by jjray on 2008-06-23 20:10:40 as read
  • Kinetic comparison of the specificity of the vancomycin resistance VanSfor two response regulators, VanR and PhoB.
    Biochemistry, Vol. 35, No. 15. (16 April 1996), pp. 4732-4740.
    by SL Fisher, SK Kim, BL Wanner, CT Walsh
    posted to two-component_system quantitative_data parameter kinetics bacteria by jjray on 2008-06-23 20:06:29 as read
  • Crosstalk between bacterial chemotaxis signal transduction proteins and regulators of transcription of the Ntr regulon: evidence that nitrogen assimilation and chemotaxis are controlled by a common phosphotransfer mechanism.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 85, No. 15. (August 1988), pp. 5492-5496.
    by AJ Ninfa, EG Ninfa, AN Lupas, A Stock, B Magasanik, J Stock
    posted to two-component_system transcriptional_regulation phosphorylation crosstalk chemotaxis bacteria by jjray on 2008-06-23 20:02:54 as read
  • Rate constants rather than biochemical mechanism determine behaviour of genetic clocks
    Journal of The Royal Society Interface
    by Emery Conrad, Avraham E Mayo, Alexander J Ninfa, Daniel B Forger
    posted to parameter oscillation mathematical_model kinetics gene_regulation gene_network feedback by jjray on 2008-06-23 20:00:00 as **
  • Purification and characterization of VanR and the cytosolic domain of VanS: a two-component regulatory system required for vancomycin resistance in Enterococcus faecium BM4147.
    Biochemistry, Vol. 32, No. 19. (18 May 1993), pp. 5057-5063.
    by GD Wright, TR Holman, CT Walsh
    posted to two-component_system quantitative_data bacteria by jjray on 2008-06-23 18:58:53 as read
  • Selection of lac gene fusions in vivo: ompR-lacZ fusions that define a functional domain of the ompR gene product.
    J. Bacteriol., Vol. 159, No. 2. (1 August 1984), pp. 750-756.
    by ML Berman, DE Jackson
    posted to two-component_system translation salmonella operon bacteria by jjray on 2008-06-23 15:22:53 as read
  • Interaction of EnvZ, a sensory histidine kinase, with phosphorylated OmpR, the cognate response regulator
    Molecular Microbiology, Vol. 46, No. 5. (2002), pp. 1283-1294.
    by Takeshi Yoshida, Sheng J Cai, Masayori Inouye
    posted to two-component_system protein_binding bacteria by jjray on 2008-06-20 23:07:24 as read
  • EnvZ-OmpR Interaction and Osmoregulation in Escherichia coli
    J. Biol. Chem., Vol. 277, No. 27. (28 June 2002), pp. 24155-24161.
    by Sheng J Cai, Masayori Inouye
    posted to two-component_system quantitative_data parameter e_coli binding_constant bacteria by jjray on 2008-06-20 22:47:40 as read
  • Signal-dependent Binding of the Response Regulators PhoP and PmrA to Their Target Promoters in Vivo
    J. Biol. Chem., Vol. 280, No. 6. (11 February 2005), pp. 4089-4094.
    by Dongwoo Shin, Eduardo A Groisman
    posted to two-component_system signaling phosphorylation gene_regulation bacteria by jjray on 2008-06-20 20:19:28 as read
  • Transcriptional autoregulation of the Salmonella typhimurium phoPQ operon.
    Journal of bacteriology, Vol. 177, No. 15. (August 1995), pp. 4364-4371.
    by FC Soncini, EG Véscovi, EA Groisman
    posted to two-component_system feedback by jjray on 2008-06-19 21:11:43 as read
  • A connector of two-component regulatory systems promotes signal amplification and persistence of expression.
    Proc Natl Acad Sci U S A (5 July 2007)
    by Akinori Kato, Alexander Y Y Mitrophanov, Eduardo A A Groisman
    posted to two-component_system signaling gene_expression by jjray on 2008-06-19 21:03:28 as read along with 3 people brianb sebastien_vigneau lilith
  • Positive feedback sharpens the anaphase switch
    Nature (15 June 2008)
    by Liam J Holt, Andrew N Krutchinsky, David O Morgan
    posted to positive_feedback feedback eukaryote cell_division by jjray on 2008-06-18 22:51:28 as **
  • Symbolic dynamics of biological feedback networks
    (2 Jun 2008)
    by Simone Pigolotti, Sandeep Krishna, Mogens H Jensen
    posted to symbolic_dynamics mathematical_model feedback dynamics by jjray on 2008-06-16 20:16:08 as ** along with 1 person ansobol
  • Human tuberculous granulomas induce peripheral lymphoid follicle-like structures to orchestrate local host defence in the lung.
    The Journal of pathology, Vol. 204, No. 2. (October 2004), pp. 217-228.
    by T Ulrichs, GA Kosmiadi, V Trusov, S Jörg, L Pradl, M Titukhina, V Mishenko, N Gushina, SH Kaufmann
    posted to mycobacterium_tuberculosis lung human granuloma by jjray on 2008-06-16 17:44:35 as read
  • Tumor necrosis factor blockade in chronic murine tuberculosis enhances granulomatous inflammation and disorganizes granulomas in the lungs.
    Infection and immunity, Vol. 76, No. 3. (March 2008), pp. 916-926.
    by SD Chakravarty, G Zhu, MC Tsai, VP Mohan, S Marino, DE Kirschner, L Huang, J Flynn, J Chan
    posted to tnf mycobacterium_tuberculosis mouse granuloma by jjray on 2008-06-16 05:08:46 as read
  • Lifespans of naive, memory and effector lymphocytes.
    Current opinion in immunology, Vol. 5, No. 3. (June 1993), pp. 433-438.
    by J Sprent
    posted to t_cell quantitative_data b_cell by jjray on 2008-06-16 04:05:04 as read
  • Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
    Cell, Vol. 133, No. 6. (13 June 2008), pp. 1106-1117.
    by Xi Chen, Han Xu, Ping Yuan, Fang Fang, Mikael Huss, Vinsensius B Vega, Eleanor Wong, Yuriy L Orlov, Weiwei Zhang, Jianming Jiang, Yuin-Han Loh, Hock C Yeo, Zhen X Yeo, Vipin Narang, Kunde R Govindarajan, Bernard Leong, Atif Shahab, Yijun Ruan, Guillaume Bourque, Wing-Kin Sung, Neil D Clarke, Chia-Lin Wei, Huck-Hui Ng
    posted to transcriptional_regulation network gene_regulation es_cell by jjray on 2008-06-13 19:29:49 as ** along with 1 person caseybrown
  • Switched or not?: the structure of unphosphorylated CheY bound to the N terminus of FliM.
    Journal of bacteriology, Vol. 188, No. 21. (November 2006), pp. 7354-7363.
    by CM Dyer, FW Dahlquist
    posted to two-component_system chemotaxis bacteria by jjray on 2008-06-11 21:52:05 as **
  • A new perspective on response regulator activation.
    Journal of bacteriology, Vol. 188, No. 21. (November 2006), pp. 7328-7330.
    by AM Stock, J Guhaniyogi
    posted to two-component_system editorial by jjray on 2008-06-11 21:51:39 as read
  • Bacterial response regulators: versatile regulatory strategies from common domains
    Trends in Biochemical Sciences, Vol. 32, No. 5. (May 2007), pp. 225-234.
    by Rong Gao, Timothy R Mack, Ann M Stock
    posted to two-component_system review bacteria 3-dimensional_structure by jjray on 2008-06-11 21:11:20 as read along with 2 people and 1 group blobbybirdman kroos Myxo group
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