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jjray library [501 articles]

最近 jjray さんのライブラリ .
  • Nucleosome Retention and the Stochastic Nature of Promoter Chromatin Remodeling for Transcription
    Cell, Vol. 133, No. 4. (16 May 2008), pp. 716-726.
    by Hinrich Boeger, Joachim Griesenbeck, Roger D Kornberg
    posted to transcription stochastic nucleosome mathematical_model gillespie_algorithm gene_expression eukaryote chromatin by jjray on 2008-05-16 20:34:56 as **
  • Stochastic Receptor Expression Allows Sensitive Bacteria to Evade Phage Attack. Part II: Theoretical Analyses
    Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 4537-4548.
    by E Chapman-Mcquiston, XL Wu
    posted to stochastic receptor phenotypic_heterogeneity persister e_coli bacteria by jjray on 2008-05-14 22:45:00 as ** along with 1 person madhadron
  • Stochastic Receptor Expression Allows Sensitive Bacteria to Evade Phage Attack. Part I: Experiments
    Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 4525-4536.
    by E Chapman-Mcquiston, XL Wu
    posted to stochastic receptor phenotypic_heterogeneity persister e_coli bacteria by jjray on 2008-05-14 22:44:46 as ** along with 1 person madhadron
  • 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 8 people deanmalmgren qwermish tmmurali skato_toyaku hryk pinney roys phoenixzxl
  • Violation of the fluctuation-dissipation theorem in a protein system.
    Biophys J (11 May 2007)
    by Kumiko Hayashi, Mitsunori Takano
    posted to spin_glass myosin molecular_dynamics fluctuation-dissipation by jjray on 2008-05-08 18:45:57 as **
  • Chromatin decouples promoter threshold from dynamic range
    Nature (16 April 2008)
    by Felix H Lam, David J Steger, Erin K O’shea
    posted to threshold_signal promoter gene_regulation dynamic_range dna_binding by jjray on 2008-05-07 21:30:41 as ** along with 1 person emptyhb
  • 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 transcriptional_regulation sensitivity promoter positive_feedback mathematical_model feedback eukaryote bistability by jjray on 2008-05-06 22:22:22 as **
  • Colored extrinsic fluctuations and stochastic gene expression
    Mol Syst Biol, Vol. 4 (6 May 2008)
    by Vahid Shahrezaei, Julien F Ollivier, Peter S Swain
    posted to stochastic gene_expression feedforward extrinsic_noise by jjray on 2008-05-06 21:09:34 as ** along with 1 person margaritis
  • 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
  • A Kinetic Model of Transcription Initiation by RNA Polymerase
    Journal of Molecular Biology, Vol. 378, No. 3. (2 May 2008), pp. 520-529.
    by Xiao-Chuan Xue, Fei Liu, Zhong-Can Ou-Yang
    posted to transcription promoter mathematical_model gibbs energy biophysics by jjray on 2008-05-05 20:46:17 as **
  • 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 ** along with 24 people 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
  • DNA dynamics vary according to macrodomain topography in the E. coli chromosome
    Molecular Microbiology, Vol. 0, No. 0. (0), pp. ???-???.
    by Olivier Espeli, Romain Mercier, Frederic Boccard
    posted to macrodomain gene_order chromosome_organization by jjray on 2008-04-30 16:55:35 as ** along with 1 person dbikard
  • 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
  • Dimensionality and dynamics in the behavior of C. elegans.
    PLoS computational biology, Vol. 4, No. 4. (April 2008)
    by GJ Stephens, B Johnson-Kerner, W Bialek, WS Ryu
    posted to eigenworm c_elegans by jjray on 2008-04-28 17:46:14 as ** along with 2 people vhphys bayesian
  • Crystal structure of the [lgr] repressor and a model for pairwise cooperative operator binding
    Nature, Vol. 452, No. 7190. (24 April 2008), pp. 1022-1025.
    by Steven Stayrook, Peera Jaru-Ampornpan, Jenny Ni, Ann Hochschild, Mitchell Lewis
    posted to transcription gene_regulation dna_binding cooperativity 3-dimensional_structure by jjray on 2008-04-23 23:37:03 as **
  • Nuclear Receptor-Enhanced Transcription Requires Motor- and LSD1-Dependent Gene Networking in Interchromatin Granules
    Cell, Vol. 132, No. 6. (21 March 2008), pp. 996-1010.
    by Esperanza Nunez, Young-Soo Kwon, Kasey R Hutt, Qidong Hu, Maria D Cardamone, Kenneth A Ohgi, Ivan Garcia-Bassets, David W Rose, Christopher K Glass, Michael G Rosenfeld, Xiang-Dong Fu
    posted to transcriptional_reprogramming transcription nucleus gene_network gene_expression chromatin by jjray on 2008-04-23 23:35:16 as ** along with 1 person dquest
  • Single-cell protein induction dynamics reveals a period of vulnerability to antibiotics in persister bacteria
    Proceedings of the National Academy of Sciences (21 April 2008), 0711712105.
    by Orit Gefen, Chana Gabay, Michael Mumcuoglu, Giora Engel, Nathalie Q Balaban
    posted to persister noise gene_expression e_coli bacteria by jjray on 2008-04-22 18:47:40 as ** along with 1 person madhadron
  • 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
  • Hysteretic and graded responses in bacterial two-component signal transduction.
    Molecular microbiology (8 April 2008)
    by Oleg A Igoshin, Rui Alves, Michael A Savageau
    posted to bacteria bistability mathematical_model two-component_system by jjray on 2008-04-16 19:32:03 as **
  • Global regulatory logic for specification of an embryonic cell lineage
    Proceedings of the National Academy of Sciences (14 April 2008), 0711220105.
    by Paola Oliveri, Qiang Tu, Eric H Davidson
    posted to gene_network gene_regulation stem_cell by jjray on 2008-04-15 18:25:49 as ** along with 2 people brant Minty
  • 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
  • Establishment of an mRNA gradient depends on the promoter: an investigation of polarity in gene expression.
    Journal of molecular biology, Vol. 378, No. 2. (25 April 2008), pp. 318-327.
    by HJ Lee, HJ Jeon, SC Ji, SH Yun, HM Lim
    posted to bacteria gene_expression gene_order gradient mrna operon promoter by jjray on 2008-04-14 17:40:02 as **
  • Energy Constraints on the Evolution of Gene Expression
    Molecular Biology and Evolution, Vol. 22, No. 6. (June 2005), pp. 1365-1374.
    by Andreas Wagner
    posted to energy evolution gene_expression transcription translation by jjray on 2008-04-03 16:05:36 as ** along with 2 people jknabe Ema
  • Tandem DNA Recognition by PhoB, a Two-Component Signal Transduction Transcriptional Activator
    Structure, Vol. 10, No. 5. (May 2002), pp. 701-713.
    by Alexandre G Blanco, Maria Sola, Xavier F Gomis-Ruth, Miquel Coll
    posted to 3-dimensional_structure dna_binding gene_regulation promoter two-component_system by jjray on 2008-04-02 21:21:22 as **
  • On the specificity of DNA-protein interactions.
    Proc Natl Acad Sci U S A, Vol. 83, No. 6. (March 1986), pp. 1608-1612.
    by PH von Hippel, OG Berg
    posted to dna_binding gene_regulation thermodynamics by jjray on 2008-04-01 20:34:15 as ** along with 3 people and 1 group stsaft cisevol lambda cis-regulatory-evolution
  • PLoS Computational Biology: A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli
    posted to dna_binding gene_regulation transcriptional_regulation by jjray on 2008-04-01 20:32:53 as ** along with 1 person and 1 group nklee Motif Discovery
  • Statistical modeling of transcription factor binding affinities predicts regulatory interactions.
    PLoS Comput Biol, Vol. 4, No. 3. (March 2008)
    by T Manke, HG Roider, M Vingron
    posted to dna_binding gene_regulation statistical_model transcription by jjray on 2008-03-31 21:37:11 as ** along with 1 person maximilianh
  • Universally Sloppy Parameter Sensitivities in Systems Biology Models
    PLoS Computational Biology, Vol. 3, No. 10. (1 October 2007), e189.
    by Ryan N Gutenkunst, Joshua J Waterfall, Fergal P Casey, Kevin S Brown, Christopher R Myers, James P Sethna
    posted to data_fitting mathematical_model parameter sensitivity_analysis by jjray on 2008-03-31 21:03:05 as ** along with 3 people aheilbut chad_davis csgillespie
  • 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 **
  • The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation.
    J Mol Biol, Vol. 181, No. 2. (20 January 1985), pp. 211-230.
    by MA Shea, GK Ackers
    posted to biophysics gene_regulation statistical_mechanics thermodynamics by jjray on 2008-03-31 18:42:35 as ** along with 1 person lambda
  • On the Relationship between Genomic Regulatory Element Organization and Gene Regulatory Dynamics
    Journal of Theoretical Biology, Vol. 195, No. 2. (21 November 1998), pp. 167-186.
    by Denise M Wolf, Frank H Eeckman
    posted to gene_regulation mathematical_model statistical_mechanics thermodynamics by jjray on 2008-03-31 18:33:46 as **
  • Gibbs measures on Brownian paths: Theory and applications
    (26 Apr 2004)
    by Volker Betz, Jozsef Lorinczi, Herbert Spohn
    posted to brownian_motion energy gibbs statistical_mechanics by jjray on 2008-03-28 18:43:19 as ** along with 1 person ansobol
  • 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
  • The TorR high-affinity binding site plays a key role in both torR autoregulation and torCAD operon expression in Escherichia coli.
    J Bacteriol, Vol. 182, No. 4. (February 2000), pp. 961-966.
    by M Ansaldi, G Simon, M Lepelletier, V Méjean
    posted to e_coli gene_regulation tor two-component_system by jjray on 2008-03-27 21:03:43 as **
  • Binding of the TorR regulator to cis-acting direct repeats activates tor operon expression.
    Mol Microbiol, Vol. 17, No. 5. (September 1995), pp. 971-980.
    by G Simon, C Jourlin, M Ansaldi, MC Pascal, M Chippaux, V Méjean
    posted to e_coli gene_regulation tor two-component_system by jjray on 2008-03-27 21:03:28 as **
  • Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli.
    Mol Microbiol, Vol. 48, No. 1. (April 2003), pp. 211-223.
    by C Bordi, L Théraulaz, V Méjean, C Jourlin-Castelli
    posted to e_coli gene_regulation tor two-component_system by jjray on 2008-03-27 20:53:18 as **
  • An unsuspected autoregulatory pathway involving apocytochrome TorC and sensor TorS in Escherichia coli.
    Proc Natl Acad Sci U S A, Vol. 98, No. 20. (25 September 2001), pp. 11615-11620.
    by S Gon, C Jourlin-Castelli, L Théraulaz, V Méjean
    posted to e_coli gene_regulation tor two-component_system by jjray on 2008-03-27 20:53:06 as **
  • Rapid Dephosphorylation of the TorR Response Regulator by the TorS Unorthodox Sensor in Escherichia coli
    J. Bacteriol., Vol. 183, No. 8. (15 April 2001), pp. 2691-2695.
    by Mireille Ansaldi, Cecile Jourlin-Castelli, Michele Lepelletier, Laurence Theraulaz, Vincent Mejean
    posted to e_coli gene_regulation tor two-component_system by jjray on 2008-03-27 20:52:42 as **
  • Stochastic switching as a survival strategy in fluctuating environments
    Nat Genet, Vol. 40, No. 4. (April 2008), pp. 471-475.
    by Murat Acar, Jerome T Mettetal, Alexander van Oudenaarden
    posted to bistability gene_expression saccharomyces_cerevisiae stochastic survival_strategy by jjray on 2008-03-27 14:56:06 as ** along with 10 people and 1 group brianb A_Olympia operon gokhan dbikard margaritis bootsy qwermish fjvico osilander GEB
  • Stimulus-dependent differential regulation in the Escherichia coli PhoQ PhoP system
    Proceedings of the National Academy of Sciences, Vol. 104, No. 41. (9 October 2007), pp. 16305-16310.
    by Tim Miyashiro, Mark Goulian
    posted to e_coli gene_expression gene_regulation transcriptional_regulation two-component_system by jjray on 2008-03-26 22:00:05 as **
  • Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways.
    Bioinformatics, Vol. 16, No. 6. (June 2000), pp. 534-547.
    by R Alves, MA Savageau
    posted to biochemical_systems_theory mathematically_controlled_comparison mathematical_model metabolism statistical_method by jjray on 2008-03-25 15:47:54 as read
  • Comparing systemic properties of ensembles of biological networks by graphical and statistical methods.
    Bioinformatics, Vol. 16, No. 6. (June 2000), pp. 527-533.
    by R Alves, MA Savageau
    posted to biochemical_systems_theory mathematically_controlled_comparison sensitivity_analysis statistical_method by jjray on 2008-03-25 15:45:54 as read
  • Transcriptional control of noise in gene expression
    Proceedings of the National Academy of Sciences (19 March 2008), 0707904105.
    by Alvaro Sanchez, Jane Kondev
    posted to gene_expression noise stochastic transcription by jjray on 2008-03-20 15:18:58 as ** along with 4 people ddcttrl balabu margaritis lambda
  • 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 ** along with 1 person madhadron
  • Failure of the work-Hamiltonian connection for free-energy calculations.
    Phys Rev Lett, Vol. 100, No. 2. (18 January 2008)
    by JM Vilar, JM Rubi
    posted to free_energy hamiltonian physics statistical_mechanics thermodynamics by jjray on 2008-03-14 17:31:10 as **
  • Ab initio thermodynamic modeling of distal multisite transcription regulation.
    Nucleic Acids Res, Vol. 36, No. 3. (February 2008), pp. 726-731.
    by L Saiz, JM Vilar
    posted to transcriptional_regulation transcription thermodynamics mathematical_model biophysics bacteria by jjray on 2008-03-14 17:29:29 as read along with 1 person maximilianh
  • Fluctuation-Dissipation: Response Theory in Statistical Physics
    (5 Mar 2008)
    by Umberto, Andrea Puglisi, Lamberto Rondoni, Angelo Vulpiani
    posted to fluctuation-dissipation review statistical_physics by jjray on 2008-03-07 16:10:04 as ** along with 1 person ansobol
  • Selection to minimise noise in living systems and its implications for the evolution of gene expression
    Mol Syst Biol, Vol. 4 (4 March 2008)
    by Ben Lehner
    posted to evolution evolvability gene_expression noise stochastic by jjray on 2008-03-05 15:28:53 as ** along with 8 people austin grahamc zwang bootsy biomcgary wilbur caseybrown michaelbarton
  • Transcriptional stochasticity in gene expression
    Journal of Theoretical Biology, Vol. 238, No. 2. (21 January 2006), pp. 348-367.
    by Tomasz Lipniacki, Pawel Paszek, Anna Marciniak-Czochra, Allan R Brasier, Marek Kimmel
    posted to mathematical_model stochastic transcription transcriptional_burst by jjray on 2008-02-27 22:03:27 as ** along with 4 people bayesian bh2 balabu cottrell
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