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jjray's network [46 articles]

当前文献位于 jjray's 文献库 标签分类为 network. You can also see everyone's network.
  • A Bacterial Cell-Cycle Regulatory Network Operating in Time and Space
    Science, Vol. 301, No. 5641. (26 September 2003), pp. 1874-1877.
    by Harley H Mcadams, Lucy Shapiro
    posted to transcriptional_regulation network mathematical_model just-in-time bacteria by jjray on 2008-07-10 18:23:52 as ** along with 6 people and 1 group balajis nickluscombe comb lshaw fishtank dylan77 EBI-regulation
  • 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 **
  • 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
  • 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 **
  • 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 2 people kengg caseybrown
  • Anticipatory Behavior Within Microbial Genetic Networks
    Science (8 May 2008), 1154456.
    by Ilias Tagkopoulos, Yir-Chung Liu, Saeed Tavazoie
    posted to simulation network evolution e_coli bacteria by jjray on 2008-06-10 22:37:00 as read along with 7 people and 2 groups stringertheory dbikard deanmalmgren djkt skumagai roys brembs Centre de Recherches Interdisciplinaires Bacterial Genome Plasticity
  • Optimal partition and effective dynamics of complex networks.
    Proc Natl Acad Sci U S A (26 February 2008)
    by Weinan E, Tiejun Li, Eric Vanden-Eijnden
    posted to network modularity markov_chain dynamics by jjray on 2008-06-10 19:57:09 as ** along with 2 people deanmalmgren maralena
  • The evolution of modularity in bacterial metabolic networks
    Proceedings of the National Academy of Sciences (6 May 2008), 0712149105.
    by Anat Kreimer, Elhanan Borenstein, Uri Gophna, Eytan Ruppin
    posted to network modularity metabolism bacteria by jjray on 2008-05-13 15:24:23 as ** along with 11 people carlk mjoach saket qwermish deanmalmgren tmmurali skato_toyaku hryk pinney roys phoenixzxl
  • Signaling cascades as cellular devices for spatial computations
    Journal of Mathematical Biology
    by Jörg Stelling, Boris Kholodenko
    posted to spatial signaling_cascade signaling network mathematical_model by jjray on 2008-05-05 20:51:13 as ** along with 2 people madhadron michaelfsp
  • Hierarchical structure and the prediction of missing links in networks
    Nature, Vol. 453, No. 7191., pp. 98-101.
    by Aaron Clauset, Cristopher Moore, MEJ Newman
    posted to network_inference network hierarchy by jjray on 2008-04-30 21:28:34 as read along with 35 people sen_cheng rds Borelli ptrobajo apwesolowski dpf cmmorel fbaroni balicea cmor kengg pbull jago Ema gtgt15 hryk nedwards i-stevenson pinney elsantosneto markusd eyliu craigwilson06 jyuh margaritis gagliol bryanhughes akshat tmmurali cactus AbnerCYH tny briordan deanmalmgren soramame_0518
  • Co-regulation of metabolic genes is better explained by flux coupling than by network distance.
    PLoS Comput Biol, Vol. 4, No. 1. (January 2008)
    by RA Notebaart, B Teusink, RJ Siezen, B Papp
    posted to saccharomyces_cerevisiae network metabolism gene_regulation gene_order e_coli by jjray on 2008-04-29 23:25:04 as ** along with 1 person maralena
  • Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction
    Proceedings of the National Academy of Sciences (17 April 2008), 0708708105.
    by Saul Lapidus, Bo Han, Jin Wang
    posted to mathematical_model network noise robustness signaling statistical_method stochastic by jjray on 2008-04-18 19:37:09 as ** along with 4 people cactus ddcttrl margaritis biehl
  • 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
  • Design principles of a bacterial signalling network
    Nature, Vol. 438, No. 7067., pp. 504-507.
    by Markus Kollmann, Linda Løvdok, Kilian Bartholomé, Jens Timmer, Victor Sourjik
    posted to design_principles gene_order network noise signaling by jjray on 2008-01-29 21:14:14 as read along with 13 people rklancer abhik monod chrn jmeppley bayesian alexg ryang balicea wnpx balabu entropy comb
  • Specificity and robustness in transcription control networks.
    Proc Natl Acad Sci U S A, Vol. 99, No. 4. (19 February 2002), pp. 2072-2077.
    by AM Sengupta, M Djordjevic, BI Shraiman
    posted to mutational_entropy network robustness transcription by jjray on 2008-01-23 21:18:48 as ** along with 1 person jstajic
  • From the Cover: Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks
    Proceedings of the National Academy of Sciences, Vol. 104, No. 41. (9 October 2007), pp. 16146-16151.
    by Marcelo Behar, Henrik G Dohlman, Timothy C Elston
    posted to kinetic_insulation kinetics network signaling signal_specificity by jjray on 2007-11-07 15:19:36 as ** along with 2 people jyuh balabu
  • 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
  • Alternative sigma factors and their roles in bacterial virulence.
    Microbiol Mol Biol Rev, Vol. 69, No. 4. (December 2005), pp. 527-543.
    by MJ Kazmierczak, M Wiedmann, KJ Boor
    posted to bacteria gene_regulation global_regulator network network_motifs review sigma_factor by jjray on 2007-08-09 21:18:11 as read along with 2 people shana gcarbajosa
  • Power-law distributions in empirical data
    (7 Jun 2007)
    by Aaron Clauset, Cosma R Shalizi, MEJ Newman
    posted to data_fitting kolmogorov-smirnov network power_law quantitative_data by jjray on 2007-06-16 03:37:53 as read along with 26 people and 1 group diamantis jyew nazareno AbnerCYH deanmalmgren stringertheory anhlc egh ansobol lfriedl itmeson dumpa madhadron sdvillal bigbossman merazzle xpontus muraken sugarexpletive jaspervoskuilen tomhebbron gi0rgi0ne amoebe jasonn pprett halukbingol EntrepreneurialRisks
  • It's a noisy business! Genetic regulation at the nanomolar scale
    Trends in Genetics, Vol. 15, No. 2. (1 February 1999), pp. 65-69.
    by Harley H Mcadams, Adam Arkin
    posted to e_coli gene_regulation gillespie_algorithm mathematical_model network noise review stochastic by jjray on 2007-06-04 18:18:49 as read along with 1 person rflrob
  • Network-based prediction of protein function
    Mol Syst Biol, Vol. 3 (13 March 2007)
    by Roded Sharan, Igor Ulitsky, Ron Shamir
    posted to graph_theory network review by jjray on 2007-05-22 15:33:26 as *** along with 11 people and 1 group ellakat carlk cmmorel wnpx julius mikaelhuss massivemayhem cjeans iris_2001 karfunkel mingzhi SysbioMPI-TCells
  • An evolutionary hybrid cellular automaton model of solid tumour growth
    Journal of Theoretical Biology, Vol. 246, No. 4. (21 June 2007), pp. 583-603.
    by P Gerlee, ARA Anderson
    posted to agent_based cellular_automaton evolutionary_dynamics mathematical_model network tumor by jjray on 2007-05-14 16:14:40 as read
  • 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
  • Noise in timing and precision of gene activities in a genetic cascade
    Mol Syst Biol, Vol. 3 (20 December 2007)
    by Amnon Amir, Oren Kobiler, Assaf Rokney, Amos B Oppenheim, Joel Stavans
    posted to mathematical_model network stochastic temporal_response by jjray on 2007-02-23 21:44:28 as *** along with 3 people balabu margaritis cjeans
  • Modeling network dynamics: the lac operon, a case study.
    J Cell Biol, Vol. 161, No. 3. (12 May 2003), pp. 471-476.
    by JM Vilar, CC Guet, S Leibler
    posted to systems_approach stochastic review quantitative_data noise network multiscale mathematical_model evolution ecology e_coli computation by jjray on 2007-02-02 19:32:22 as read along with 7 people and 2 groups rklancer jstajic bayesian balicea johncumbers wilsoros carmaus dIEMoSIRIS MoSi-Rostock
  • 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
  • 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
  • Computational Analysis of Biochemical Systems : A Practical Guide for Biochemists and Molecular Biologists
    (04 September 2000)
    by Eberhard O Voit
    posted to biochemical_systems_theory biology_as_engineering book evolution feedback gene_regulation mathematical_model mathematically_controlled_comparison metabolism multiscale network network_motifs oscillation power_law robustness sensitivity_analysis systems_approach theory by jjray on 2005-09-02 20:35:25 as read along with 2 people csgillespie cangiani
  • Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions.
    J Theor Biol, Vol. 25, No. 3. (December 1969), pp. 365-369.
    by MA Savageau
    posted to biochemical_systems_theory biochemistry mathematical_model metabolism network sensitivity_analysis systems_approach theory by jjray on 2005-08-31 20:40:25 as read
  • Subunit structure of regulator proteins influences the design of gene circuitry: analysis of perfectly coupled and completely uncoupled circuits.
    J Mol Biol, Vol. 248, No. 4. (12 May 1995), pp. 739-755.
    by WS Hlavacek, MA Savageau
    posted to biochemical_systems_theory evolution feedback gene_regulation mathematical_model mathematically_controlled_comparison network network_motifs robustness systems_approach temporal_response transcription by jjray on 2005-08-31 20:38:54 as read
  • Rules for coupled expression of regulator and effector genes in inducible circuits.
    J Mol Biol, Vol. 255, No. 1. (12 January 1996), pp. 121-139.
    by WS Hlavacek, MA Savageau
    posted to biochemical_systems_theory evolution feedback gene_regulation mathematical_model mathematically_controlled_comparison network network_motifs robustness systems_approach temporal_response transcription by jjray on 2005-08-31 20:35:12 as read
  • Completely uncoupled and perfectly coupled gene expression in repressible systems.
    J Mol Biol, Vol. 266, No. 3. (28 February 1997), pp. 538-558.
    by WS Hlavacek, MA Savageau
    posted to biochemical_systems_theory evolution feedback gene_regulation mathematical_model mathematically_controlled_comparison network network_motifs systems_approach transcription by jjray on 2005-08-31 20:33:45 as read
  • Alternative designs for a genetic switch: analysis of switching times using the piecewise power-law representation.
    Math Biosci, Vol. 180 (c 2002), pp. 237-253.
    by MA Savageau
    posted to biochemical_systems_theory feedback gene_regulation mathematical_model mathematically_controlled_comparison network network_motifs piecewise_power-law systems_approach theory by jjray on 2005-08-31 20:29:04 as read
  • Design principles for elementary gene circuits: Elements, methods, and examples.
    Chaos, Vol. 11, No. 1. (March 2001), pp. 142-159.
    by Michael A. A Savageau
    posted to biochemical_systems_theory biology_as_engineering evolution feedback gene_regulation mathematical_model mathematically_controlled_comparison network network_motifs review robustness sensitivity_analysis systems_approach theory by jjray on 2005-08-31 20:26:48 as read along with 3 people and 1 group rklancer macowell monod BUiGEM
  • The use of oscillatory signals in the study of genetic networks.
    Proc Natl Acad Sci U S A (9 May 2005)
    by Ovidiu Lipan, Wing H H Wong
    posted to gene_regulation mathematical_model network oscillation stochastic systems_approach by jjray on 2005-08-30 21:50:55 as read along with 1 person rklancer
  • Multiple functions of a feed-forward-loop gene circuit.
    J Mol Biol, Vol. 349, No. 3. (10 June 2005), pp. 501-514.
    by ME Wall, MJ Dunlop, WS Hlavacek
    posted to biochemistry feedforward gene_regulation mathematical_model mathematically_controlled_comparison network network_motifs systems_approach temporal_response by jjray on 2005-08-30 21:43:41 as read along with 1 person bayesian
  • Improved methods for the mathematically controlled comparison of biochemical systems.
    Theor Biol Med Model, Vol. 1, No. 1. (4 June 2004)
    by John H Schwacke, Eberhard O Voit
    posted to biochemical_systems_theory biochemistry mathematical_model mathematically_controlled_comparison network network_motifs sensitivity_analysis systems_approach theory by jjray on 2005-08-30 21:29:27 as read
  • Computation and analysis of time-dependent sensitivities in Generalized Mass Action systems.
    J Theor Biol, Vol. 236, No. 1. (7 September 2005), pp. 21-38.
    by JH Schwacke, EO Voit
    posted to biochemical_systems_theory biochemistry mathematical_model network sensitivity_analysis theory by jjray on 2005-08-30 21:27:58 as read
  • Quantifying the relevance of different mediators in the human immune cell network.
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1639-1643.
    by P Tieri, S Valensin, V Latora, GC Castellani, M Marchiori, D Remondini, C Franceschi
    posted to component_relevance_ranking cytokine graph_theory immune_activation network systems_approach by jjray on 2005-08-30 21:07:38 as read
  • GeneNet database: description and modeling of gene networks.
    In Silico Biol, Vol. 2, No. 2. (2002), pp. 97-110.
    by NA Kolchanov, EA Nedosekina, EA Ananko, VA Likhoshvai, NL Podkolodny, AV Ratushny, IL Stepanenko, OA Podkolodnaya, EV Ignatieva, YG Matushkin
    posted to human_macrophage immune_activation mathematical_model network nitric_oxide quantitative_data systems_approach by jjray on 2005-08-30 21:03:04 as read
  • Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.
    J Biol, Vol. 4, No. 2. (2005)
    by LV Zhang, OD King, SL Wong, DS Goldberg, AH Tong, G Lesage, B Andrews, H Bussey, C Boone, FP Roth
    posted to feedforward network network_motifs saccharomyces_cerevisiae systems_approach by jjray on 2005-08-30 20:57:22 as *** along with 10 people and 1 group ksiek carlk lfriedl marcora ssb benny nirfriedman koller iris_2001 gwcarter kdl
  • An evolutionary and functional assessment of regulatory network motifs.
    Genome Biol, Vol. 6, No. 4. (2005)
    by A Mazurie, S Bottani, M Vergassola
    posted to evolution fragility network network_motifs saccharomyces_cerevisiae systems_approach by jjray on 2005-08-30 20:55:01 as *** along with 2 people madhadron gcalda
  • Network motifs in the transcriptional regulation network of Escherichia coli
    Nat Genet, Vol. 31, No. 1. (May 2002), pp. 64-68.
    by Shai S Shen-Orr, Ron Milo, Shmoolik Mangan, Uri Alon
    posted to dense_overlapping_regulon e_coli feedforward network network_motifs systems_approach transcription by jjray on 2005-08-30 19:25:14 as read along with 12 people and 1 group hannahrajasingh Borelli jstajic ssb nickluscombe gurkanbebek jtaylor jayster4 karfunkel blobbybirdman zibuyu maralena EBI-regulation
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