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jjray library [607 articles]

最近 jjray さんのライブラリ (優先度順).
  • Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels
    J. Phys. Chem. A, Vol. 104, No. 9. (9 March 2000), pp. 1876-1889.
    by MA Gibson, J Bruck
    posted to algorithm simulation stochastic by jjray on 2007-12-11 22:30:52 as ***** along with 5 people and 1 group petermilner jstajic jberro matthewhflamm rcaze Projet_ENSIMAG
  • Equation of State Calculations by Fast Computing Machines
    The Journal of Chemical Physics, Vol. 21, No. 6. (1953), pp. 1087-1092.
    by Nicholas Metropolis, Arianna W Rosenbluth, Marshall N Rosenbluth, Augusta H Teller, Edward Teller
    posted to computation metropolis_rule monte_carlo by jjray on 2007-08-12 19:22:20 as ***** along with 10 people and 1 group petermilner apostola chad_davis tobin mkurc rabio gcalda Akimasa Bc91 guxiyou LIGO
  • Evolution of chromosome organization driven by selection for reduced gene expression noise
    Nature Genetics, Vol. 39, No. 8. (27 July 2007), pp. 945-949.
    by Nizar N Batada, Laurence D Hurst
    posted to chromosome_organization evolution gene_expression noise by jjray on 2007-08-06 21:29:43 as ***** along with 5 people and 2 groups dpollard ealloza djkt lusk zwang EisenLab BioinfoCIPF
  • Lectures in Theoretical Biophysics
    (23 April 2000)
    by K Schulten, Kosztin
    posted to biophysics notes stochastic by jjray on 2008-02-13 17:32:46 as ***
  • Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon
    Journal of Molecular Biology, Vol. 372, No. 3. (21 September 2007), pp. 817-845.
    by Pier F Gherardini, Mark N Wass, Manuela Helmer-Citterich, Michael J Sternberg
    posted to convergent_evolution enzyme evolution by jjray on 2007-08-31 14:35:10 as *** along with 6 people and 2 groups sim82 barry tjimenez chad_davis tny Minty structural_bioinformatics Bioinformatics
  • Gene regulation at the single-cell level
    Science, Vol. 307, No. 5717. (Mar 2005), pp. 1962-5.
    by Nitzan Rosenfeld, Jonathan W Young, Uri Alon, Peter S Swain, Michael B Elowitz
    posted to gene_expression gene_regulation single_cell stochastic by jjray on 2007-08-19 20:47:02 as *** along with 1 person and 1 group macowell BUiGEM
  • In vivo dynamics of RNA polymerase II transcription.
    Nat Struct Mol Biol (5 August 2007)
    by Xavier Darzacq, Yaron Shav-Tal, Valeria de Turris, Yehuda Brody, Shailesh M M Shenoy, Robert D D Phair, Robert H H Singer
    posted to gene_expression kinetics mrna single_cell transcription by jjray on 2007-08-13 21:20:53 as *** along with 5 people and 3 groups dpollard dchughes madhadron cwbrown margaritis EisenLab G4ID Genetics-of-Gambling
  • Negative feedback predominates over cross-regulation to control ERK MAPK activity in response to FGF signalling in embryos
    FEBS Letters, Vol. 580, No. 17. (24 July 2006), pp. 4242-4245.
    by Terence G Smith, Maria Karlsson, Simon J Lunn, Maxwell C Eblaghie, Iain D Keenan, Elizabeth R Farrell, Cheryll Tickle, Kate G Storey, Stephen M Keyse
    posted to crosstalk feedback network_motifs by jjray on 2007-08-12 19:41:27 as *** along with 1 person arne
  • Space as the final frontier in stochastic simulations of biological systems
    FEBS Letters, Vol. 579, No. 8. (21 March 2005), pp. 1789-1794.
    by Caroline Lemerle, Barbara Di Ventura, Luis Serrano
    posted to mathematical_model simulation spatial stochastic by jjray on 2007-08-12 19:39:50 as *** along with 1 person arne
  • Effect of feedback regulation on stochastic gene expression
    Journal of Theoretical Biology, Vol. 247, No. 4. (21 August 2007), pp. 827-836.
    by Yi Tao, Xiudeng Zheng, Yuehua Sun
    posted to feedback gene_expression mathematical_model noise stochastic by jjray on 2007-07-31 15:30:16 as ***
  • Noise in Gene Expression Determines Cell Fate in Bacillus subtilis.
    Science (14 June 2007)
    by Hédia Maamar, Arjun Raj, David Dubnau
    posted to development gene_expression phenotypic_heterogeneity stochastic by jjray on 2007-07-27 17:46:52 as *** along with 4 people sebastien_vigneau margaritis cjeans cabbagezs
  • Combinatorial promoter design for engineering noisy gene expression
    PNAS (24 July 2007), 0608451104.
    by Kevin F Murphy, Gabor Balazsi, James J Collins
    posted to biology_as_engineering gene_expression gillespie_algorithm mathematical_model noise stochastic by jjray on 2007-07-25 15:29:52 as *** along with 1 person margaritis
  • Stochastic gene expression in switching environments
    Journal of Mathematical Biology, Vol. 55, No. 2. (2007), pp. 249-269.
    by Martin Gander, Christian Mazza, Hansklaus Rummler
    posted to gene_expression mathematical_model stochastic by jjray on 2007-07-23 15:02:55 as ***
  • Genetic Properties Influencing the Evolvability of Gene Expression.
    Science (24 May 2007)
    by Christian R R Landry, Bernardo Lemos, Scott A A Rifkin, W J J Dickinson, Daniel L L Hartl
    posted to evolution evolvability gene_expression gene_regulation stochastic by jjray on 2007-07-18 21:04:29 as *** along with 10 people and 3 groups klo brant balicea sebastien_vigneau grahamc emarker heliopais cisevol caseybrown emptyhb EisenLab ParkinsonLab_at_MaRS cis-regulatory-evolution
  • Probing the Limits to Positional Information
    Cell, Vol. 130, No. 1. (13 July 2007), pp. 153-164.
    by Thomas Gregor, David W Tank, Eric F Wieschaus, William Bialek
    posted to biophysics development drosophila information physical_limit by jjray on 2007-07-17 18:01:51 as ***
  • Quantifying noise levels of intercellular signals
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 75, No. 6. (2007)
    by Kai Wang, Wouter J Rappel, Rex Kerr, Herbert Levine
    posted to biophysics mathematical_model monte_carlo noise stochastic by jjray on 2007-06-25 23:21:30 as ***
  • A chemical uncertainty principle challenge
    Analytical and Bioanalytical Chemistry, Vol. 387, No. 5. (March 2007), pp. 1583-1584.
    by Meija, Juris
    posted to frequency uncertainty_principle by jjray on 2007-06-08 21:47:02 as ***
  • Sparse time-frequency representations
    PNAS, Vol. 103, No. 16. (18 April 2006), pp. 6094-6099.
    by Timothy J Gardner, Marcelo O Magnasco
    posted to frequency mathematical_model by jjray on 2007-06-08 21:43:30 as *** along with 3 people bayesian Borelli proportional
  • Uncertainty principle of genetic information in a living cell
    Theoretical Biology and Medical Modelling, Vol. 2, No. 1. (2005)
    by Pierluigi Strippoli, Silvia Canaider, Francesco Noferini, Pietro D'Addabbo, Lorenza Vitale, Federica Facchin, Luca Lenzi, Raffaella Casadei, Paolo Carinci, Maria Zannotti, Flavia Frabetti
    posted to biological_uncertainty_principle genetics information by jjray on 2007-06-08 21:37:45 as *** along with 3 people and 1 group arne epigenetics asddd dIEMoSIRIS
  • Computational methods for diffusion-influenced biochemical reactions.
    Bioinformatics (30 May 2007)
    by Maciej Dobrzynski, Jordi Vidal Rodríguez, Jaap A A Kaandorp, Joke G G Blom
    posted to biochemistry mathematical_model noise review simulation stochastic by jjray on 2007-06-04 16:47:09 as *** along with 2 people balabu dagmar
  • Diffusion of transcription factors can drastically enhance the noise in gene expression.
    Biophys J, Vol. 91, No. 12. (15 December 2006), pp. 4350-4367.
    by JS van Zon, MJ Morelli, S Tănase-Nicola, PR ten Wolde
    posted to gene_regulation gillespie_algorithm mathematical_model noise stochastic transcription by jjray on 2007-05-30 19:23:39 as *** along with 3 people ddcttrl balabu margaritis
  • Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell
    Science, Vol. 316, No. 5828. (25 May 2007), pp. 1191-1194.
    by Johan Elf, Gene-Wei Li, Sunney X Xie
    posted to biophysics e_coli gene_regulation transcription by jjray on 2007-05-25 19:47:51 as *** along with 7 people and 3 groups ras austin dpollard madhadron balabu nickluscombe samjlord EisenLab EBI-regulation moernerlab
  • 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
  • Signal transduction network motifs and biological memory
    Journal of Theoretical Biology, Vol. 246, No. 4. (21 June 2007), pp. 755-761.
    by Zhangang Han, Thomas M Vondriska, Ling Yang, Robb, James N Weiss, Zhilin Qu
    posted to feedback feedforward mathematical_model motif_compositions network_motifs signaling by jjray on 2007-05-14 16:23:30 as *** along with 1 person and 4 groups jwdietrich MathBio Cybernetics Biomedical_Cybernetics AQUA-FONTIS-Study
  • Deterministic characterization of stochastic genetic circuits
    PNAS, Vol. 104, No. 18. (1 May 2007), pp. 7402-7407.
    by Matthew Scott, Terence Hwa, Brian Ingalls
    posted to gene_regulation mathematical_model noise stochastic by jjray on 2007-05-01 19:40:41 as *** along with 2 people balabu margaritis
  • Noisy information processing through transcriptional regulation.
    Proc Natl Acad Sci U S A (9 April 2007)
    by Eric Libby, Theodore J J Perkins, Peter S S Swain
    posted to bayesian_inference gene_regulation mathematical_model noise by jjray on 2007-04-24 19:46:00 as *** along with 2 people margaritis shigepong
  • Oscillation patterns in negative feedback loops.
    Proc Natl Acad Sci U S A, Vol. 104, No. 16. (17 April 2007), pp. 6533-6537.
    by S Pigolotti, S Krishna, MH Jensen
    posted to feedback mathematical_model oscillation theory by jjray on 2007-04-24 18:31:12 as ***
  • Emergence of cooperation and evolutionary stability in finite populations
    Nature, Vol. 428, No. 6983. (April 2004), pp. 646-650.
    by Martin A Nowak, Akira Sasaki, Christine Taylor, Drew Fudenberg
    posted to ess evolution game_theory mathematical_model by jjray on 2007-04-11 19:24:31 as *** along with 5 people and 1 group zono adriandefroment Koh CareyNadell sharmiamala ikeg-lab
  • Complete genetic linkage can subvert natural selection
    PNAS, Vol. 104, No. 15. (10 April 2007), pp. 6266-6271.
    by Philip J Gerrish, Alexandre Colato, Alan S Perelson, Paul D Sniegowski
    posted to evolution genetic_linkage mathematical_model by jjray on 2007-04-10 19:28:48 as ***
  • 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
  • Adaptive response of a gene network to environmental changes by fitness-induced attractor selection.
    PLoS ONE, Vol. 1 (2006)
    by A Kashiwagi, I Urabe, K Kaneko, T Yomo
    posted to evolution gene_regulation mathematical_model theory by jjray on 2007-04-02 20:27:04 as *** along with 1 person madhadron
  • An Algorithmic Introduction to Numerical Simulation of Stochastic Differential Equations
    SIAM Review, Vol. 43, No. 3. (2001), pp. 525-546.
    by Desmond
    posted to review sde simulation by jjray on 2007-03-21 17:01:00 as *** along with 3 people ansobol Borelli Guff32
  • Towards a physics of evolution: Existence of gales of creative deconstruction in evolving technological networks
    (8 Mar 2007)
    by Rudolf Hanel, Stuart A Kauffman, Stefan Thurner
    posted to evolution mathematical_model thermodynamics by jjray on 2007-03-19 17:53:45 as *** along with 1 person madhadron
  • 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 pbellec daed aheilbut alexg
  • Spectral methods for parametric sensitivity in stochastic dynamical systems.
    Biophys J, Vol. 92, No. 2. (15 January 2007), pp. 379-393.
    by D Kim, BJ Debusschere, HN Najm
    posted to gillespie_algorithm mathematical_model noise stochastic theory by jjray on 2007-03-05 20:13:47 as *** along with 1 person balabu
  • 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
  • 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 ***
  • Microbial cell individuality and the underlying sources of heterogeneity
    Nature Reviews Microbiology, Vol. 4, No. 8., pp. 577-587.
    by Simon V Avery
    posted to stochastic review phenotypic_heterogeneity noise gene_regulation by jjray on 2007-01-31 20:54:47 as *** along with 3 people madhadron balabu aswin
  • 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
  • Stochastic gene expression in fluctuating environments.
    Genetics, Vol. 167, No. 1. (May 2004), pp. 523-530.
    by M Thattai, A van Oudenaarden
    posted to stochastic phenotypic_heterogeneity oscillation noise mathematical_model growth_rate gene_regulation evolution ecology by jjray on 2007-01-30 16:26:01 as *** along with 6 people rklancer balabu dbikard mhucka timflutre margaritis
  • Feedback inhibition of calcineurin and Ras by a dual inhibitory protein Carabin
    Nature (17 January 2007)
    by Fan Pan, Luo Sun, David B Kardian, Katharine A Whartenby, Drew M Pardoll, Jun O Liu
    posted to quantitative_data network_motifs immune_activation gene_regulation feedback dual_feedback_motif by jjray on 2007-01-25 17:22:02 as *** along with 1 person and 4 groups jwdietrich MathBio Cybernetics Biomedical_Cybernetics AQUA-FONTIS-Study
  • Phenotypic heterogeneity can enhance rare-cell survival in stress-sensitive yeast populations
    Molecular Microbiology, Vol. 63, No. 2. (January 2007), pp. 507-520.
    by Bishop, L Amy, Rab, A Faiza, Sumner, R Edward, Avery, V Simon
    posted to stochastic saccharomyces_cerevisiae phenotypic_heterogeneity noise gene_regulation by jjray on 2007-01-22 15:20:37 as *** along with 1 person madhadron
  • Noise can play an organizing role for the recurrent dynamics in excitable media
    PNAS, Vol. 104, No. 3. (16 January 2007), pp. 702-707.
    by Cyrill B Muratov, Eric Vanden-Eijnden, Weinan E
    posted to stochastic pattern_formation noise mathematical_model by jjray on 2007-01-16 21:24:50 as *** along with 2 people balabu margaritis
  • 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 brant dpollard emilyhare adepace aswin skoch3 blobbybirdman emptyhb 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 *** 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
  • Deviant effects in molecular reaction pathways
    Nature Biotechnology, Vol. 24, No. 10. (10 October 2006), pp. 1235-1240.
    by Michael S Samoilov, Adam P Arkin
    posted to commentary mathematical_model theory by jjray on 2006-10-11 19:10:10 as *** along with 2 people balabu dbikard
  • 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
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