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Group: baker-group - with tag systems_biology [149 articles]

Neue Artikel von Mitliedern der Gruppe baker-group Gruppe with tag systems_biology
  • Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis
    PLoS ONE, Vol. 3, No. 5. (28 May 2008), e2249.
    by Elife Z Bagci, Yoram Vodovotz, Timothy R Billiar, Bard Ermentrout, Ivet Bahar
    posted to nitric_oxide systems_biology by sobolevnrm to the group baker-group on 2008-07-23 12:11:10 as read
  • The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks.
    Eur J Biochem, Vol. 271, No. 14. (July 2004), pp. 2905-2922.
    by HG Holzhütter
    posted to nitric_oxide systems_biology by sobolevnrm to the group baker-group on 2008-06-18 22:36:56 as read along with 3 people alexg pmendes JeremyZucker
  • Controlling the rates of biochemical reactions and signaling networks by shape and volume changes
    Proceedings of the National Academy of Sciences, Vol. 105, No. 11. (18 March 2008), pp. 4099-4104.
    by L Lizana, B Bauer, O Orwar
    posted to diffusion systems_biology by sobolevnrm to the group baker-group on 2008-05-19 11:22:52 as read along with 1 person rmorenoe
  • Bayesian Ranking of Biochemical System Models.
    Bioinformatics (5 December 2007)
    by Vladislav Vyshemirsky, Mark A A Girolami
    posted to bioinformatics statistics systems_biology by sobolevnrm to the group baker-group on 2008-04-24 11:32:12 as read along with 5 people ggallone jyuh bootsy lenov keithvass
  • Modularization of biochemical networks based on classification of Petri net t-invariants
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Eva G Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Bjorn Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch
    posted to graph_theory systems_biology by sobolevnrm to the group baker-group on 2008-02-08 12:20:33 as read along with 5 people reyez jyuh bootsy maralena roys
  • Variable-free exploration of stochastic models: a gene regulatory network example
    (6 Nov 2006)
    by Radek Erban, Thomas A Frewen, Xiao Wang, Timothy C Elston, Ronald Coifman, Boaz Nadler, Ioannis G Kevrekidis
    posted to kinetics multiscale systems_biology by sobolevnrm to the group baker-group on 2008-02-01 21:23:37 as ***** along with 1 person j_vinals
  • Getting Started in Probabilistic Graphical Models
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e252.
    by Edoardo M Airoldi
    posted to bioinformatics systems_biology by sobolevnrm to the group baker-group on 2008-02-01 12:54:37 as read along with 12 people jyuh balicea AbnerCYH stajich cjeans GustavoLacerda GeeSharpMinor cabbagezs nklee biehl softsimu jfr
  • A mathematical tool for exploring the dynamics of biological networks
    Proceedings of the National Academy of Sciences (21 November 2007), 0709955104.
    by Paolo E Barbano, Marina Spivak, Marc Flajolet, Angus C Nairn, Paul Greengard, Leslie Greengard
    posted to mathematics systems_biology by sobolevnrm to the group baker-group on 2008-01-10 12:32:48 as read along with 9 people tmmurali cjeans zwang cactus forgoston lenov sdbneuro mdramirez phoenixzxl
  • On anti-portfolio effects in science and technology with application to reaction kinetics, chemical synthesis, and molecular biology
    Proceedings of the National Academy of Sciences, Vol. 104, No. 47. (20 November 2007), pp. 18398-18403.
    by Marcel O Vlad, Alexandru D Corlan, Vlad T Popa, John Ross
    posted to mathematics systems_biology by sobolevnrm to the group baker-group on 2007-12-21 12:32:30 as read along with 1 person RamuAnandakrishnan
  • Robustness and modular design of the Drosophila segment polarity network
    Mol Syst Biol, Vol. 2 (12 December 2006)
    by Wenzhe Ma, Luhua Lai, Qi Ouyang, Chao Tang
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-12-20 12:21:09 as read along with 2 people faisalm Heute
  • 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 systems_biology by sobolevnrm to the group baker-group on 2007-11-09 12:12:44 as read along with 6 people biomcgary faisalm fishtank cjeans afenley entropy
  • Toward realistic modeling of dynamic processes in cell signaling: Quantification of macromolecular crowding effects
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007)
    by Jian Sun, Harel Weinstein
    posted to diffusion kinetics systems_biology by sobolevnrm to the group baker-group on 2007-11-06 12:40:05 as read along with 3 people jonesn ARobson cactus
  • From Pathways Databases to Network Models of Switching Behavior
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e152.
    by Baltazar D Aguda, Andrew B Goryachev
    posted to bioinformatics systems_biology by sobolevnrm to the group baker-group on 2007-10-04 12:52:53 as read along with 5 people balicea cjeans GustavoLacerda thomaskelder tharris
  • Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems
    Biotechnol. Prog. (26 September 2007)
    by H Li, Y Cao, LR Petzold, DT Gillespie
    posted to kinetics mathematics systems_biology by sobolevnrm to the group baker-group on 2007-10-02 12:42:54 as read along with 1 person and 1 group dagmar compneur
  • Towards a theory of biological robustness
    Mol Syst Biol, Vol. 3 (2007)
    by Hiroaki Kitano
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-09-25 12:30:28 as read along with 8 people jjray dullhunk margaritis massivemayhem fishtank bootsy Ema jf76
  • Roles of Hemoglobin Allostery in Hypoxia-induced Metabolic Alterations in Erythrocytes: SIMULATION AND ITS VERIFICATION BY METABOLOME ANALYSIS
    J. Biol. Chem., Vol. 282, No. 14. (6 April 2007), pp. 10731-10741.
    by Ayako Kinoshita, Kosuke Tsukada, Tomoyoshi Soga, Takako Hishiki, Yuki Ueno, Yoichi Nakayama, Masaru Tomita, Makoto Suematsu
    posted to systems_biology nitric_oxide by sobolevnrm to the group baker-group on 2007-09-18 14:18:57 as read
  • Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology
    J. Biol. Chem., Vol. 282, No. 34. (24 August 2007), pp. 24525-24537.
    by Fan Wu, Feng Yang, Kalyan C Vinnakota, Daniel A Beard
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-08-22 12:25:15 as read along with 1 person paulschlesinger
  • Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
    Proceedings of the National Academy of Sciences of the United States of America (in press)
    by QK Beg, A Vazquez, J Ernst, MA de Menezes, Bar Z Joseph, AL Barabási, ZN Oltvai
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-07-25 13:01:34 as read
  • Metabolic Engineering
    Annual Review of Biomedical Engineering, Vol. 1 (1999), pp. 535-57.
    by M Koffas, C Roberge, K Lee, G Stephanopoulos
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-07-11 13:28:13 as read
  • Automated reverse engineering of nonlinear dynamical systems
    Proceedings of the National Academy of Sciences of the United States of America (in press)
    by J Bongard, H Lipson
    posted to teaching systems_biology mathematics by sobolevnrm to the group baker-group on 2007-06-18 13:08:48 as read along with 1 person trichner
  • Multi-Resolution-Analysis Scheme for Uncertainty Quantification in Chemical Systems
    SIAM Journal on Scientific Computing, Vol. 29, No. 2. (2007), pp. 864-89.
    by OP Le Ma\itre, HN Najm, PP Pébay, RG Ghanem, OM Knio
    posted to systems_biology mathematics by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as read
  • Regularizing capacity of metabolic networks
    Physical Review E, Vol. 75 (2007)
    by C Marr, Müller M Linow, MT Hütt
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as read
  • Self-organization of actin filament orientation in the dendritic-nucleation/array-treadmilling model
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 17. (2007), pp. 7086-91.
    by TE Schaus, EW Taylor, GG Borisy
    posted to systems_biology cytoskeleton biomembranes by sobolevnrm to the group baker-group on 2007-05-25 14:37:08 as read
  • Deterministic characterization of stochastic genetic circuits
    Proceedings of the National Academy of Sciences of the United States of America (in press)
    by M Scott, T Hwa, B Ingalls
    posted to systems_biology kinetics by sobolevnrm to the group baker-group on 2007-05-25 14:37:08 as read
  • Numerical Matrices Method for Nonlinear System Identification and Description of Dynamics of Biochemical Reaction Networks
    Biophysical Journal, Vol. 92, No. 10. (2007), pp. 3459-73.
    by AV Karnaukhov, EV Karnaukhova, JR Williamson
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:37:07 as read
  • Parameter estimation in ordinary differential equations for biochemical processes using the method of multiple shooting
    IET Systems Biology, Vol. 1, No. 2. (2007), pp. 78-88.
    by M Peifer, J Timmer
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:37:07 as read
  • Efficient algorithms for ordinary differential equation model identification of biological systems
    IET Systems Biology, Vol. 1, No. 2. (2007), pp. 120-9.
    by P Gennemark, D Wedelin
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:37:07 as read
  • Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation
    PLoS Computational Biology, Vol. 3, No. 3. (2007)
    by A Ciliberto, F Capuani, JJ Tyson
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:37:06 as read
  • Bridging from molecular simulation to biochemical networks
    Current Opinion in Structural Biology (in press)
    by M Stein, RR Gabdoulline, RC Wade
    posted to systems_biology multiscale kinetics diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:37:06 as read
  • Simplicity in biology
    Nature, Vol. 446, No. 7135. (2007)
    by U Alon
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:36:49 as read
  • Classical versus Stochastic Kinetics Modeling of Biochemical Reaction Systems
    Biophysical Journal, Vol. 92, No. 7. (2007), pp. 2350-65.
    by J Goutsias
    posted to systems_biology kinetics by sobolevnrm to the group baker-group on 2007-05-25 14:36:49 as read
  • Discrimination of dynamical system models for biological and chemical processes
    Journal of Computational Chemistry (in press)
    by S Lorenz, E Diederichs, R Telgmann, C Schã¼tte
    posted to systems_biology kinetics by sobolevnrm to the group baker-group on 2007-05-25 14:36:48 as read
  • Multinomial tau-leaping method for stochastic kinetic simulations
    Journal of Chemical Physics, Vol. 126 (2007)
    by MF Pettigrew, H Resat
    posted to systems_biology kinetics by sobolevnrm to the group baker-group on 2007-05-25 14:36:29 as read
  • In Silico Biology: From Simulation to Understanding
    Current Biology, Vol. 17 (2007), pp. R132-R134.
    by M Kollmann, V Sourjik
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:36:29 as read
  • Tuning Bulk Electrostatics to Regulate Protein Function
    Cell, Vol. 128 (2007), pp. 441-4.
    by Z Serber, Jr
    posted to systems_biology electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:28 as read
  • Thermodynamics-Based Metabolic Flux Analysis
    Biophysical Journal, Vol. 92, No. 5. (2007), pp. 1792-805.
    by CS Henry, LJ Broadbelt, V Hatzimanikatis
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:36:28 as read
  • Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems
    Biotechnology and Bioengineering, Vol. 71, No. 4. (2001), pp. 286-306.
    by CH Schilling, JS Edwards, D Letscher, BO Palsson
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:36:28 as read
  • Bayesian-based selection of metabolic objective functions
    Bioinformatics (in press)
    by AL Knorr, R Jain, R Srivastava
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:36:28 as read
  • SBaddon: High Performance Simulation for the Systems Biology Toolbox for MATLAB
    Bioinformatics (in press)
    by H Schmidt
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:36:05 as read
  • Thematic review series: Systems Biology Approaches to Metabolic and Cardiovascular Disorders. Multi-organ whole-genome measurements and reverse engineering to uncover gene networks underlying complex traits
    Journal of Lipid Research, Vol. 48, No. 2. (2007), pp. 267-77.
    by J Tegnér, J Skogsberg, J Björkegren
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:36:05 as read
  • A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors
    Science, Vol. 315, No. 5809. (2007), pp. 233-7.
    by SJ Maerkl, SR Quake
    posted to systems_biology protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Large-Scale Statistical Parameter Estimation in Complex Systems with an Application to Metabolic Models
    Multiscale Modeling and Simulation, Vol. 5, No. 4. (2006), pp. 1333-66.
    by D Calvetti, E Somersalo
    posted to systems_biology mathematics by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Reduction and solution of the chemical master equation using time scale separation and finite state projection
    Journal of Chemical Physics, Vol. 125 (2006)
    by S Peles, B Munsky, M Khammash
    posted to systems_biology mathematics diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:33:55 as **
  • Metabolic Processes Account for the Majority of the Intracellular Water in Log-Phase Escherichia coli Cells As Revealed by Hydrogen Isotopes
    Biochemistry, Vol. 45, No. 45. (2006), pp. 13622-30.
    by Kreuzer HW Martin, MJ Lott, JR Ehleringer, EL Hegg
    posted to systems_biology solvation by sobolevnrm to the group baker-group on 2007-05-25 14:24:57 as read
  • Stochastic Simulation of Chemical Kinetics
    Annual Review of Physical Chemistry (in press)
    by DT Gillespie
    posted to systems_biology mathematics by sobolevnrm to the group baker-group on 2007-05-25 14:24:56 as read
  • Biological network design strategies: discovery through dynamic optimization
    Molecular BioSystems (in press)
    by BS Adiwijaya, PI Barton, B Tidor
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:24:56 as read
  • Export by red blood cells of nitric oxide bioactivity
    Nature, Vol. 409, No. 6820. (2001), pp. 622-6.
    by JR Pawlowski, DT Hess, JS Stamler
    posted to systems_biology nitric_oxide diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:24:56 as read
  • Recovering metabolic pathways via optimisation
    Bioinformatics (in press)
    by JM Beasley, FJ Planes
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:24:56 as read
  • Biochemistry of Nitric Oxide and Its Redox-Activated Forms
    Science, Vol. 258, No. 5090. (1992), pp. 1898-902.
    by JS Stamler, DJ Singel, J Loscalzo
    posted to systems_biology nitric_oxide diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:24:56 as read
  • Reconstruction and Functional Characterization of the Human Mitochondrial Metabolic Network Based on Proteomic and Biochemical Data
    Journal of Biological Chemistry, Vol. 279, No. 38. (2004), pp. 39532-40.
    by TD Vo, HJ Greenberg, BO Palsson
    posted to systems_biology by sobolevnrm to the group baker-group on 2007-05-25 14:24:56 as read
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