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pmendes library [128 articles]

Статьи, недавно добавленные в библиотеку pmendes .
  • No free lunch theorems for optimization
    Evolutionary Computation, IEEE Transactions on, Vol. 1, No. 1. (1997), pp. 67-82.
    by DH Wolpert, WG Macready
    posted to theory optimization algorithm by pmendes on 2008-07-09 10:25:53 as read along with 10 people and 3 groups japarejo abhik balicea fghorow nojhan yog mmunson petrposik Bc91 aberlan EvolutionaryComputation Metaheuristics Optimization
  • An Introduction to the Conjugate Gradient Method Without the Agonizing Pain
    (1994)
    by Jonathan R Shewchuk
    posted to optimization algorithm by pmendes on 2008-07-09 10:23:19 as ** along with 10 people and 2 groups ansobol dsquared aufrank kutabar fghorow rblake iff thomast2 Zaphod nafets ur-cls uiuc-cs
  • Something from nothing -- bridging the gap between constraint-based and kinetic modelling
    FEBS Journal, Vol. 274, No. 21. (November 2007), pp. 5576-5585.
    by Kieran Smallbone, Evangelos Simeonidis, David S Broomhead, Douglas B Kell
    posted to modelling metabolism kinetics by pmendes on 2008-06-26 14:17:15 as ** along with 2 people and 1 group peterli dbk dbk-lab
  • Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics.
    Metabolic engineering, Vol. 5, No. 3. (July 2003), pp. 164-176.
    by D Visser, JJ Heijnen
    posted to modelling mca kinetics by pmendes on 2008-06-26 13:58:38 as **
  • Approximative kinetic formats used in metabolic network modeling
    Biotechnology and Bioengineering, Vol. 91, No. 5. (2005), pp. 534-545.
    by Joseph J Heijnen
    posted to review modelling kinetics by pmendes on 2008-06-26 13:56:14 as *** along with 1 person fishtank
  • Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 18. (6 May 2008), pp. 6608-6613.
    by B Schmierer, AL Tournier, PA Bates, CS Hill
    posted to used-copasi signalling parameter-estimation modelling by pmendes on 2008-05-22 20:29:19 as **
  • Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation
    Algorithms in Bioinformatics (2007), pp. 420-430.
    by Geoffrey Koh, Lisa Tucker-Kellogg, David Hsu, P Thiagarajan
    posted to used-copasi parameter-estimation modelling by pmendes on 2008-05-22 20:26:42 as **
  • 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 simulation pentose-phosphate-pathway optimization modelling metabolism is-in-biomodels glycolysis erythrocyte by pmendes on 2008-05-19 11:06:33 as read along with 3 people and 1 group JeremyZucker sobolevnrm alexg baker-group
  • Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
    J. Comput. Phys., Vol. 206, No. 2. (2005), pp. 395-411.
    by Yang Cao, Dan Gillespie, Linda Petzold
    posted to stochastic simulation multi-scale modelling algorithm by pmendes on 2008-05-13 01:56:11 as ** along with 2 people ptupper LarryT
  • Stochastic simulation of chemical kinetics.
    Annu Rev Phys Chem, Vol. 58 (2007), pp. 35-55.
    by DT Gillespie
    posted to stochastic simulation review modelling kinetics by pmendes on 2008-05-12 00:05:35 as ** along with 3 people and 3 groups jjray dbikard carmaus Centre de Recherches Interdisciplinaires dIEMoSIRIS MoSi-Rostock
  • Extraction of elementary rate constants from global network analysis of E. coli central metabolism
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Jiao Zhao, Douglas Ridgway, Gordon Broderick, Andriy Kovalenko, Michael Ellison
    posted to parameter-estimation modelling kinetics by pmendes on 2008-05-11 16:59:38 as read along with 1 person jrbanga
  • Algorithms for Minimisation Without Derivatives
    (1973)
    by Richard P Brent
    posted to optimization algorithm by pmendes on 2008-05-10 09:48:30 as **
  • An efficient method for finding the minimum of a function of several variables without calculating derivatives
    The Computer Journal, Vol. 7, No. 2. (1 February 1964), pp. 155-162.
    by MJD Powell
    posted to optimization algorithm by pmendes on 2008-05-10 09:15:44 as read along with 2 people yocchiman vandoormaal
  • Particle swarm optimization
    Neural Networks, 1995. Proceedings., IEEE International Conference on, Vol. 4 (1995), pp. 1942-1948 vol.4.
    by J Kennedy, R Eberhart
    posted to stochastic particle-swarm optimization algorithm by pmendes on 2008-05-10 09:02:20 as read along with 9 people and 2 groups peskin nigham sdvillal pescar238 dilbert rodrhern mahmoodr laura_prada Iainios SORG uchile_int_computacional
  • Discrete stochastic simulation of cell signaling: comparison of computational tools
    Engineering in Medicine and Biology Society, 2006. EMBS '06. 28th Annual International Conference of the IEEE (2006), pp. 2013-2016.
    by Tiina Manninen, Eeva Makiraatikka, Antti Ylipaa, Antti Pettinen, Kalle Leinonen, Marja-Leena Linne
    posted to stochastic software simulation review copasi comparison by pmendes on 2008-04-29 23:58:17 as **
  • Synthesis of dihydropyridines and pyridines from imines and alkynes via C-H activation.
    Journal of the American Chemical Society, Vol. 130, No. 11. (19 March 2008), pp. 3645-3651.
    by DA Colby, RG Bergman, JA Ellman
    posted to used-copasi by pmendes on 2008-04-29 23:56:06 as **
  • Using process diagrams for the graphical representation of biological networks
    Nature Biotechnology, Vol. 23, No. 8. (04 August 2005), pp. 961-966.
    by Hiroaki Kitano, Akira Funahashi, Yukiko Matsuoka, Kanae Oda
    posted to visualization systems-biology networks bioinformatics by pmendes on 2008-04-28 03:05:16 as read along with 6 people csanford srp33 lenov dullhunk massivemayhem maralena
  • Maximum Likelihood from Incomplete Data via the EM Algorithm
    Journal of the Royal Statistical Society. Series B (Methodological), Vol. 39, No. 1. (1977), pp. 1-38.
    by AP Dempster, NM Laird, DB Rubin
    posted to theory stochastic parameter-estimation algorithm by pmendes on 2008-04-28 00:36:57 as **
  • Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate
    Nature Cell Biology, Vol. 9, No. 3. (18 February 2007), pp. 324-330.
    by Silvia DM Santos, Peter J Verveer, Philippe IH Bastiaens
    posted to signalling reverse-engineering by pmendes on 2008-04-27 18:50:36 as ** along with 1 person and 1 group balabu Bioinformatics
  • Microarray data analysis methods and their applications to gene expression data analysis for Saccharomyces cerevisiae under oxidative stress.
    (2006)
    by Wei Sha
    posted to transcriptomics gene-networks bioinformatics by pmendes on 2008-04-27 02:45:59 as **
  • Stochastic ranking for constrained evolutionary optimization
    IEEE Transactions on Evolutionary Computation, Vol. 4 (2000), pp. 284-294.
    by T Runarsson, X Yao
    posted to parameter-estimation optimization evolution-strategy evolutionary-algorithm algorithm by pmendes on 2008-04-27 00:08:59 as read
  • The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks.
    J Mol Biol, Vol. 334, No. 2. (21 November 2003), pp. 197-204.
    by S Mangan, A Zaslaver, U Alon
    posted to theory modelling gene-networks by pmendes on 2008-04-26 17:48:51 as ** along with 2 people jstajic karfunkel
  • A connectionist model of development.
    Journal of theoretical biology, Vol. 152, No. 4. (21 October 1991), pp. 429-453.
    by E Mjolsness, DH Sharp, J Reinitz
    posted to theory modelling gene-networks by pmendes on 2008-04-26 17:04:57 as **
  • A mathematical framework for describing and analysing gene regulatory networks.
    Journal of theoretical biology, Vol. 176, No. 2. (21 September 1995), pp. 291-300.
    by T Mestl, E Plahte, SW Omholt
    posted to theory modelling gene-networks by pmendes on 2008-04-26 16:37:30 as **
  • Modeling gene expression with differential equations.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Vol. 4 (1999), pp. 29-40.
    by T Chen, HL He, GM Church
    posted to modelling gene-networks by pmendes on 2008-04-26 15:57:59 as read
  • A computational algebra approach to the reverse engineering of gene regulatory networks.
    Journal of theoretical biology, Vol. 229, No. 4. (21 August 2004), pp. 523-537.
    by R Laubenbacher, B Stigler
    posted to systems-biology reverse-engineering modelling gene-networks discrete by pmendes on 2008-04-26 15:30:50 as read
  • Homeostasis and differentiation in random genetic control networks.
    Nature, Vol. 224, No. 5215. (11 October 1969), pp. 177-178.
    by S Kauffman
    posted to simulation modelling gene-networks boolean by pmendes on 2008-04-26 15:13:41 as **
  • Gene regulation networks: a theory for their global structure and behaviors.
    Curr Top Dev Biol, Vol. 6, No. 6. (1971), pp. 145-182.
    by S Kauffman
    posted to simulation review modelling gene-networks boolean by pmendes on 2008-04-26 15:12:25 as **
  • The large scale structure and dynamics of gene control circuits: an ensemble approach.
    Journal of theoretical biology, Vol. 44, No. 1. (March 1974), pp. 167-190.
    by S Kauffman
    posted to simulation modelling gene-networks boolean by pmendes on 2008-04-26 15:10:30 as **
  • Metabolic stability and epigenesis in randomly constructed genetic nets.
    J Theor Biol, Vol. 22, No. 3. (March 1969), pp. 437-467.
    by SA Kauffman
    posted to simulation modelling gene-networks boolean by pmendes on 2008-04-26 15:07:34 as ** along with 2 people hito gurkanbebek
  • Parameter optimization in S-system models
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Marco Vilela, Chun I Chou, Susana Vinga, Ana T Vasconcelos, Eberhard Voit, Jonas Almeida
    posted to reverse-engineering parameter-estimation bst by pmendes on 2008-04-25 13:35:51 as ***
  • Insights into Zn2+ homeostasis in neurons from experimental and modeling studies.
    American journal of physiology. Cell physiology, Vol. 294, No. 3. (March 2008), pp. C726-C742.
    by RA Colvin, AI Bush, I Volitakis, CP Fontaine, D Thomas, K Kikuchi, WR Holmes
    posted to used-gepasi used-copasi simulation modelling metabolism kinetics by pmendes on 2008-04-23 19:46:51 as **
  • LibSBML: An API Library for SBML
    Bioinformatics (5 February 2008), btn051.
    by Benjamin J Bornstein, Sarah M Keating, Akiya Jouraku, Michael Hucka
    posted to systems-biology standards software sbml by pmendes on 2008-04-23 19:22:28 as ** along with 5 people jyuh chad_davis dullhunk lenov maralena
  • Full-scale model of glycolysis in Saccharomyces cerevisiae
    Biophysical Chemistry, Vol. 94, No. 1-2. (11 December 2001), pp. 121-163.
    by F Hynne, S Dano, PG Sorensen
    posted to yeast simulation parameter-estimation nonlinear-dynamics modelling metabolism kinetics by pmendes on 2008-04-23 19:13:35 as ** along with 1 person westoll
  • Metabolic control analysis of moiety-conserved cycles
    European Journal of Biochemistry, Vol. 155, No. 3. (1986), pp. 631-640.
    by Jan, Henrik Kacser, Kirsten J Merwe
    posted to theory modelling metabolism mca by pmendes on 2008-04-23 19:09:45 as read along with 1 person athleem
  • Metabolic Control Analysis of Glycerol Synthesis in Saccharomyces cerevisiae
    Appl. Environ. Microbiol., Vol. 68, No. 9. (1 September 2002), pp. 4448-4456.
    by Garth R Cronwright, Johann M Rohwer, Bernard A Prior
    posted to simulation modelling metabolism kinetics by pmendes on 2008-04-23 19:04:31 as read along with 1 person athleem
  • Metabolic control mechanisms. 5. A solution for the equations representing interaction between glycolysis and respiration in ascites tumor cells.
    The Journal of Biological Chemistry, Vol. 235 (August 1960), pp. 2426-2439.
    by B Chance, D Garfinkel, J Higgins, B Hess
    posted to simulation modelling metabolism kinetics computer-archeology by pmendes on 2008-04-23 18:45:28 as read
  • Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology
    (14 December 1998)
    by Gerhard Michal
    posted to visualization metabolism by pmendes on 2008-04-23 17:36:10 as read along with 1 person fishtank
  • BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by N Le Novère, B Bornstein, A Broicher, M Courtot, M Donizelli, H Dharuri, L Li, H Sauro, M Schilstra, B Shapiro, JL Snoep, M Hucka
    posted to sbml modelling database by pmendes on 2008-04-23 01:34:07 as read along with 4 people and 2 groups wnpx dullhunk dagmar lenov dIEMoSIRIS compneur
  • Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use
    Bio/Technology, Vol. 12, No. 10. (October 1994), pp. 994-998.
    by Amit Varma, Bernhard O Palsson
    posted to metabolism fba by pmendes on 2008-04-23 01:11:19 as * along with 2 people roys Ema
  • Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era.
    Biotechnol Prog, Vol. 15, No. 3. (n 1999), pp. 296-303.
    by CH Schilling, S Schuster, BO Palsson, R Heinrich
    posted to theory network-structure metabolism extreme-pathways elementary-modes by pmendes on 2008-04-23 01:04:53 as read along with 1 person and 1 group camster dbk-lab
  • Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism.
    J Math Biol, Vol. 45, No. 2. (August 2002), pp. 153-181.
    by S Schuster, C Hilgetag, JH Woods, DA Fell
    posted to network-structure metabolism elementary-modes by pmendes on 2008-04-23 01:02:04 as read along with 2 people and 1 group camster Borelli dbk-lab
  • Metabolic control theory: A structural approach
    Journal of Theoretical Biology, Vol. 135 (1988), pp. 175-201.
    by C Reder
    posted to theory network-structure metabolism mca by pmendes on 2008-04-23 00:55:12 as read along with 1 person tomrevilla
  • The theory of oscillating reactions
    Industrial & Engineering Chemistry, Vol. 59, No. 5. (1967), pp. 18-62.
    by JJ Higgins
    posted to simulation oscillations nonlinear-dynamics modelling metabolism kinetics computer-archeology by pmendes on 2008-04-22 22:07:46 as ****
  • Analogue and digital representations of enzyme kinetics
    J. Biol. Chem., Vol. 235 (1960), pp. 2440-2443.
    by B Chance
    posted to simulation kinetics computer-archeology by pmendes on 2008-04-22 21:45:08 as read
  • A hybrid computer for the investigation of chemical reactions: the Johnson Foundation electronic computer, mark II
    Annals of the New York Academy of Sciences, Vol. 115 (31 July 1964), pp. 1025-1037.
    by JJ Higgins
    posted to simulation kinetics computer-archeology by pmendes on 2008-04-22 21:41:27 as ****
  • Cyclic and oscillatory responses of metabolic pathways involving chemical feedback and their computer representations
    Annals of the New York Academy of Sciences, Vol. 115 (31 July 1964), pp. 1010-1024.
    by B Chance, A Ghosh, JJ Higgins, PK Maitra
    posted to simulation oscillations modelling metabolism by pmendes on 2008-04-22 21:36:57 as ****
  • Analysis of sequential reactions
    Annals of the New York Academy of Sciences, Vol. 108 (1963), pp. 305-321.
    by JJ Higgins
    posted to modelling mca kinetics by pmendes on 2008-04-22 21:35:23 as read
  • Analogue and digital computer representations of biochemical processes.
    Federation proceedings, Vol. 21 (b 1962), pp. 75-86.
    by B Chance, JJ Higgins, D Garfinkel
    posted to systems-biology simulation modelling metabolism by pmendes on 2008-04-22 21:32:02 as read
  • The possible effect of the aggregation of the molecules of hæmoglobin.
    J. Physiol., Vol. 40 (1910), pp. iv-vii.
    by AV Hill
    posted to kinetics hill hemaglobin cooperativity by pmendes on 2008-04-22 21:15:33 as read
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