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jjray feedback [60 articles]

Recent papers added to jjray library classified by the tag feedback. You can also see everyone's feedback.
  • A genetic timer through noise-induced stabilization of an unstable state
    Proceedings of the National Academy of Sciences (3 October 2008)
    by Marc Turcotte, Jordi Garcia-Ojalvo, Gürol M Süel
    posted to synthetic_biology stability noise mathematical_model gene_regulation feedback by jjray on 2008-10-05 21:38:11 as **
  • Stochastic Modeling of Gene Positive Autoregulation Networks Involving Signal Molecules
    Biophys. J., Vol. 95, No. 7. (1 October 2008), pp. 3137-3145.
    by Xin Fang, William E Bentley, Evanghelos Zafiriou
    posted to stochastic signaling quorum_sensing positive_feedback feedback e_coli by jjray on 2008-09-23 16:19:24 as **
  • On the spontaneous emergence of cell polarity
    Nature, Vol. 454, No. 7206., pp. 886-889.
    by Steven J Altschuler, Sigurd B Angenent, Yanqin Wang, Lani F Wu
    posted to feedback mathematical_model positive_feedback signaling stochastic by jjray on 2008-08-14 18:02:34 as **
  • Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems.
    Proc Natl Acad Sci U S A, Vol. 101, No. 7. (17 February 2004), pp. 1822-1827.
    by D Angeli, JE Ferrell, ED Sontag
    posted to bifurcation bistability feedback hysteresis method positive_feedback by jjray on 2008-08-04 05:03:19 as read along with 6 people and 2 groups rklancer dbk jyuh monod holan jbchang streptomyces dbk-lab
  • Positive Receptor Feedback during Lineage Commitment Can Generate Ultrasensitivity to Ligand and Confer Robustness to a Bistable Switch
    Biophys. J., Vol. 95, No. 4. (15 August 2008), pp. 1575-1589.
    by Santhosh Palani, Casim A Sarkar
    posted to bifurcation bistability development feedback goldbeter-koshland positive_feedback robustness sensitivity stem_cell by jjray on 2008-07-24 21:24:55 as **
  • Estimation of the Source-by-Source Effect of Autorepression on Genetic Noise
    Biophys. J., Vol. 95, No. 3. (1 August 2008), pp. 1063-1074.
    by Hiroyuki Okano, Tetsuya J Kobayashi, Hirokazu Tozaki, Hidenori Kimura
    posted to extrinsic_noise feedback gene_regulation noise by jjray on 2008-07-21 22:57:14 as **
  • Positive feedback of G1 cyclins ensures coherent cell cycle entry
    Nature, Vol. 454, No. 7202., pp. 291-296.
    by Jan M Skotheim, Stefano Di Talia, Eric D Siggia, Frederick R Cross
    posted to cell_cycle feedback positive_feedback by jjray on 2008-07-16 21:32:50 as ** along with 2 people madhadron entropy
  • An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/Crc Mathematical and Computational Biology Series)
    (07 July 2006)
    by Uri Alon
    posted to biochemistry design_principles feedback mathematical_model response_time robustness synthetic_biology systems_approach by jjray on 2008-07-16 16:31:47 as ** along with 8 people and 2 groups joseph_x_zhou aalibes balajis balicea mattjb fishtank akastrin azazello ComplexAdaptiveSystems DSTO-CAS
  • Autoamplification of a two-component regulatory system results in "learning" behavior.
    Journal of bacteriology, Vol. 183, No. 16. (August 2001), pp. 4914-4917.
    by SM Hoffer, HV Westerhoff, KJ Hellingwerf, PW Postma, J Tommassen
    posted to bacteria feedback gene_regulation two-component_system by jjray on 2008-07-13 19:31:16 as read
  • Coherent Coupling of Feedback Loops: A Design Principle of Cell Signaling Networks.
    Bioinformatics (Oxford, England) (2 July 2008)
    by Yung-Keun K Kwon, Kwang-Hyun H Cho
    posted to boolean_network coherent_coupling design_principles feedback robustness by jjray on 2008-07-11 17:20:28 as ** along with 4 people maralena bootsy lemke reyez
  • Functional organisation of Escherichia coli transcriptional regulatory network
    Journal of Molecular Biology, Vol. 381, No. 1. (1 August 2008), pp. 238-247.
    by Agustino Martínez-Antonio, Sarath C Janga, Denis Thieffry
    posted to bacteria e_coli feedback global_regulator positive_feedback transcriptional_regulation by jjray on 2008-07-11 17:13:23 as ** along with 1 person maralena
  • 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 adiabatic_elimination feedback noise oscillation stochastic by jjray on 2008-06-30 16:13:24 as ** along with 1 person balicea
  • 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 boolean_network dynamics feedback by jjray on 2008-06-26 18:12:12 as ** along with 1 person abduljarrah
  • 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 design_principles feedback mathematical_model metabolism saccharomyces_cerevisiae by jjray on 2008-06-24 19:56:11 as ** along with 4 people djkt marck michaelbarton zwang
  • 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 feedback mathematical_model positive_feedback review two-component_system by jjray on 2008-06-23 22:52:24 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 feedback gene_network gene_regulation kinetics mathematical_model oscillation parameter by jjray on 2008-06-23 20:00:00 as **
  • 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 feedback two-component_system by jjray on 2008-06-19 21:11:43 as read
  • Positive feedback sharpens the anaphase switch
    Nature (15 June 2008)
    by Liam J Holt, Andrew N Krutchinsky, David O Morgan
    posted to cell_division eukaryote feedback positive_feedback 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 dynamics feedback mathematical_model symbolic_dynamics by jjray on 2008-06-16 20:16:08 as ** along with 1 person ansobol
  • A Positive Feedback Loop Promotes Transcription Surge That Jump-Starts Salmonella Virulence Circuit
    Science, Vol. 314, No. 5805. (8 December 2006), pp. 1607-1609.
    by Dongwoo Shin, Eun-Jin Lee, Henry Huang, Eduardo A Groisman
    posted to bacteria feedback gene_expression gene_regulation phopq salmonella two-component_system by jjray on 2008-05-26 16:27:20 as read
  • Ultrasensitive gene regulation by positive feedback loops in nucleosome modification
    Mol Syst Biol, Vol. 4 (15 April 2008)
    by Kim Sneppen, Mille A Micheelsen, Ian B Dodd
    posted to bistability eukaryote feedback mathematical_model positive_feedback promoter sensitivity transcriptional_regulation by jjray on 2008-05-06 22:22:22 as **
  • Comparison of classical and autogenous systems of regulation in inducible operons
    Nature, Vol. 252, No. 5484. (13 December 1974), pp. 546-549.
    by Michael A Savageau
    posted to biochemical_systems_theory feedback mathematical_model network response_time by jjray on 2008-04-15 17:26:39 as read along with 1 person marcio
  • Transcription and noise in negative feedback loops
    Biosystems, Vol. 91, No. 1. (January 2008), pp. 76-82.
    by JC Nacher, T Ochiai
    posted to feedback gene_regulation noise transcription by jjray on 2008-03-31 18:54:43 as **
  • Continuous control in bacterial regulatory circuits.
    J Bacteriol, Vol. 186, No. 22. (November 2004), pp. 7618-7625.
    by E Batchelor, TJ Silhavy, M Goulian
    posted to bacteria feedback gene_regulation by jjray on 2008-03-28 17:15:33 as **
  • Robust control in bacterial regulatory circuits.
    Curr Opin Microbiol, Vol. 7, No. 2. (April 2004), pp. 198-202.
    by M Goulian
    posted to feedback feedforward gene_regulation review robustness by jjray on 2008-03-28 17:12:37 as ** along with 2 people rklancer monod
  • Positive feedback and noise activate the stringent response regulator rel in mycobacteria.
    PLoS ONE, Vol. 3, No. 3. (2008)
    by K Sureka, B Ghosh, A Dasgupta, J Basu, M Kundu, I Bose
    posted to feedback hysteresis mathematical_model mycobacteria noise by jjray on 2008-03-16 16:53:11 as read along with 1 person madhadron
  • Design of gene circuits: lessons from bacteria.
    Nat Rev Genet, Vol. 5, No. 1. (January 2004), pp. 34-42.
    by ME Wall, WS Hlavacek, MA Savageau
    posted to bacteria design_principles feedback gene_order gene_regulation review by jjray on 2008-01-30 15:15:54 as read along with 5 people and 2 groups rklancer icases monod dbikard grahamc TNT SynBioSys
  • Analysis of sigma32 mutants defective in chaperone-mediated feedback control reveals unexpected complexity of the heat shock response.
    Proc Natl Acad Sci U S A, Vol. 104, No. 45. (6 November 2007), pp. 17638-17643.
    by T Yura, E Guisbert, M Poritz, CZ Lu, E Campbell, CA Gross
    posted to feedback gene_order heat_shock sigma_factor by jjray on 2008-01-29 21:16:42 as **
  • SOCS proteins, cytokine signalling and immune regulation
    Nature Reviews Immunology, Vol. 7, No. 6. (18 May 2007), pp. 454-465.
    by Akihiko Yoshimura, Tetsuji Naka, Masato Kubo
    posted to feedback review socs1 by jjray on 2007-09-05 04:58:03 as read along with 1 person jyuh
  • Negative autoregulation speeds the response times of transcription networks.
    J Mol Biol, Vol. 323, No. 5. (8 November 2002), pp. 785-793.
    by N Rosenfeld, MB Elowitz, U Alon
    posted to feedback mathematical_model network response_time synthetic_biology transcription by jjray on 2007-09-05 04:09:24 as read along with 3 people rklancer bayesian margaritis
  • Negative feedback predominates over cross-regulation to control ERK MAPK activity in response to FGF signalling in embryos
    FEBS Letters, Vol. 580, No. 17. (24 July 2006), pp. 4242-4245.
    by Terence G Smith, Maria Karlsson, Simon J Lunn, Maxwell C Eblaghie, Iain D Keenan, Elizabeth R Farrell, Cheryll Tickle, Kate G Storey, Stephen M Keyse
    posted to crosstalk feedback network_motifs by jjray on 2007-08-12 19:41:27 as *** along with 1 person arne
  • Effect of feedback regulation on stochastic gene expression
    Journal of Theoretical Biology, Vol. 247, No. 4. (21 August 2007), pp. 827-836.
    by Yi Tao, Xiudeng Zheng, Yuehua Sun
    posted to feedback gene_expression mathematical_model noise stochastic by jjray on 2007-07-31 15:30:16 as ***
  • Regulation of cytokine signaling and inflammation
    Cytokine & Growth Factor Reviews, Vol. 13, No. 4-5. ( 2002), pp. 413-421.
    by Toshitkatsu Hanada, Akihiko Yoshimura
    posted to cytokine feedback gene_regulation immune_activation inflammation network_motifs nf-kappab review tnf by jjray on 2007-05-14 18:28:18 as read along with 1 person LenaBuchner
  • Signal transduction network motifs and biological memory
    Journal of Theoretical Biology, Vol. 246, No. 4. (21 June 2007), pp. 755-761.
    by Zhangang Han, Thomas M Vondriska, Ling Yang, Robb, James N Weiss, Zhilin Qu
    posted to feedback feedforward mathematical_model motif_compositions network_motifs signaling by jjray on 2007-05-14 16:23:30 as *** along with 1 person and 4 groups jwdietrich MathBio Cybernetics Biomedical_Cybernetics AQUA-FONTIS-Study
  • Roles of noise in single and coupled multiple genetic oscillators
    The Journal of Chemical Physics, Vol. 126, No. 11. (2007)
    by Mitsumasa Yoda, Tomohiro Ushikubo, Wataru Inoue, Masaki Sasai
    posted to feedback gene_regulation mathematical_model noise oscillation phase_coherence repressilator stochastic synthetic_biology by jjray on 2007-04-27 21:13:40 as read along with 1 person ullahmukhtar
  • Oscillation patterns in negative feedback loops.
    Proc Natl Acad Sci U S A, Vol. 104, No. 16. (17 April 2007), pp. 6533-6537.
    by S Pigolotti, S Krishna, MH Jensen
    posted to feedback mathematical_model oscillation theory by jjray on 2007-04-24 18:31:12 as ***
  • Hierarchy and feedback in the evolution of the Escherichia coli transcription network
    PNAS, Vol. 104, No. 13. (27 March 2007), pp. 5516-5520.
    by Cosentino, P Jona, B Bassetti, H Isambert
    posted to e_coli evolution feedback feedforward gene_regulation network_motifs systems_approach by jjray on 2007-04-10 19:33:31 as read along with 3 people cjeans zwang dquest
  • Dynamical Motifs: Building Blocks of Complex Dynamics in Sparsely Connected Random Networks
    Physical Review Letters, Vol. 92, No. 23. (2004)
    by Valentin P Zhigulin
    posted to chaos feedback graph_theory network network_motifs theory by jjray on 2007-04-03 16:08:53 as *** along with 2 people and 5 groups jwdietrich watson MathBio Cybernetics NeuralNetworks Biomedical_Cybernetics AQUA-FONTIS-Study
  • Chemical combination effects predict connectivity in biological systems
    Mol Syst Biol, Vol. 3 (27 February 2007)
    by Joseph Lehar, Grant R Zimmermann, Andrew S Krueger, Raymond A Molnar, Jebediah T Ledell, Adrian M Heilbut, Glenn F Short, Leanne C Giusti, Garry P Nolan, Omar A Magid, Margaret S Lee, Alexis A Borisy, Brent R Stockwell, Curtis T Keith
    posted to feedback mathematical_model network_inference synergistic_signals systems_approach by jjray on 2007-03-13 15:06:17 as *** along with 4 people aheilbut pbellec alexg daed
  • Combinatorial synthesis of genetic networks.
    Science, Vol. 296, No. 5572. (24 May 2002), pp. 1466-1470.
    by CC Guet, MB Elowitz, W Hsing, S Leibler
    posted to synthetic_biology network_motifs gene_regulation feedback e_coli by jjray on 2007-02-07 20:38:45 as read along with 5 people rklancer tmmurali monod johncumbers dbikard
  • Who puts the tubercle in tuberculosis?
    Nature Reviews Microbiology, Vol. 5, No. 1. (11 December 2006), pp. 39-47.
    by David G Russell
    posted to review neutrophil mycobacterium_tuberculosis macrophage_deactivation macrophage_activation immune_cell_kinetics host-pathogen_interaction granuloma feedback cytokine chemokine by jjray on 2007-02-07 19:14:42 as read
  • Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast
    Nature Genetics, Vol. 38, No. 9. (27 August 2006), pp. 1082-1087.
    by Stephen A Ramsey, Jennifer J Smith, David Orrell, Marcello Marelli, Timothy W Petersen, Pedro de Atauri, Hamid Bolouri, John D Aitchison
    posted to systems_approach saccharomyces_cerevisiae phenotypic_heterogeneity network_motifs mathematical_model gene_regulation feedback dual_feedback_motif by jjray on 2007-01-30 16:38:32 as read along with 1 person balabu
  • Robustness of cellular functions.
    Cell, Vol. 118, No. 6. (17 September 2004), pp. 675-685.
    by J Stelling, U Sauer, Z Szallasi, FJ Doyle, J Doyle
    posted to systems_approach robustness review network_motifs network mathematical_model gene_regulation feedback biology_as_engineering by jjray on 2007-01-30 16:33:02 as *** along with 7 people and 1 group camster rklancer monod bayesian javierFellow fishtank perpetuale dbk-lab
  • Feedback inhibition of calcineurin and Ras by a dual inhibitory protein Carabin
    Nature (17 January 2007)
    by Fan Pan, Luo Sun, David B Kardian, Katharine A Whartenby, Drew M Pardoll, Jun O Liu
    posted to quantitative_data network_motifs immune_activation gene_regulation feedback dual_feedback_motif by jjray on 2007-01-25 17:22:02 as *** along with 1 person and 4 groups jwdietrich MathBio Cybernetics Biomedical_Cybernetics AQUA-FONTIS-Study
  • An HIV Feedback Resistor: Auto-Regulatory Circuit Deactivator and Noise Buffer.
    PLoS Biol, Vol. 5, No. 1. (26 December 2006)
    by Leor S S Weinberger, Thomas Shenk
    posted to noise mathematical_model hiv feedback by jjray on 2007-01-17 21:37:24 as read along with 1 person aswin
  • Modularity and Dynamics of Cellular Networks
    PLoS Computational Biology, Vol. 2, No. 12. (1 December 2006), e174.
    by Yuan Qi, Hui Ge
    posted to systems_approach saccharomyces_cerevisiae robustness review network_motifs network gene_regulation feedforward feedback dense_overlapping_regulon by jjray on 2007-01-10 16:18:25 as *** along with 3 people and 1 group teuder dolhuis mikaelhuss SNE
  • Requirement for multiple activation signals by anti-inflammatory feedback in macrophages.
    J Theor Biol, Vol. 241, No. 2. (21 July 2006), pp. 276-294.
    by JC Ray, DE Kirschner
    posted to biochemical_systems_theory evolution feedback gene_regulation ifn-gamma immune_activation inos iron lps mathematical_model mathematically_controlled_comparison murine_macrophage network network_motifs nf-kappab nitric_oxide piecewise_power-law power_law response_time robustness sensitivity_analysis signaling stat1 synergistic_signals systems_approach by jjray on 2006-09-28 21:24:15 as read
  • NO suppresses while peroxynitrite sustains NF-[kappa]B: a paradigm to rationalize cytoprotective and cytotoxic actions attributed to NO
    Cardiovascular Research, Vol. 63, No. 1. (1 July 2004), pp. 31-40.
    by Yoshiyuki Hattori, Kikuo Kasai, Steven S Gross
    posted to biochemistry feedback immune_activation network_motifs nf-kappab nitric_oxide by jjray on 2006-09-20 20:52:59 as read
  • Re-examination of the role of suppressor of cytokine signaling 1 (SOCS1) in the regulation of toll-like receptor signaling.
    J Biol Chem, Vol. 279, No. 52. (24 December 2004), pp. 54702-54707.
    by S Gingras, E Parganas, A de Pauw, JN Ihle, PJ Murray
    posted to feedback immune_activation lps murine_macrophage network_motifs nf-kappab signaling socs1 toll-like_receptor type-1_ifn by jjray on 2006-08-03 17:32:50 as read
  • Suppressor of cytokine signaling (SOCS) proteins indirectly regulate toll-like receptor signaling in innate immune cells.
    J Biol Chem, Vol. 279, No. 52. (24 December 2004), pp. 54708-54715.
    by A Baetz, M Frey, K Heeg, AH Dalpke
    posted to feedback immune_activation lps murine_macrophage network_motifs nf-kappab signaling socs1 toll-like_receptor type-1_ifn by jjray on 2006-08-03 17:31:03 as read
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