jjray's robustness [44 articles] Export

Recent papers added to jjray's library classified by the tag robustness. You can also see everyone's robustness.

	The multi-step phosphorelay mechanism of unorthodox two-component systems in E. coli realizes ultrasensitivity to stimuli while maintaining robustness to noises. [My Copy] Computational biology and chemistry, Vol. 30, No. 6. (December 2006), pp. 438-444. by Jeong-Rae R. Kim, Kwang-Hyun H. Cho posted to two-component_system simulation sensitivity robustness phosphorylation noise mathematical_model e_coli bacteria by jjray on 2009-11-19 18:06:21 as
	Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits [My Copy] Cell, Vol. 139, No. 3. (30 October 2009), pp. 512-522. by Tolga Çağatay, Marc Turcotte, Michael B. Elowitz, Jordi Garcia-Ojalvo, Gürol M. Süel posted to stochastic robustness noise network gene_regulation dynamics development bacteria by jjray on 2009-11-03 21:37:58 as along with 4 people maren dbikard samubernard venancio
	Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments [My Copy] (23 Oct 2009) by Ramon Grima posted to stochastic robustness noise kinetics intracellular enzyme biophysics by jjray on 2009-10-26 23:46:26 as along with 1 person apocapoc
	Emergent Network Structure, evolvable Robustness and non-linear Effects of Point Mutations in an Artificial Genome Model [My Copy] (25 Aug 2009) by Thimo Rohlf, Christopher R. Winkler posted to robustness network mutation modularity genome evolution by jjray on 2009-08-26 15:47:22 as along with 1 person sigoldberg1
	Identification of a topological characteristic responsible for the biological robustness of regulatory networks. [My Copy] PLoS computational biology, Vol. 5, No. 7. (24 July 2009), e1000442. by Yangle Wu, Xiaomeng Zhang, Jianglei Yu, Qi Ouyang posted to yeast robustness network_motifs network information gene_regulation by jjray on 2009-08-25 21:00:03 as along with 7 people and 2 groups roys jago winterstream phoenixzxl reyez tinatoni TRHvidsten Software-Architecture Integrative Expertise for Global Health
	Role of Translational Coupling in Robustness of Bacterial Chemotaxis Pathway [My Copy] PLoS Biol, Vol. 7, No. 8. (18 August 2009), e1000171. by Linda Løvdok, Kajetan Bentele, Nikita Vladimirov, et al.Anette Müller, Ferencz S. Pop, Dirk Lebiedz, Markus Kollmann, Victor Sourjik posted to signaling robustness evolution chromosome_organization chemotaxis bacteria by jjray on 2009-08-25 17:31:36 as along with 2 people vladimirov biomcgary
	Robustness and epistasis in mutation-selection models [My Copy] Physical Biology, Vol. 6, No. 3. (September 2009), 036007. by Andrea Wolff, Joachim Krug posted to robustness mathematical_model evolution epistasis biophysics by jjray on 2009-08-23 14:12:56 as
	Robust synthetic biology design: stochastic game theory approach [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1822-1830. by Bor-Sen Chen, Chia-Hung Chang, Hsiao-Ching Lee posted to game_theory robustness stochastic synthetic_biology by jjray on 2009-07-02 17:06:07 as along with 5 people and 1 group abhishek_tiwari melo_mcr dswan sjcockell phoenixzxl Synthetic Biology
	The nature of robustness in development. [My Copy] BioEssays : news and reviews in molecular, cellular and developmental biology, Vol. 24, No. 6. (June 2002), pp. 553-563. by H. F. Nijhout posted to canalization development evolution robustness by jjray on 2009-06-04 20:52:12 as
	A coordinated network of transporters with overlapping specificities provides a robust survival strategy [My Copy] Proceedings of the National Academy of Sciences (18 May 2009) by Nir Tal, Shimon Schuldiner posted to antibiotics bacteria crosstalk e_coli robustness by jjray on 2009-05-22 23:20:11 as along with 2 people viktor21614 trfield
	Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks [My Copy] PLoS Comput Biol, Vol. 5, No. 1. (2 January 2009), e1000256. by Adel Dayarian, Madalena Chaves, Eduardo D. Sontag, Anirvan M. Sengupta posted to geometric mathematical_model method network robustness by jjray on 2009-05-18 19:53:32 as along with 2 people TRHvidsten agomez
	Funnel landscape and mutational robustness as a result of evolution under thermal noise [My Copy] (7 Apr 2009) by Ayaka Sakata, Koji Hukushima, Kunihiko Kaneko posted to biophysics evolution evolutionary_dynamics fitness_landscape hamiltonian mutational_robustness noise robustness by jjray on 2009-04-20 18:29:53 as
	A framework for evolutionary systems biology [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 27. by Laurence Loewe posted to evolution review robustness theory by jjray on 2009-02-26 20:03:56 as along with 16 people and 1 group tomhebbron pawelsobko leemond31 maren gwenknight Scis0000002 agomez dswan bertelsen JeremyZucker JoeDunckley Zephyrus michaelbarton trfield VGreiff druvus Roswell Cancer Crosstalk
	Sexual reproduction selects for robustness and negative epistasis in artificial gene networks [My Copy] Nature, Vol. 440, No. 7080. (2006), pp. 87-90. by Ricardo B. R. Azevedo, Rolf Lohaus, Suraj Srinivasan, Kristen K. Dang, Christina L. Burch posted to evolution gene_network robustness by jjray on 2009-01-08 20:17:27 as along with 4 people and 2 groups adamnellis eldan cmm mjoach GEB FAB-lab
	Cell-to-Cell Stochastic Variation in Gene Expression Is a Complex Genetic Trait. [My Copy] PLoS genetics, Vol. 4, No. 4. (April 2008) by J. Ansel, H. Bottin, C. Rodriguez-Beltran, et al.C. Damon, M. Nagarajan, S. Fehrmann, J. François, G. Yvert posted to gene_expression genetics noise robustness stochastic by jjray on 2009-01-05 22:12:26 as along with 4 people and 1 group Zephyrus balicea erel10 xingxu Roswell Cancer Crosstalk
	Spontaneous Reaction Silencing in Metabolic Optimization [My Copy] PLoS Comput Biol, Vol. 4, No. 12. (5 December 2008), e1000236. by Takashi Nishikawa, Natali Gulbahce, Adilson E. Motter posted to bacteria metabolism optimization robustness by jjray on 2009-01-05 18:12:45 as along with 2 people agomez tnishi0
	Robustness and dissipation of mitogen-activated protein kinases signal transduction network: Underlying funneled landscape against stochastic fluctuations [My Copy] The Journal of Chemical Physics, Vol. 129, No. 13. (2008) by Jin Wang, Kun Zhang, Erkwang Wang posted to brownian_dynamics mathematical_model robustness signaling stochastic by jjray on 2008-10-07 20:14:16 as
	Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 34. (26 August 2008), pp. 12271-12276. by Jin Wang, Li Xu, Erkang Wang posted to dynamical_system entropy limit_cycle mathematical_model non-equilibrium oscillation potential robustness by jjray on 2008-08-22 16:38:16 as along with 2 people and 1 group joseph_x_zhou sg45653 bioNetwork_sysBio
	Input–output robustness in simple bacterial signaling systems [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 50. (11 December 2007), pp. 19931-19935. by Guy Shinar, Ron Milo, María R. Martínez, Uri Alon posted to bacteria mathematical_model phopq robustness signaling two-component_system by jjray on 2008-08-20 20:04:44 as along with 5 people abhishek_tiwari ajitkumar22 yonatanf madhadron Ema
	High-order combination effects and biological robustness [My Copy] Mol Syst Biol, Vol. 4 (2008) by Joseph Lehar, Andrew Krueger, Grant Zimmermann, Alexis Borisy posted to complexity method robustness by jjray on 2008-08-13 20:33:35 as along with 11 people niallhaslam colmryan ipark-kaist frohike michaelbarton tomhebbron guhjy tmmurali pengchy bootsy Ema
	Positive Receptor Feedback during Lineage Commitment Can Generate Ultrasensitivity to Ligand and Confer Robustness to a Bistable Switch [My Copy] 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
	Parasites lead to evolution of robustness against gene loss in host signaling networks [My Copy] Molecular Systems Biology, Vol. 4 (15 July 2008) by Marcel Salathe, Orkun S. Soyer posted to host-pathogen_interaction robustness signaling by jjray on 2008-07-16 16:39:35 as along with 6 people tomhebbron beete grahamc zwang renatomilani Retchless
	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 18 people and 4 groups Sergey_gerbek dbikard fastjoe23 bertelsen ilyashl Scis0000002 fgibson reyez flyme dullhunk joseph_x_zhou aalibes balajis balicea mattjb fishtank akastrin azazello Systems_Biology Computational_Systems_Biology ComplexAdaptiveSystems DSTO-CAS
	Coherent Coupling of Feedback Loops: A Design Principle of Cell Signaling Networks. [My Copy] 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
	Shaping robust system through evolution [My Copy] Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 18, No. 2. (2008) by Kunihiko Kaneko posted to artificial_evolution evolution mathematical_model network noise robustness by jjray on 2008-07-01 00:06:37 as
	Input reconstruction of chaos sensors [My Copy] Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 18, No. 2. (2008) by Dongchuan Yu, Fang Liu, Pik Y. Lai posted to chaos mathematical_model robustness signaling by jjray on 2008-06-30 23:49:25 as
	Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction [My Copy] 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 biehl margaritis ddcttrl cactus
	Robust control in bacterial regulatory circuits. [My Copy] 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
	Robustness and the cycle of phosphorylation and dephosphorylation in a two-component regulatory system [My Copy] Proceedings of the National Academy of Sciences, Vol. 100, No. 2. (21 January 2003), pp. 691-696. by Eric Batchelor, Mark Goulian posted to bacteria biochemistry mathematical_model robustness two-component_system by jjray on 2008-02-13 23:17:21 as along with 1 person yonatanf
	A simple principle concerning the robustness of protein complex activity to changes in gene expression [My Copy] BMC Systems Biology, Vol. 2, No. 1. (2008) by Jennifer Semple, Tanya Vavouri, Ben Lehner posted to design_principles modularity overexpression robustness by jjray on 2008-02-11 16:30:58 as along with 3 people biehl Ema guhjy
	Module-based analysis of robustness tradeoffs in the heat shock response system. [My Copy] PLoS Comput Biol, Vol. 2, No. 7. (28 July 2006) by H. Kurata, H. El-Samad, R. Iwasaki, et al.H. Ohtake, J. C. Doyle, I. Grigorova, C. A. Gross, M. Khammash posted to design_principles gene_order heat_shock robustness by jjray on 2008-01-29 21:20:22 as
	Surviving heat shock: Control strategies for robustness and performance [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 8. (22 February 2005), pp. 2736-2741. by H. El-Samad, H. Kurata, J. C. Doyle, C. A. Gross, M. Khammash posted to design_principles gene_order heat_shock robustness by jjray on 2008-01-29 21:18:41 as along with 4 people karthikraman jporternj monod madhadron
	Robust filtering circuit design for stochastic gene networks under intrinsic and extrinsic molecular noises. [My Copy] Mathematical biosciences, Vol. 211, No. 2. (February 2008), pp. 342-355. by Bor-Sen S. Chen, Wei-Sheng S. Wu posted to gene_regulation noise robustness stochastic synthetic_biology by jjray on 2008-01-24 15:41:12 as along with 2 people bertelsen austin
	Specificity and robustness in transcription control networks. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 4. (19 February 2002), pp. 2072-2077. by A. M. Sengupta, M. Djordjevic, B. I. Shraiman posted to mutational_entropy network robustness transcription by jjray on 2008-01-23 21:18:48 as along with 2 people rouault jstajic
	Towards a theory of biological robustness [My Copy] Mol Syst Biol, Vol. 3 (18 September 2007) by Hiroaki Kitano posted to design_principles mathematical_model review robustness theory by jjray on 2007-10-12 15:32:45 as along with 12 people and 1 group abhishek_tiwari xxavx VGreiff sjayanthi dullhunk margaritis massivemayhem fishtank bootsy sobolevnrm Ema jf76 baker-group
	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
	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
	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
	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
	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
	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
	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

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bacteria	292
mathematical_model	257
gene_regulation	256
stochastic	198
signaling	157
evolution	145
mycobacterium_tuberculosis	139
e_coli	134
two-component_system	134
noise	133
network	131
feedback	129
review	103
biophysics	101
gene_expression	85
t_cell	60
immune_activation	59
method	58
biochemistry	57
transcription	56
bacillus_subtilis	54
tnf	53
theory	52
murine_macrophage	51
physics	51
chemokine	50
chemotaxis	48
robustness	44
metabolism	38
network_motifs	38
nitric_oxide	38
quantitative_data	37
sporulation	37
systems_approach	37
thermodynamics	36
bistability	34
phopq	34
simulation	34
dynamical_system	33
spo0	33
phosphorylation	32
ifn-gamma	30
regulatory_t_cell	30
salmonella	30
development	29
human_macrophage	29
information	29
kinetics	29
mrna	29
promoter	29
oscillation	28
granuloma	27
spatial	26
synthetic_biology	26
transcriptional_regulation	26
nf-kappab	25
stability	25
eukaryote	23
macrophage	22
dynamics	21
gillespie_algorithm	21
yeast	21
biochemical_systems_theory	20
complexity	20
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sigma_factor	20
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iron	19
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inos	16
bara	15
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atp	9
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lam	9
lps	9
mouse	9
operon	9
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jf	6
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tor	5
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persister	4
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endothelium	3
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ferritin	3
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foxp3	3
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nucleus	3
phobr	3
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potential	3
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roi	3
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ess	1
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maximum_likelihood	1
memristor	1
met-leu-phe	1
metropolis-hastings	1
metropolis_rule	1
michaelis-menten	1
microfluidics	1
migration	1
mitochondria	1
mixed_feedback	1
molecular_dynamics	1
motility	1
mtsa-10	1
multimerization	1
mycobacteria	1
mycobacterium_marinum	1
mycobacterium_smegmatis	1
myd88	1
myosin	1
myxobacteria	1
nkt	1
non-human_primate	1
organization	1
overshoot	1
oxidative_stress	1
percolation	1
phase_coherence	1
phase_transition	1
phenotypic_mutation	1
philosophy	1
pleiotropy	1
potts_model	1
ppar-gamma	1
propensity	1
proteasome	1
protein_export	1
protein_function	1
proteome	1
quantitative_response	1
quantum_field_theory	1
rapamycin	1
reciprocal_adaptation	1
refseq	1
relativity	1
ribosome	1
rna	1
rnase	1
sampling	1
sde	1
series	1
siphon	1
sirna	1
smoluchowski_diffusion	1
speculation	1
stochastic_resonance	1
stoichiometry	1
substrate_competition	1
supercoiling	1
superoxide	1
superstatistics	1
symbolic_dynamics	1
szilard	1
tgfbeta	1
th1	1
time	1
transcriptional_attentuation	1
transendothelial_migration	1
triad	1
volume	1

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