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jjray systems_approach [33 articles]

Recent papers added to jjray library classified by the tag systems_approach. You can also see everyone's systems_approach.
  • 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
  • Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations
    Science, Vol. 316, No. 5824. (27 April 2007), pp. 593-597.
    by Nobuyoshi Ishii, Kenji Nakahigashi, Tomoya Baba, Martin Robert, Tomoyoshi Soga, Akio Kanai, Takashi Hirasawa, Miki Naba, Kenta Hirai, Aminul Hoque, Pei Y Ho, Yuji Kakazu, Kaori Sugawara, Saori Igarashi, Satoshi Harada, Takeshi Masuda, Naoyuki Sugiyama, Takashi Togashi, Miki Hasegawa, Yuki Takai, Katsuyuki Yugi, Kazuharu Arakawa, Nayuta Iwata, Yoshihiro Toya, Yoichi Nakayama, Takaaki Nishioka, Kazuyuki Shimizu, Hirotada Mori, Masaru Tomita
    posted to e_coli metabolism robustness systems_approach by jjray on 2007-04-27 21:49:27 as read along with 4 people and 1 group raiyar dylan77 ytoya IgorG steinmetzlab
  • 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
  • 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
  • Computational analysis of the synergy among multiple interacting genes
    Mol Syst Biol, Vol. 3 (13 February 2007)
    by Dimitris Anastassiou
    posted to gene_regulation synergistic_signals systems_approach theory by jjray on 2007-02-28 00:35:14 as read along with 1 person frohike
  • Key Role of Local Regulation in Chemosensing Revealed by a New Molecular Interaction-Based Modeling Method
    PLoS Computational Biology, Vol. 2, No. 7. (1 July 2006), e82.
    by Martin Meier-Schellersheim, Xuehua Xu, Bastian Angermann, Eric J Kunkel, Tian Jin, Ronald N Germain
    posted to mathematical_model signaling systems_approach theory by jjray on 2007-02-22 19:33:01 as ***
  • 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
  • Transcriptional noise and cellular heterogeneity in mammalian macrophages
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 495-506.
    by S Ramsey, A Ozinsky, A Clark, KD Smith, P de Atauri, V Thorsson, D Orrell, H Bolouri
    posted to toll-like_receptor systems_approach stochastic signaling noise nf-kappab network_motifs murine_macrophage mathematical_model mammalian macrophage_activation immune_activation gene_regulation feedforward by jjray on 2007-01-30 16:48:47 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
  • A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors
    Science, Vol. 315, No. 5809. (12 January 2007), pp. 233-237.
    by Sebastian J Maerkl, Stephen R Quake
    posted to transcription systems_approach microfluidics gene_regulation biophysics by jjray on 2007-01-12 19:57:23 as *** along with 8 people and 2 groups dpollard emilyhare adepace aswin skoch3 blobbybirdman emptyhb brant EisenLab Koch_Lab
  • Rules for modeling signal-transduction systems.
    Sci STKE, Vol. 2006, No. 344. (17 July 2006)
    by WS Hlavacek, JR Faeder, ML Blinov, RG Posner, M Hucka, W Fontana
    posted to theory systems_approach signaling mathematical_model by jjray on 2007-01-10 19:30:31 as read along with 3 people wnpx eukfn josepe
  • Variability and memory of protein levels in human cells
    Nature (19 November 2006)
    by Alex Sigal, Ron Milo, Ariel Cohen, Naama Geva-Zatorsky, Yael Klein, Yuvalal Liron, Nitzan Rosenfeld, Tamar Danon, Natalie Perzov, Uri Alon
    posted to transcription systems_approach stochastic noise gene_regulation by jjray on 2007-01-10 19:17:14 as *** along with 4 people and 3 groups icases marcius margaritis cjeans BioinfoCIPF SGU-CIPF TNT
  • 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
  • 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 crosstalk gene_regulation noise promoter systems_approach transcription by jjray on 2007-01-04 16:57:06 as *** along with 1 person margaritis
  • 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
  • Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli.
    Genetics, Vol. 149, No. 4. (August 1998), pp. 1677-1691.
    by MA Savageau
    posted to demand_theory e_coli evolution gene_regulation mathematical_model systems_approach transcription by jjray on 2005-08-31 20:31:36 as read along with 1 person i41m
  • 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
  • A new measure of the robustness of biochemical networks.
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2698-2705.
    by BS Chen, YC Wang, WS Wu, WH Li
    posted to biochemical_systems_theory biochemistry fragility mathematical_model robustness sensitivity_analysis systems_approach theory by jjray on 2005-08-30 21:40:32 as read
  • 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
  • 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 lfriedl marcora ssb benny nirfriedman koller iris_2001 gwcarter carlk ksiek 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 gcalda madhadron
  • 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 13 people and 1 group jstajic ssb nickluscombe gurkanbebek jtaylor jayster4 karfunkel blobbybirdman zibuyu maralena hannahrajasingh Borelli ethkim EBI-regulation
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