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タグ: mathematical_model [111 articles]

Recent papers classified by the tag mathematical_model.
  • 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
  • Stochastic mRNA Synthesis in Mammalian Cells
    PLoS Biology, Vol. 4, No. 10. (1 October 2006), e309.
    by Arjun Raj, Charles S Peskin, Daniel Tranchina, Diana Y Vargas, Sanjay Tyagi
    posted to gene_regulation mammalian mathematical_model mrna noise stochastic transcription transcriptional_burst by jjray on 2006-09-12 21:07:11 as read along with 7 people nirfriedman madhadron balabu cottrell qfwills johncumbers margaritis
  • 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 HIV Feedback Resistor: Auto-Regulatory Circuit Deactivator and Noise Buffer.
    PLoS Biol, Vol. 5, No. 1. (26 December 2006)
    by Leor S S Weinberger, Thomas Shenk
    posted to noise mathematical_model hiv feedback by jjray on 2007-01-17 21:37:24 as read along with 1 person aswin
  • 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
  • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    Journal of Computational Physics, Vol. 22, No. 4. (December 1976), pp. 403-434.
    by Daniel T Gillespie
    posted to gillespie_algorithm mathematical_model simulation stochastic by jjray on 2007-04-10 16:07:55 as *** along with 6 people and 1 group matthewhflamm petermilner jberro rjoy mazzucco ptupper Projet_ENSIMAG
  • 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
  • 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
  • Understanding biology by reverse engineering the control.
    Proc Natl Acad Sci U S A, Vol. 102, No. 12. (22 March 2005), pp. 4219-4220.
    by CJ Tomlin, JD Axelrod
    posted to biology_as_engineering commentary feedback mathematical_model by jjray on 2005-08-30 21:34:14 as read
  • A Mathematical Model for Neutrophil Gradient Sensing and Polarization
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e36.
    by Matthew Onsum, Christopher V Rao
    posted to cell_polarization chemotaxis mathematical_model neutrophil by jjray on 2007-03-30 22:06:52 as read
  • The mean and noise of stochastic gene transcription
    Journal of Theoretical Biology, Vol. 253, No. 2. (21 July 2008), pp. 271-280.
    by Moxun Tang
    posted to transcription stochastic noise mathematical_model gene_expression by jjray on 2008-06-30 16:19:47 as ** along with 1 person balicea
  • 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
  • Cost–benefit theory and optimal design of gene regulation functions
    Phys. Biol., Vol. 4, No. 4. (December 2007), 229.
    by Tomer Kalisky, Erez Dekel, Uri Alon
    posted to cost-benefit gene_regulation mathematical_model theory by jjray on 2008-01-15 19:40:58 as ** along with 2 people and 1 group dbikard Pascalichouchou SynBioSys
  • Mathematical and computational models of immune-receptor signalling.
    Nat Rev Immunol, Vol. 4, No. 6. (June 2004), pp. 445-456.
    by B Goldstein, JR Faeder, WS Hlavacek
    posted to immune_activation mathematical_model receptor_binding review signaling by jjray on 2005-08-30 21:32:04 as read
  • Dependence of Macrophage Phagocytic Efficacy on Antibody Concentration
    Infect. Immun., Vol. 75, No. 4. (1 April 2007), pp. 1904-1915.
    by Natasa Macura, Tong Zhang, Arturo Casadevall
    posted to macrophage mathematical_model phagocytosis by jjray on 2007-05-29 16:58:15 as read
  • Shaping robust system through evolution
    Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 18, No. 2. (2008)
    by Kunihiko Kaneko
    posted to robustness noise network mathematical_model evolution artificial_evolution by jjray on 2008-07-01 00:06:37 as **
  • 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
  • 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 ***
  • How regulatory CD25+CD4+T cells impinge on tumor immunobiology? On the existence of two alternative dynamical classes of tumors
    Journal of Theoretical Biology, Vol. 247, No. 1. (7 July 2007), pp. 122-137.
    by Kalet Leon, Karina Garcia, Jorge Carneiro, Agustin Lage
    posted to mathematical_model regulatory_t_cell t_cell tumor by jjray on 2007-05-25 19:18:05 as read
  • Computation and analysis of time-dependent sensitivities in Generalized Mass Action systems.
    J Theor Biol, Vol. 236, No. 1. (7 September 2005), pp. 21-38.
    by JH Schwacke, EO Voit
    posted to biochemical_systems_theory biochemistry mathematical_model network sensitivity_analysis theory by jjray on 2005-08-30 21:27:58 as read
  • A method of estimating the noise level in a chaotic time series
    Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 18, No. 2. (2008)
    by AW Jayawardena, Pengcheng Xu, WK Li
    posted to time_series noise mathematical_model chaos by jjray on 2008-06-30 23:59:02 as **
  • Universal occurrence of the phase-flip bifurcation in time-delay coupled systems
    Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 18, No. 2. (2008)
    by Awadhesh Prasad, Syamal K Dana, Rajat Karnatak, Jürgen Kurths, Bernd Blasius, Ramakrishna Ramaswamy
    posted to mathematical_model ecology dynamical_system delay chaos bifurcation by jjray on 2008-06-30 23:55:49 as **
  • 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
  • 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 ***
  • Substrate competition as a source of ultrasensitivity in the inactivation of wee1.
    Cell, Vol. 128, No. 6. (23 March 2007), pp. 1133-1145.
    by SY Kim, JE Ferrell
    posted to biochemistry mathematical_model signaling substrate_competition zero-order_ultrasensitivity by jjray on 2008-02-18 16:55:50 as ** along with 1 person and 1 group arne dIEMoSIRIS
  • How gene order is influenced by the biophysics of transcription regulation
    PNAS (20 August 2007), 0700672104.
    by Grigory Kolesov, Zeba Wunderlich, Olga N Laikova, Mikhail S Gelfand, Leonid A Mirny
    posted to biophysics gene_order gene_regulation mathematical_model transcription by jjray on 2007-08-21 15:24:30 as *** along with 6 people madhadron margaritis zwang Jporci maximilianh lambda
  • 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
  • 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
  • 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 **
  • 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 **
  • 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
  • Towards a theory of biological robustness
    Mol Syst Biol, Vol. 3 (2007)
    by Hiroaki Kitano
    posted to design_principles mathematical_model review robustness theory by jjray on 2007-10-12 15:32:45 as read along with 8 people and 1 group jf76 dullhunk margaritis massivemayhem fishtank bootsy sobolevnrm Ema baker-group
  • 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 ***
  • Input reconstruction of chaos sensors
    Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 18, No. 2. (2008)
    by Dongchuan Yu, Fang Liu, Pik Y Lai
    posted to signaling robustness mathematical_model chaos 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
    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
  • Negative autoregulation speeds the response times of transcription networks.
    J Mol Biol, Vol. 323, No. 5. (8 November 2002), pp. 785-793.
    by N Rosenfeld, MB Elowitz, U Alon
    posted to feedback mathematical_model network response_time synthetic_biology transcription by jjray on 2007-09-05 04:09:24 as read along with 3 people rklancer bayesian margaritis
  • Evolvability is a selectable trait.
    Proc Natl Acad Sci U S A, Vol. 101, No. 32. (10 August 2004), pp. 11531-11536.
    by DJ Earl, MW Deem
    posted to evolution evolvability mathematical_model by jjray on 2008-02-07 19:21:02 as ** along with 4 people and 1 group tomhebbron eldan Retchless adepace EisenLab
  • 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
  • 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
    posted to stochastic pattern_formation noise mathematical_model by jjray on 2007-01-16 21:24:50 as *** along with 2 people balabu margaritis
  • Estimation of the rate of killing by cytotoxic T lymphocytes in vivo
    PNAS, Vol. 104, No. 5. (30 January 2007), pp. 1599-1603.
    by Roland R Regoes, Daniel L Barber, Rafi Ahmed, Rustom Antia
    posted to mathematical_model quantitative_data t_cell by jjray on 2007-04-06 17:56:09 as read
  • Noise in genetic and neural networks.
    Chaos, Vol. 16, No. 2. (June 2006)
    by PS Swain, A Longtin
    posted to noise neural_network mathematical_model gene_network by jjray on 2008-07-01 18:09:49 as ** along with 3 people and 2 groups bayesian cudmore suizan APprecision 801
  • 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
  • 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 along with 1 person marcio
  • Intrinsic and extrinsic contributions to stochasticity in gene expression.
    Proc Natl Acad Sci U S A, Vol. 99, No. 20. (1 October 2002), pp. 12795-12800.
    by PS Swain, MB Elowitz, ED Siggia
    posted to stochastic noise mathematical_model gene_regulation gene_expression by jjray on 2008-07-01 18:08:59 as ** along with 5 people JKelly555 madhadron balabu timflutre margaritis
  • 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 ***
  • The mechanism of cell differentiation in Bacillus subtilis
    Nature, Vol. 441, No. 7091., pp. 371-374.
    by Dagmar Iber, Joanna Clarkson, Michael D Yudkin, Iain D Campbell
    posted to bacillus_subtilis bacteria mathematical_model sigma_factor by jjray on 2007-08-09 21:29:15 as read along with 2 people balabu comb
  • 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
  • Intrinsic noise in gene regulatory networks.
    Proc Natl Acad Sci U S A, Vol. 98, No. 15. (17 July 2001), pp. 8614-8619.
    by M Thattai, A van Oudenaarden
    posted to noise network mathematical_model gene_regulation by jjray on 2008-07-01 18:07:54 as ** along with 3 people bayesian timflutre margaritis
  • 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
  • Stochastic fluctuations in metabolic pathways
    PNAS, Vol. 104, No. 22. (29 May 2007), pp. 9224-9229.
    by Erel Levine, Terence Hwa
    posted to biochemistry mathematical_model metabolism noise stochastic by jjray on 2007-05-30 19:20:03 as *** along with 1 person balabu
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