m_j's library 51 articles Export

	A new algorithm for Monte Carlo simulation of Ising spin systems1 [My Copy] Journal of Computational Physics, Vol. 17, No. 1. (January 1975), pp. 10-18. by A. Bortz, M. Kalos, J. Lebowitz posted to ssa simulation by m_j on 2009-11-23 10:58:49 as along with 1 person matthewhflamm
	Continuous System Simulation [My Copy] (15 March 2006) by Francois E. Cellier, Ernesto Kofman posted to simulation models modeling by m_j on 2009-11-18 08:36:37 as along with 1 person winko
	Introductory Statistics: Concepts, Models, and Applications, Second Edition [My Copy] by David Stockburger posted to models modeling by m_j on 2009-11-17 14:06:46 as
	A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology [My Copy] Nat Biotech, Vol. 26, No. 10. (09 October 2008), pp. 1155-1160. by Markus J. Herrgard, Neil Swainston, Paul Dobson, et al.Warwick B. Dunn, K. Yalcin Arga, Mikko Arvas, Nils Buthgen, Simon Borger, Roeland Costenoble, Matthias Heinemann, Michael Hucka, Nicolas Le Novere, Peter Li, Wolfram Liebermeister, Monica L. Mo, Ana P. Oliveira, Dina Petranovic, Stephen Pettifer, Evangelos Simeonidis, Kieran Smallbone, Irena Spasie, Dieter Weichart, Roger Brent, David S. Broomhead, Hans V. Westerhoff, Betul Kurdar, Merja Penttila, Edda Klipp, Bernhard O. Palsson, Uwe Sauer, Stephen G. Oliver, Pedro Mendes, Jens Nielsen, Douglas B. Kell posted to systems_biology models by m_j on 2009-11-03 14:36:32 as along with 22 people and 2 groups pmendes windman83 jfr raiyar neilswainston irenas JeremyZucker chasmand schwartzjmc pinney pauldobson alaninmcr allysonlister zwang guhjy dbk michaelbarton ptrobajo neils dullhunk pengchy tmmurali MetabolicModeling BergmanLab
	The ²-Catenin/TCF-4 Complex Imposes a Crypt Progenitor Phenotype on Colorectal Cancer Cells [My Copy] Vol. 111, No. 2. (18 October 2002), pp. 241-250. by Marc van de Wetering, Elena Sancho, Cornelis Verweij, et al.Wim de Lau, Irma Oving, Adam Hurlstone, Karin van der Horn, Eduard Batlle, Damien Coudreuse, Anna-Pavlina Haramis, Menno Tjon-Pon-Fong, Petra Moerer, Maaike van den Born, Gwen Soete, Steven Pals, Martin Eilers, Rene Medema, Hans Clevers posted to wnt_pathway by m_j on 2009-11-03 14:16:32 as
	A Wnt survival guide: from flies to human disease. [My Copy] The Journal of investigative dermatology, Vol. 129, No. 7. (July 2009), pp. 1614-1627. by Andy J. Chien, William H. Conrad, Randall T. Moon posted to wnt_pathway by m_j on 2009-11-03 13:20:10 as
	Expression and Function of the Developmental Gene Wnt-4 during Experimental Acute Renal Failure in Rats [My Copy] J Am Soc Nephrol, Vol. 14, No. 5. (1 May 2003), pp. 1223-1233. by Yoshio Terada, Hiroyuki Tanaka, Tomokazu Okado, et al.Haruko Shimamura, Seiji Inoshita, Michio Kuwahara, Sei Sasaki posted to wnt_pathway by m_j on 2009-11-03 10:42:05 as along with 1 person guhjy
	Increased expression of Wnt-1 in schizophrenic brains [My Copy] Schizophrenia Research, Vol. 38, No. 1. (27 July 1999), pp. 1-6. by T. Miyaoka posted to wnt_pathway by m_j on 2009-11-03 10:35:51 as
	WNT and \|[beta]\|-catenin signalling: diseases and therapies [My Copy] Nat Rev Genet, Vol. 5, No. 9. (01 September 2004), pp. 691-701. by Randall T. Moon, Aimee D. Kohn, Giancarlo V. Ferrari, Ajamete Kaykas posted to wnt_pathway by m_j on 2009-11-03 10:25:09 as along with 1 person borisrebolledo
	Wnt signaling and cancer. [My Copy] Genes & development, Vol. 14, No. 15. (1 August 2000), pp. 1837-1851. by P. Polakis posted to wnt_pathway by m_j on 2009-11-03 10:12:14 as along with 2 people ajaymalik gsk3
	Linking colorectal cancer to Wnt signaling. [My Copy] Cell, Vol. 103, No. 2. (13 October 2000), pp. 311-320. by M. Bienz, H. Clevers posted to wnt_pathway by m_j on 2009-11-03 10:11:28 as
	Wnt signaling in disease and in development. [My Copy] Cell research, Vol. 15, No. 1. (January 2005), pp. 28-32. by Roel Nusse posted to wnt_pathway by m_j on 2009-11-03 09:48:58 as
	Spatial gradients of cellular phospho-proteins [My Copy] FEBS Letters, Vol. 457, No. 3. (03 September 1999), pp. 452-454. by Guy C. Brown, Boris N. Kholodenko posted to spatial_simulation diffusion by m_j on 2009-09-29 13:58:31 as
	Modeling 2D and 3D Diffusion [My Copy] Methods in Membrane Lipids (2007), pp. 295-321. by Michael J. Saxton posted to spatial_simulation particle_based diffusion brownian_dynamics by m_j on 2009-09-16 14:50:58 as
	The multivariate Langevin and Fokker--Planck equations [My Copy] American Journal of Physics, Vol. 64, No. 10. (1996), pp. 1246-1257. by Daniel T. Gillespie posted to stochastic_simulation brownian_dynamics by m_j on 2009-09-16 09:18:58 as
	Insight or illusion? Seeing inside the cell with mesoscopic simulations. [My Copy] HFSP journal, Vol. 2, No. 1. (February 2008), pp. 1-6. by J. C. Shillcock posted to brownian_dynamics molecular_dynamics stochastic_simulation by m_j on 2009-07-27 01:30:12 as
	Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus [My Copy] Computational Methods in Systems Biology (2007), pp. 184-199. by Andrew Phillips, Luca Cardelli posted to stochastic_simulation by m_j on 2009-05-04 15:03:15 as along with 1 person mattis23
	A multi-algorithm, multi-timescale method for cell simulation [My Copy] Bioinformatics, Vol. 20, No. 4. (1 March 2004), pp. 538-546. by Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita posted to multi-scale stochastic_simulation by m_j on 2009-05-04 08:33:29 as along with 7 people and 3 groups arjunan fierykylin chrn carmaus dagmar lenov csanford dIEMoSIRIS MoSi-Rostock compneur
	Abundance, complexation, and trafficking of Wnt/beta-catenin signaling elements in response to Wnt3. [My Copy] J Mol Signal, Vol. 2, No. 1. (25 October 2007) by Noriko Yokoyama, Dezhong Yin, Craig C. Malbon posted to wnt_pathway by m_j on 2009-01-08 16:53:24 as along with 1 person tibbitts
	Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics [My Copy] The Journal of Chemical Physics, Vol. 127, No. 10. (2007) by Tatiana, Kevin Burrage posted to spatial_simulation stochastic_simulation tau_leaping by m_j on 2009-01-07 14:30:12 as along with 1 person and 1 group dagmar compneur
	Identifying Optimal Lipid Raft Characteristics Required To Promote Nanoscale Protein-Protein Interactions on the Plasma Membrane [My Copy] Mol. Cell. Biol., Vol. 26, No. 1. (1 January 2006), pp. 313-323. by Dan V. Nicolau, Kevin Burrage, Robert G. Parton, John F. Hancock posted to lipid_rafts plasma_membrane stochastic_simulation by m_j on 2008-12-03 14:49:04 as along with 1 person ARobson
	Perilipin Targets a Novel Pool of Lipid Droplets for Lipolytic Attack by Hormone-sensitive Lipase [My Copy] J. Biol. Chem., Vol. 280, No. 52. (30 December 2005), pp. 43109-43120. by Hsiao-Ping H. Moore, Robert B. Silver, Emilio P. Mottillo, David A. Bernlohr, James G. Granneman posted to lipid_droplets by m_j on 2008-12-03 09:52:09 as
	The multiple faces of caveolae [My Copy] Nature Reviews Molecular Cell Biology, Vol. 8, No. 3., pp. 185-194. by Robert G. Parton, Kai Simons posted to caveolae by m_j on 2008-12-03 09:38:14 as along with 3 people and 1 group tkershaw tsjipko samjlord moernerlab
	Lipid droplets: a unified view of a dynamic organelle [My Copy] Nature Reviews Molecular Cell Biology, Vol. 7, No. 5. (08 March 2006), pp. 373-378. by Sally Martin, Robert G. Parton posted to caveolae lipid_droplets by m_j on 2008-12-03 09:35:03 as along with 2 people paulschlesinger ma_ko
	Multiplicity of the interactions of Wnt proteins and their receptors. [My Copy] Cell Signal, Vol. 19, No. 4. (April 2007), pp. 659-671. by A. Kikuchi, H. Yamamoto, S. Kishida posted to beta_catenin wnt_pathway by m_j on 2008-12-03 09:33:58 as along with 1 person guhjy
	Triacylglycerol Is Synthesized in a Specific Subclass of Caveolae in Primary Adipocytes [My Copy] J. Biol. Chem., Vol. 280, No. 1. (7 January 2005), pp. 5-8. by Anita Ost, Unn Ortegren, Johanna Gustavsson, Fredrik H. Nystrom, Peter Stralfors posted to brownian_dynamics caveolae lipid_droplets by m_j on 2008-12-03 09:32:11 as
	Oscillatory regulation of Hes1: Discrete stochastic delay modelling and simulation. [My Copy] PLoS Comput Biol, Vol. 2, No. 9. (8 September 2006) by M. Barrio, K. Burrage, A. Leier, T. Tian posted to stochastic_simulation by m_j on 2008-11-19 11:03:59 as along with 1 person lenov
	Modelling and simulation of intracellular dynamics: Choosing an appropriate framework [My Copy] IEEE Transactions on NanoBioscience, Vol. 3 (2004), pp. 200-207. by Olaf Wolkenhauer, Mukhtar Ullah, Walter Kolch, Kwang-Hyun Cho posted to deterministic stochastic_simulation by m_j on 2008-11-04 16:14:39 as
	Elucidating the interactions between the adhesive and transcriptional functions of ββ-catenin in normal and cancerous cells [My Copy] Journal of Theoretical Biology, Vol. 247, No. 1. (07 July 2007), pp. 77-102. by I. Vanleeuwen, H. Byrne, O. Jensen, J. King posted to beta_catenin wnt_pathway by m_j on 2008-10-30 08:56:40 as
	The untapped potential of virtual game worlds to shed light on real world epidemics [My Copy] The Lancet Infectious Diseases, Vol. 7, No. 9. (September 2007), pp. 625-629. by Eric T. Lofgren, Nina H. Fefferman posted to epidemics game wow by m_j on 2008-10-30 08:41:32 as along with 9 people rcrane skembel knowlengr dumpa madhadron lshaw ibschwartz Torsten_Holmer tminze
	Protein mobility in the cytoplasm of Escherichia coli. [My Copy] J Bacteriol, Vol. 181, No. 1. (January 1999), pp. 197-203. by M. B. Elowitz, M. G. Surette, P. E. Wolf, J. B. Stock, S. Leibler posted to diffusion molecular_crowding by m_j on 2008-10-20 14:25:43 as along with 3 people ocs csanford gabe_rosser
	Computational methods for diffusion-influenced biochemical reactions. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 15. (1 August 2007), pp. 1969-1977. by Maciej Dobrzynski, Jordi Vidal V. Rodríguez, Jaap A. Kaandorp, Joke G. Blom posted to brownian_dynamics diffusion stochastic_simulation by m_j on 2008-10-20 13:52:38 as along with 6 people and 1 group gabe_rosser jjray ocs balabu dagmar jmccammon McCammon
	Stochastic vs. Deterministic Modeling of Intracellular Viral Kinetics [My Copy] Journal of Theoretical Biology, Vol. 218, No. 3. (07 October 2002), pp. 309-321. by R. Srivastava, L. You, J. Summers, J. Yin posted to deterministic modeling stochastic_simulation by m_j on 2008-10-20 11:07:55 as
	A general method for numerically simulating the stochastic time evolution of coupled chemical reactions [My Copy] Journal of Computational Physics, Vol. 22, No. 4. (December 1976), pp. 403-434. by D. Gillespie posted to gillespie ssa stochastic_simulation by m_j on 2008-09-11 15:45:49 as along with 13 people and 1 group Dangerfc bertelsen devinli fierykylin jporternj hadesnumb jberro rjoy mazzucco ptupper petermilner matthewhflamm jjray Projet_ENSIMAG
	Nonequilibrium chemical potentials and free energies for enzyme-catalyzed reactions [My Copy] Cell Biochemistry and Biophysics, Vol. 11, No. 1. (3 December 1987), pp. 331-344. by Joel Keizer posted to reaction_rate_constants reactions by m_j on 2008-09-11 12:25:39 as
	Brownian Dynamics Simulation of Protein-Protein Diffusional Encounter [My Copy] Methods, Vol. 14, No. 3. (March 1998), pp. 329-341. by Razif R. Gabdoulline, Rebecca C. Wade posted to brownian_dynamics diffusion simulation by m_j on 2008-09-10 11:55:58 as along with 2 people and 2 groups barry Martin8223 structural_bioinformatics Bioinformatics
	Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli [My Copy] Bioinformatics, Vol. 22, No. 15. (1 August 2006), pp. 1895-1901. by Jordi V. Rodríguez, Jaap A. Kaandorp, Maciej Dobrzynski, Joke G. Blom posted to gillespie reactions simulator ssa_alternative by m_j on 2008-09-09 15:56:22 as along with 2 people and 1 group fierykylin dagmar compneur
	Cellular Automata Approaches to Enzymatic Reaction Networks [My Copy] Cellular Automata (2002), pp. 294-303. by Jörg Weimar posted to cellular_automata reactions by m_j on 2008-09-09 15:45:26 as
	Simulating reaction-diusion cellular automata with JCASim [My Copy] In Discrete Modelling and Discrete Algorithms in Continuum Mechanics (2001), pp. 217-226. by Jorg R. Weimar posted to cellular_automata reactions by m_j on 2008-09-09 15:44:04 as
	Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws1 [My Copy] Progress in Biophysics and Molecular Biology*, Vol. 85, No. 2-3. (July 2004), pp. 235-260. by S. Schnell posted to cellular_automata molecular_crowding by m_j on 2008-09-09 15:42:34 as along with 5 people and 1 group mhellmann gabe_rosser schnell ras csanford IU_Informatics_CX
	Multiscale Modeling of Chemical Kinetics via the Master Equation [My Copy] Multiscale Modeling & Simulation, Vol. 6, No. 4. (2008), pp. 1146-1168. by Shev Macnamara, Kevin Burrage, Roger B. Sidje posted to master_equation multi_scale by m_j on 2008-06-26 13:26:17 as along with 1 person ocs
	Stochastic modeling and simulation of gene networks - A review of the state-of-the-art research on stochastic simulations [My Copy] Signal Processing Magazine, IEEE In Signal Processing Magazine, IEEE, Vol. 24, No. 1. (2007), pp. 27-36. by X. Cai, X. Wang posted to stochastic_simulation by m_j on 2008-06-23 15:35:20 as
	Conservative Parallel Simulation of Continuous Time Markov Chains Using Uniformization [My Copy] IEEE Trans. Parallel Distrib. Syst., Vol. 4, No. 8. (August 1993), pp. 906-921. by P. Heidelberger, D. M. Nicol posted to markov_process parallel by m_j on 2008-06-23 15:25:01 as
	Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: dynamics. [My Copy] Physical review. E, Statistical, nonlinear, and soft matter physics, Vol. 66, No. 5 Pt 1. (November 2002) by A. R. Kinjo, S. Takada posted to molecular_crowding by m_j on 2008-06-23 15:22:50 as
	Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: Statics [My Copy] Phys. Rev. E, Vol. 66, No. 3. (September 2002), 031911. by A. R. Kinjo, S. Takada posted to molecular_crowding by m_j on 2008-06-23 15:21:09 as
	Molecular-dynamics studies of annihilation reactions [My Copy] Europhysics Letters, Vol. 67 (September 2004), pp. 900-906. by F. Baras, M. Salazar, E. Kestemont, M. M. Mansour posted to molecular_dynamics reactions by m_j on 2008-06-23 15:11:23 as
	Pre-sampling as an approach for exploiting temporal uncertainty [My Copy] In PADS '00: Proceedings of the fourteenth workshop on Parallel and distributed simulation (2000), pp. 157-164. by Margaret L. Loper, Richard M. Fujimoto posted to network_simulation simulation by m_j on 2008-06-18 13:24:26 as
	Three-dimensional Cellular Automata for Reaction-Diffusion Systems [My Copy] by Jorg Weimar posted to cellular_automata by m_j on 2008-05-14 13:51:51 as
	Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. [My Copy] Phys Biol, Vol. 1, No. 3-4. (December 2004), pp. 137-151. by S. S. Andrews, D. Bray posted to particle_based simulation stochastic_simulation spatial_simulation by m_j on 2008-05-14 13:40:44 as along with 9 people and 3 groups vladimirov jjray fierykylin roland_ewald dagmar csanford lenov gabe_rosser arjunan dIEMoSIRIS MoSi-Rostock compneur
	Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico. [My Copy] FEBS letters, Vol. 579, No. 8. (21 March 2005), pp. 1783-1788. by Kouichi Takahashi, Satya Nanda Vel N. Arjunan, Masaru Tomita posted to molecular_crowding simulation systems_biology spatial_simulation by m_j on 2008-05-14 13:37:02 as along with 11 people and 3 groups gabe_rosser ddcttrl ocs monocyte biplabbose chrn biosv carmaus dagmar csanford arjunan dIEMoSIRIS MoSi-Rostock compneur

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stochastic_simulation	13
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brownian_dynamics	6
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cellular_automata	5
diffusion	5
reactions	5
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spatial_simulation	5
modeling	4
caveolae	3
models	3
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deterministic	2
gillespie	2
molecular_dynamics	2
ssa	2
systems_biology	2
beta_catenin	2
particle_based	2
plasma_membrane	1
game	1
multi_scale	1
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tau_leaping	1
master_equation	1
multi-scale	1
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epidemics	1
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