Tag systems_approach [36 articles] Export

Recent papers classified by the tag systems_approach.

	Universally Sloppy Parameter Sensitivities in Systems Biology Models [My Copy] PLoS Comput Biol, Vol. 3, No. 10. (5 October 2007), e189. by Ryan N. Gutenkunst, Joshua J. Waterfall, Fergal P. Casey, Kevin S. Brown, Christopher R. Myers, James P. Sethna posted to systems_approach sensitivity mathematical_model biophysics by jjray on 2009-08-25 19:57:54 as along with 12 people and 2 groups dadiamah arne mhasoba Borelli cjryan biomcgary faisalm fishtank cjeans sobolevnrm afenley entropy Savage Lab, UCLA baker-group
	Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture [My Copy] Molecular Systems Biology, Vol. 5 (18 August 2009) by Raja Jothi, S. Balaji, Arthur Wuster, et al.Joshua A. Grochow, Jorg Gsponer, Teresa M. Przytycka, L. Aravind, Madan M. Babu posted to systems_approach network gene_regulation dynamics by jjray on 2009-08-19 16:52:48 as along with 12 people ashishanand apocapoc brianb dswan sjcockell zwang fenghezi rdiaz megraw poirel TRHvidsten biomcgary
	A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches [My Copy] Cell, Vol. 137, No. 1. (03 April 2009), pp. 172-181. by Irene Cantone, Lucia Marucci, Francesco Iorio, et al.Maria A. Ricci, Vincenzo Belcastro, Mukesh Bansal, Stefania Santini, Mario di Bernardo, Diego di Bernardo, Maria P. Cosma posted to yeast information mathematical_model network synthetic_biology systems_approach by jjray on 2009-04-03 16:21:06 as along with 8 people and 1 group frohike Borelli absterga coela stasaki behindtherabbit zwang phoenixzxl cube_and_beyond
	SYSTEMS BIOLOGY: Attractors and Democratic Dynamics [My Copy] Science, Vol. 323, No. 5917. (20 February 2009), pp. 1016-1017. by Yaneer Bar-Yam, Dion Harmon, Benjamin de Bivort posted to dynamical_system gene_regulation network opinion systems_approach by jjray on 2009-02-20 16:38:54 as along with 6 people mjoach davidcsterratt rdiaz agomez kieran101 renatomilani
	An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/Crc Mathematical and Computational Biology) [My Copy] (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 17 people and 2 groups dbikard fastjoe23 bertelsen ilyashl Scis0000002 fgibson reyez flyme dullhunk 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. [My Copy] Science (New York, N.Y.), Vol. 316, No. 5824. (27 April 2007), pp. 593-597. by Nobuyoshi Ishii, Kenji Nakahigashi, Tomoya Baba, et al.Martin Robert, Tomoyoshi Soga, Akio Kanai, Takashi Hirasawa, Miki Naba, Kenta Hirai, Aminul Hoque, Pei Yee 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 along with 8 people and 1 group JeremyZucker ynaito cgaugain thomaskelder raiyar dylan77 ytoya IgorG steinmetzlab
	Hierarchy and feedback in the evolution of the Escherichia coli transcription network [My Copy] Proceedings of the National Academy of Sciences, 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 along with 4 people arjun_citeulike cjeans zwang dquest
	Chemical combination effects predict connectivity in biological systems [My Copy] Mol Syst Biol, Vol. 3 (27 February 2007) by Joseph Lehar, Grant R. Zimmermann, Andrew S. Krueger, et al.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 6 people mingzhi ipark-kaist aheilbut pbellec alexg daed
	Computational analysis of the synergy among multiple interacting genes [My Copy] 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 along with 6 people yenisy shikin Borelli ipark-kaist Sonix frohike
	Key Role of Local Regulation in Chemosensing Revealed by a New Molecular Interaction-Based Modeling Method [My Copy] 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. [My Copy] J Cell Biol, Vol. 161, No. 3. (12 May 2003), pp. 471-476. by J. M. Vilar, C. C. 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 along with 7 people and 2 groups rklancer jstajic bayesian balicea johncumbers wilsoros carmaus dIEMoSIRIS MoSi-Rostock
	Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast [My Copy] Nature Genetics, Vol. 38, No. 9. (27 August 2006), pp. 1082-1087. by Stephen A. Ramsey, Jennifer J. Smith, David Orrell, et al.Marcello Marelli, Timothy W. Petersen, Pedro de Atauri, Hamid Bolouri, John D. Aitchison posted to yeast systems_approach phenotypic_heterogeneity network_motifs mathematical_model gene_regulation feedback dual_feedback_motif by jjray on 2007-01-30 16:38:32 as along with 1 person balabu
	Robustness of Cellular Functions [My Copy] Cell, Vol. 118, No. 6. (17 September 2004), pp. 675-685. by Jörg Stelling, Uwe Sauer, Zoltan Szallasi, Francis J. Doyle Iii, John 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 9 people and 1 group winterstream cryptochrome camster rklancer monod bayesian javierFellow fishtank perpetuale dbk-lab
	A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors [My Copy] 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 9 people and 2 groups absterga dpollard emilyhare adepace aswin skoch3 blobbybirdman emptyhb brant EisenLab Koch_Lab
	Rules for modeling signal-transduction systems. [My Copy] Sci STKE, Vol. 2006, No. 344. (17 July 2006) by W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka, W. Fontana posted to theory systems_approach signaling mathematical_model by jjray on 2007-01-10 19:30:31 as along with 5 people aheilbut tonamswish wnpx eukfn josepe
	Variability and memory of protein levels in human cells [My Copy] Nature (19 November 2006) by Alex Sigal, Ron Milo, Ariel Cohen, et al.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 [My Copy] PLoS Computational Biology, Vol. 2, No. 12. (1 December 2006), e174. by Yuan Qi, Hui Ge posted to yeast systems_approach 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 [My Copy] 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. [My Copy] J Theor Biol, Vol. 241, No. 2. (21 July 2006), pp. 276-294. by J. C. Ray, D. E. 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
	Computational Analysis of Biochemical Systems : A Practical Guide for Biochemists and Molecular Biologists [My Copy] (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 along with 1 person cangiani
	Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. [My Copy] J Theor Biol, Vol. 25, No. 3. (December 1969), pp. 365-369. by M. A. 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
	Subunit structure of regulator proteins influences the design of gene circuitry: analysis of perfectly coupled and completely uncoupled circuits. [My Copy] J Mol Biol, Vol. 248, No. 4. (12 May 1995), pp. 739-755. by W. S. Hlavacek, M. A. 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
	Rules for coupled expression of regulator and effector genes in inducible circuits. [My Copy] J Mol Biol, Vol. 255, No. 1. (12 January 1996), pp. 121-139. by W. S. Hlavacek, M. A. 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
	Completely uncoupled and perfectly coupled gene expression in repressible systems. [My Copy] J Mol Biol, Vol. 266, No. 3. (28 February 1997), pp. 538-558. by W. S. Hlavacek, M. A. 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
	Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli. [My Copy] Genetics, Vol. 149, No. 4. (August 1998), pp. 1677-1691. by M. A. 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 along with 1 person i41m
	Alternative designs for a genetic switch: analysis of switching times using the piecewise power-law representation. [My Copy] Math Biosci, Vol. 180 (c 2002), pp. 237-253. by M. A. 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
	Design principles for elementary gene circuits: Elements, methods, and examples. [My Copy] 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 along with 4 people and 1 group bertelsen rklancer macowell monod BUiGEM
	The use of oscillatory signals in the study of genetic networks. [My Copy] 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 along with 2 people mmcclean rklancer
	Multiple functions of a feed-forward-loop gene circuit. [My Copy] J Mol Biol, Vol. 349, No. 3. (10 June 2005), pp. 501-514. by M. E. Wall, M. J. Dunlop, W. S. 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 along with 1 person bayesian
	A new measure of the robustness of biochemical networks. [My Copy] Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2698-2705. by B. S. Chen, Y. C. Wang, W. S. Wu, W. H. 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
	Improved methods for the mathematically controlled comparison of biochemical systems. [My Copy] 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
	Quantifying the relevance of different mediators in the human immune cell network. [My Copy] Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1639-1643. by P. Tieri, S. Valensin, V. Latora, et al.G. C. 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
	GeneNet database: description and modeling of gene networks. [My Copy] In Silico Biol, Vol. 2, No. 2. (2002), pp. 97-110. by N. A. Kolchanov, E. A. Nedosekina, E. A. Ananko, et al.V. A. Likhoshvai, N. L. Podkolodny, A. V. Ratushny, I. L. Stepanenko, O. A. Podkolodnaya, E. V. Ignatieva, Y. G. 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
	Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network [My Copy] Journal of Biology, Vol. 4, No. 2. (2005), 6. by Lan Zhang, Oliver King, Sharyl Wong, et al.Debra Goldberg, Amy Tong, Guillaume Lesage, Brenda Andrews, Howard Bussey, Charles Boone, Frederick Roth posted to yeast feedforward network network_motifs systems_approach by jjray on 2005-08-30 20:57:22 as along with 11 people and 1 group colmryan lfriedl marcora ssb benny nirfriedman koller iris_2001 gwcarter carlk ksiek kdl
	An evolutionary and functional assessment of regulatory network motifs. [My Copy] Genome Biol, Vol. 6, No. 4. (2005) by A. Mazurie, S. Bottani, M. Vergassola posted to yeast evolution fragility network network_motifs 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 [My Copy] Nature Genetics, Vol. 31, No. 1. (22 April 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 along with 18 people and 1 group vtraag sergiun mtagaya kaarsinogen cswinburne jstajic ssb nickluscombe gurkanbebek jtaylor jayster4 karfunkel blobbybirdman zibuyu maralena hannahrajasingh Borelli ethkim EBI-regulation

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mathematical_model	23
network	22
gene_regulation	20
network_motifs	16
feedback	13
biochemical_systems_theory	10
evolution	10
robustness	10
mathematically_controlled_comparison	9
theory	9
transcription	8
sensitivity_analysis	6
biochemistry	5
e_coli	5
feedforward	5
yeast	5
review	4
biology_as_engineering	3
immune_activation	3
metabolism	3
noise	3
signaling	3
stochastic	3
synergistic_signals	3
temporal_response	3
biophysics	2
dense_overlapping_regulon	2
fragility	2
multiscale	2
nitric_oxide	2
oscillation	2
piecewise_power-law	2
power_law	2
quantitative_data	2
response_time	2
synthetic_biology	2
book	1
component_relevance_ranking	1
computation	1
crosstalk	1
cytokine	1
demand_theory	1
design_principles	1
dual_feedback_motif	1
dynamical_system	1
dynamics	1
ecology	1
graph_theory	1
human_macrophage	1
ifn-gamma	1
information	1
inos	1
iron	1
lps	1
microfluidics	1
murine_macrophage	1
network_inference	1
nf-kappab	1
opinion	1
phenotypic_heterogeneity	1
promoter	1
sensitivity	1
stat1	1

Tag systems_approach [36 articles] Export

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