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	METAMOD: software for steady-state modeling and control analysis of metabolic pathways on the BBC microcomputer. [My Copy] Computer Applications in the Biosciences, Vol. 2, No. 4. (1986), pp. 243-249. by J. H. S. Hofmeyr, K. J. van der Merwe posted to software simulation modelling by pmendes on 2009-11-12 20:53:45 as
	Metabolic control analysis of moiety-conserved cycles. [My Copy] European Journal of Biochemistry, Vol. 155, No. 3. (1986), pp. 631-641. by J. H. S. Hofmeyr, H. Kacser, K. J. van der Merwe posted to theory modelling metabolism mca by pmendes on 2009-11-12 20:53:45 as
	Control pattern analysis of metabolic pathways. Flux and concentration control in linear pathways. [My Copy] Euopean Journal of Biochemistry, Vol. 186, No. 1-2. (1989), pp. 343-354. by J. H. S. Hofmeyr posted to theory modelling metabolism mca by pmendes on 2009-11-12 20:53:45 as
	Steady-state modeling of metabolic pathways. A guide for the prospective simulator. [My Copy] Computer Applications in the Biosciences, Vol. 2, No. 1. (1986), pp. 5-11. by J. H. S. Hofmeyr posted to theory review modelling by pmendes on 2009-11-12 20:53:45 as
	Metabolic regulation: a control analytic perspective [My Copy] Journal of Bioenergetics and Biomembranes, Vol. 27, No. 5. (1995), pp. 479-490. by J. H. Hofmeyr posted to theory modelling metabolism mca kinetics by pmendes on 2009-11-12 20:53:43 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 yeast systems-biology semantics sbml reconstruction modelling metabolism mcisb community_approach by pmendes on 2009-10-14 11:57:02 as along with 23 people and 2 groups dadiamah m_j windman83 jfr raiyar neilswainston irenas JeremyZucker chasmand schwartzjmc pinney pauldobson alaninmcr allysonlister zwang guhjy dbk michaelbarton ptrobajo neils dullhunk pengchy tmmurali MetabolicModeling BergmanLab
	Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis. [My Copy] Eur J Biochem, Vol. 269, No. 16. (August 2002), pp. 3894-3904. by L. Pritchard, D. B. Kell posted to yeast used-gepasi simulation parameter-estimation modelling metabolism glycolysis by pmendes on 2009-10-14 11:54:13 as along with 6 people and 2 groups schwartzjmc peterli michaelbarton dbk LeightonP dullhunk streptomyces dbk-lab
	The Systems Biology Graphical Notation [My Copy] Nature Biotechnology, Vol. 27, No. 8. (07 August 2009), pp. 735-741. by Nicolas L. Novere, Michael Hucka, Huaiyu Mi, et al.Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit I. Aladjem, Sarala M. Wimalaratne, Frank T. Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji, Lu Li, Yukiko Matsuoka, Alice Villeger, Sarah E. Boyd, Laurence Calzone, Melanie Courtot, Ugur Dogrusoz, Tom C. Freeman, Akira Funahashi, Samik Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin, Douglas B. Kell, Chris Sander, Herbert Sauro, Jacky L. Snoep, Kurt Kohn, Hiroaki Kitano posted to visualization systems-biology standards software signalling networks modelling metabolism gene-networks by pmendes on 2009-08-19 17:25:13 as along with 42 people and 3 groups agomez heliopais kshameer nuin singhsh greg tonamswish pablocarb josepe abc623 daforerog abhishek_tiwari robertrentzsch ngehlenborg pekrau thegoose bertelsen fgibson Borelli thomaskelder dullhunk polivares chasmand brianb roys torfinnnome guhjy Zephyrus lenov reyez allysonlister apocapoc renatomilani VGreiff druvus sjcockell jandot megraw leliavski frohike fpattyn jhyang Orengo Group Journal Picks Journal picks Neuroblastoma
	Something from nothing -- bridging the gap between constraint-based and kinetic modelling [My Copy] FEBS Journal, Vol. 274, No. 21. (November 2007), pp. 5576-5585. by Kieran Smallbone, Evangelos Simeonidis, David S. Broomhead, Douglas B. Kell posted to kinetics metabolism modelling by pmendes on 2008-06-26 14:17:15 as along with 5 people and 1 group abhishek_tiwari dadiamah schwartzjmc dbk peterli dbk-lab
	Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. [My Copy] Metabolic engineering, Vol. 5, No. 3. (July 2003), pp. 164-176. by D. Visser, J. J. Heijnen posted to kinetics mca modelling by pmendes on 2008-06-26 13:58:38 as
	Approximative kinetic formats used in metabolic network modeling. [My Copy] Biotechnology and bioengineering, Vol. 91, No. 5. (5 September 2005), pp. 534-545. by Joseph J. Heijnen posted to kinetics modelling review by pmendes on 2008-06-26 13:56:14 as along with 2 people bertelsen fishtank
	Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. [My Copy] 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, A. L. Tournier, P. A. Bates, C. S. Hill posted to modelling parameter-estimation signalling used-copasi by pmendes on 2008-05-22 20:29:19 as along with 2 people heliopais guhjy
	Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation [My Copy] Algorithms in Bioinformatics (2007), pp. 420-430. by Geoffrey Koh, Lisa Tucker-Kellogg, David Hsu, P. Thiagarajan posted to modelling parameter-estimation used-copasi 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. [My Copy] Eur J Biochem, Vol. 271, No. 14. (July 2004), pp. 2905-2922. by H. G. Holzhütter posted to erythrocyte glycolysis is-in-biomodels metabolism modelling optimization pentose-phosphate-pathway simulation by pmendes on 2008-05-19 11:06:33 as along with 4 people and 1 group schwartzjmc alexg sobolevnrm JeremyZucker baker-group
	Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems [My Copy] J. Comput. Phys., Vol. 206, No. 2. (2005), pp. 395-411. by Yang Cao, Dan Gillespie, Linda Petzold posted to algorithm modelling multi-scale simulation stochastic by pmendes on 2008-05-13 01:56:11 as along with 2 people ptupper LarryT
	Stochastic simulation of chemical kinetics. [My Copy] Annual review of physical chemistry, Vol. 58, No. 1. (2007), pp. 35-55. by Daniel T. Gillespie posted to kinetics modelling review simulation stochastic by pmendes on 2008-05-12 00:05:35 as along with 9 people and 3 groups gabe_rosser timflutre fierykylin devinli cannin jlidmar carmaus dbikard jjray dIEMoSIRIS MoSi-Rostock Centre de Recherches Interdisciplinaires
	Extraction of elementary rate constants from global network analysis of E. coli central metabolism [My Copy] BMC Systems Biology, Vol. 2, No. 1. (2008) by Jiao Zhao, Douglas Ridgway, Gordon Broderick, Andriy Kovalenko, Michael Ellison posted to kinetics modelling parameter-estimation by pmendes on 2008-05-11 16:59:38 as along with 1 person jrbanga
	The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. [My Copy] J Mol Biol, Vol. 334, No. 2. (21 November 2003), pp. 197-204. by S. Mangan, A. Zaslaver, U. Alon posted to gene-networks modelling theory by pmendes on 2008-04-26 17:48:51 as along with 2 people jstajic karfunkel
	A connectionist model of development. [My Copy] Journal of theoretical biology, Vol. 152, No. 4. (21 October 1991), pp. 429-453. by E. Mjolsness, D. H. Sharp, J. Reinitz posted to gene-networks modelling theory by pmendes on 2008-04-26 17:04:57 as
	A mathematical framework for describing and analysing gene regulatory networks. [My Copy] Journal of theoretical biology, Vol. 176, No. 2. (21 September 1995), pp. 291-300. by T. Mestl, E. Plahte, S. W. Omholt posted to gene-networks modelling theory by pmendes on 2008-04-26 16:37:30 as
	Modeling gene expression with differential equations. [My Copy] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Vol. 4 (1999), pp. 29-40. by T. Chen, H. L. He, G. M. Church posted to gene-networks modelling by pmendes on 2008-04-26 15:57:59 as along with 3 people dadiamah schwartzjmc nicholasflann
	A computational algebra approach to the reverse engineering of gene regulatory networks. [My Copy] Journal of theoretical biology, Vol. 229, No. 4. (21 August 2004), pp. 523-537. by R. Laubenbacher, B. Stigler posted to discrete gene-networks modelling reverse-engineering systems-biology by pmendes on 2008-04-26 15:30:50 as
	Homeostasis and differentiation in random genetic control networks. [My Copy] Nature, Vol. 224, No. 5215. (11 October 1969), pp. 177-178. by S. Kauffman posted to boolean gene-networks modelling simulation by pmendes on 2008-04-26 15:13:41 as
	Gene regulation networks: a theory for their global structure and behaviors. [My Copy] Curr Top Dev Biol, Vol. 6, No. 6. (1971), pp. 145-182. by S. Kauffman posted to boolean gene-networks modelling review simulation by pmendes on 2008-04-26 15:12:25 as
	The large scale structure and dynamics of gene control circuits: an ensemble approach. [My Copy] Journal of theoretical biology, Vol. 44, No. 1. (March 1974), pp. 167-190. by S. Kauffman posted to boolean gene-networks modelling simulation by pmendes on 2008-04-26 15:10:30 as
	Metabolic stability and epigenesis in randomly constructed genetic nets. [My Copy] J Theor Biol, Vol. 22, No. 3. (March 1969), pp. 437-467. by S. A. Kauffman posted to boolean gene-networks modelling simulation by pmendes on 2008-04-26 15:07:34 as along with 3 people jmenche hito gurkanbebek
	Insights into Zn2+ homeostasis in neurons from experimental and modeling studies. [My Copy] American journal of physiology. Cell physiology, Vol. 294, No. 3. (March 2008), pp. C726-C742. by R. A. Colvin, A. I. Bush, I. Volitakis, et al.C. P. Fontaine, D. Thomas, K. Kikuchi, W. R. Holmes posted to kinetics metabolism modelling simulation used-copasi used-gepasi by pmendes on 2008-04-23 19:46:51 as
	Full-scale model of glycolysis in Saccharomyces cerevisiae [My Copy] Biophysical Chemistry, Vol. 94, No. 1-2. (11 December 2001), pp. 121-163. by F. Hynne, S. Dano, P. G. Sorensen posted to kinetics metabolism modelling nonlinear-dynamics parameter-estimation simulation yeast by pmendes on 2008-04-23 19:13:35 as along with 4 people and 1 group dadiamah schwartzjmc tlse65 westoll smac
	Metabolic control analysis of moiety-conserved cycles [My Copy] European Journal of Biochemistry, Vol. 155, No. 3. (1986), pp. 631-640. by Jan, Henrik Kacser, Kirsten J. Merwe posted to mca metabolism modelling theory by pmendes on 2008-04-23 19:09:45 as along with 1 person athleem
	Metabolic Control Analysis of Glycerol Synthesis in Saccharomyces cerevisiae [My Copy] 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 kinetics metabolism modelling simulation by pmendes on 2008-04-23 19:04:31 as along with 1 person athleem
	Metabolic control mechanisms. 5. A solution for the equations representing interaction between glycolysis and respiration in ascites tumor cells. [My Copy] The Journal of Biological Chemistry, Vol. 235 (August 1960), pp. 2426-2439. by B. Chance, D. Garfinkel, J. Higgins, B. Hess posted to computer-archeology kinetics metabolism modelling simulation by pmendes on 2008-04-23 18:45:28 as
	BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. [My Copy] Nucleic acids research, Vol. 34, No. Database issue. (1 January 2006), pp. D689-D691. by N. Le Novère, B. Bornstein, A. Broicher, et al.M. Courtot, M. Donizelli, H. Dharuri, L. Li, H. Sauro, M. Schilstra, B. Shapiro, J. L. Snoep, M. Hucka posted to database modelling sbml by pmendes on 2008-04-23 01:34:07 as along with 11 people and 2 groups irenas jporternj yujiangwang peterli behindtherabbit allysonlister shikin wnpx dullhunk dagmar lenov dIEMoSIRIS compneur
	The theory of oscillating reactions [My Copy] Industrial & Engineering Chemistry, Vol. 59, No. 5. (1967), pp. 18-62. by J. J. Higgins posted to computer-archeology kinetics metabolism modelling nonlinear-dynamics oscillations simulation by pmendes on 2008-04-22 22:07:46 as
	Cyclic and oscillatory responses of metabolic pathways involving chemical feedback and their computer representations [My Copy] Annals of the New York Academy of Sciences, Vol. 115 (31 July 1964), pp. 1010-1024. by B. Chance, A. Ghosh, J. J. Higgins, P. K. Maitra posted to metabolism modelling oscillations simulation by pmendes on 2008-04-22 21:36:57 as
	Analysis of sequential reactions [My Copy] Annals of the New York Academy of Sciences, Vol. 108 (1963), pp. 305-321. by J. J. Higgins posted to kinetics mca modelling by pmendes on 2008-04-22 21:35:23 as
	Analogue and digital computer representations of biochemical processes. [My Copy] Federation proceedings, Vol. 21 (b 1962), pp. 75-86. by B. Chance, J. J. Higgins, D. Garfinkel posted to metabolism modelling simulation systems-biology by pmendes on 2008-04-22 21:32:02 as
	The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models [My Copy] Comput. Appl. Biosci., Vol. 13, No. 4. (1 August 1997), pp. 377-385. by Jan-Hendrik S. Hofmeyr, Hofmeyr Cornish-Bowden posted to cooperativity kinetics modelling by pmendes on 2008-04-22 21:11:20 as along with 1 person and 1 group athleem JJJ
	Role of substrate inhibition kinetics in enzymatic chemical oscillations. [My Copy] Biophysical journal, Vol. 67, No. 4. (October 1994), pp. 1414-1428. by P. Shen, R. Larter posted to kinetics metabolism modelling oscillations by pmendes on 2008-04-22 16:50:19 as
	A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker's yeast [My Copy] FEBS Journal, Vol. 273, No. 15. (August 2006), pp. 3520-3533. by Jorg Schaber, Bente Kofahl, Axel Kowald, Edda Klipp posted to modelling simulation systems-biology yeast by pmendes on 2008-04-11 10:42:04 as along with 2 people and 1 group jtaylor arne dIEMoSIRIS
	Exact Stochastic Simulation of Coupled Chemical Reactions [My Copy] The Journal of Physical Chemistry, Vol. 81, No. 25. (1977), pp. 2340-2361. by D. T. Gillespie posted to algorithm modelling simulation stochastic by pmendes on 2008-03-27 00:02:28 as along with 1 person and 1 group dagmar compneur
	On the killing of mycobacteria by macrophages [My Copy] Cellular Microbiology, Vol. 10, No. 2. (February 2008), pp. 529-548. by Luisa Jordao, Christopher K. Bleck, Luis Mayorga, Gareth Griffiths, Elsa Anes posted to immunology modelling simulation used-copasi by pmendes on 2008-03-25 11:03:30 as
	Kinetic model of sucrose accumulation in maturing sugarcane culm tissue [My Copy] Phytochemistry In Dynamic Metabolic Networks, Vol. 68, No. 16-18. ( 2007), pp. 2375-2392. by Lafras Uys, Frederik C. Botha, Jan-Hendrik S. Hofmeyr, Johann M. Rohwer posted to mca modelling used-copasi by pmendes on 2008-03-25 10:54:10 as along with 1 person lafras
	Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress [My Copy] Journal of Biology, Vol. 6 (21 December 2007), 10. by Markus Ralser, Mirjam M. Wamelink, Axel Kowald, et al.Birgit Gerisch, Gino Heeren, Eduard A. Struys, Edda Klipp, Cornelis Jakobs, Michael Breitenbach, Hans Lehrach, Sylvia Krobitsch posted to kinetics metabolism modelling pentose-phosphate-pathway used-copasi by pmendes on 2008-03-17 09:33:02 as along with 4 people and 1 group bertelsen thegoose2 guhjy tharris C. elegans / WormBase
	Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. [My Copy] European journal of biochemistry / FEBS, Vol. 267, No. 17. (September 2000), pp. 5313-5329. by B. Teusink, J. Passarge, C. A. Reijenga, et al.E. Esgalhado, C. C. van der Weijden, M. Schepper, M. C. Walsh, B. M. Bakker, K. van Dam, H. V. Westerhoff, J. L. Snoep posted to glycolysis metabolism modelling simulation by pmendes on 2008-03-02 18:01:04 as along with 6 people dadiamah schwartzjmc peterli dullhunk marcio michaelbarton
	Simulation of biochemical networks using COPASI: a complex pathway simulator [My Copy] In WSC '06: Proceedings of the 37th conference on Winter simulation (2006), pp. 1698-1706. by Sven Sahle, Ralph Gauges, J&\#252;rgen Pahle, et al.Natalia Simus, Ursula Kummer, Stefan Hoops, Christine Lee, Mudita Singhal, Liang Xu, Pedro Mendes posted to copasi mendes modelling simulation by pmendes on 2008-02-29 17:59:13 as along with 1 person and 2 groups carmaus dIEMoSIRIS MoSi-Rostock
	Channelling can decrease pool size. [My Copy] Eur J Biochem, Vol. 204, No. 1. (15 February 1992), pp. 257-266. by P. Mendes, D. B. Kell, H. V. Westerhoff posted to mendes metabolic-channelling metabolism modelling simulation used-gepasi by pmendes on 2008-02-29 17:44:37 as along with 1 person and 2 groups dbk streptomyces dbk-lab
	GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. [My Copy] Comput Appl Biosci, Vol. 9, No. 5. (October 1993), pp. 563-571. by P. Mendes posted to gepasi mendes modelling simulation software by pmendes on 2008-02-29 17:43:42 as along with 4 people and 4 groups tlse65 chrn beapen cfornari smac Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics
	On the role of enzyme kinetic parameters in determining the effectiveness with which channelling can decrease the size of a metabolite pool. [My Copy] Acta Biotheor, Vol. 41, No. 1-2. (June 1993), pp. 63-73. by P. Mendes, D. B. Kell posted to mendes metabolic-channelling metabolism modelling simulation used-gepasi by pmendes on 2008-02-29 17:43:05 as along with 1 person and 2 groups dbk streptomyces dbk-lab
	A series of cases in which metabolic channelling can decrease the pool size at constant net flux in a simple dynamic channel. [My Copy] Biochem Soc Trans, Vol. 23, No. 2. (May 1995) by P. Mendes, D. B. Kell, H. V. Westerhoff posted to mendes metabolic-channelling metabolism modelling simulation by pmendes on 2008-02-29 17:42:34 as along with 1 person and 2 groups dbk streptomyces dbk-lab
	On the analysis of the inverse problem of metabolic pathways using artificial neural networks. [My Copy] Biosystems, Vol. 38, No. 1. (1996), pp. 15-28. by P. Mendes, D. B. Kell posted to kinetics mendes modelling neural-networks reverse-engineering simulation used-gepasi by pmendes on 2008-02-29 17:41:33 as along with 1 person and 2 groups dbk streptomyces dbk-lab

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