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	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
	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
	Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel. [My Copy] Biochim Biophys Acta, Vol. 1289, No. 2. (15 March 1996), pp. 175-186. 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 17:40:42 as along with 1 person and 2 groups dbk streptomyces dbk-lab
	Making cells work--metabolic engineering for everyone. [My Copy] Trends Biotechnol, Vol. 15, No. 1. (January 1997), pp. 6-7. by P. Mendes, D. Kell posted to meeting-report mendes metabolic-engineering by pmendes on 2008-02-29 17:39:53 as
	Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. [My Copy] Trends in biochemical sciences, Vol. 22, No. 9. (September 1997), pp. 361-363. by P. Mendes posted to gepasi mendes modelling simulation software by pmendes on 2008-02-29 17:38:57 as along with 3 people and 3 groups peterli beapen csanford Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics
	Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 14, No. 10. (1 November 1998), pp. 869-883. by P. Mendes, D. Kell posted to gepasi mendes modelling optimization parameter-estimation simulation software by pmendes on 2008-02-29 17:38:17 as along with 6 people and 1 group nicholasflann peterli yujiangwang dullhunk dagmar csgillespie compneur
	ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. [My Copy] Bioinformatics, Vol. 17, No. 1. (January 2001), pp. 83-94. by A. Siepel, A. Farmer, A. Tolopko, et al.M. Zhuang, P. Mendes, W. Beavis, B. Sobral posted to bioinformatics component-based mendes visualization by pmendes on 2008-02-29 17:37:39 as along with 1 person dullhunk
	MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. [My Copy] Bioinformatics, Vol. 17, No. 3. (March 2001), pp. 288-289. by P. Mendes, D. B. Kell posted to gepasi mendes modelling simulation by pmendes on 2008-02-29 17:34:11 as along with 3 people and 2 groups camster dbk LeightonP streptomyces dbk-lab
	Bioinformatics for rice resources. [My Copy] Novartis Found Symp, Vol. 236 (2001) by B. W. Sobral, H. Mangalam, A. Siepel, P. Mendes, R. Pecherer, G. McLaren posted to bioinformatics mendes by pmendes on 2008-02-29 17:33:41 as
	In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae. [My Copy] Eur J Biochem, Vol. 268, No. 14. (July 2001), pp. 3930-3936. by A. M. Martins, P. Mendes, C. Cordeiro, A. P. Freire posted to glx kinetics mendes used-gepasi yeast by pmendes on 2008-02-29 17:33:05 as
	Emerging bioinformatics for the metabolome. [My Copy] Brief Bioinform, Vol. 3, No. 2. (June 2002), pp. 134-145. by P. Mendes posted to mendes metabolomics review by pmendes on 2008-02-29 17:31:42 as along with 3 people and 1 group irenas katerinakal JeremyZucker dbk-lab
	Linking the genes: inferring quantitative gene networks from microarray data. [My Copy] Trends Genet, Vol. 18, No. 8. (August 2002), pp. 395-398. by A. de la Fuente, P. Brazhnik, P. Mendes posted to gene-networks mendes reverse-engineering systems-biology transcriptomics by pmendes on 2008-02-29 17:31:10 as along with 2 people and 3 groups beapen heliopais Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics
	Metabolic control in integrated biochemical systems. [My Copy] Eur J Biochem, Vol. 269, No. 18. (September 2002), pp. 4399-4408. by A. de la Fuente, J. L. Snoep, H. V. Westerhoff, P. Mendes posted to gene-expression-metabolism mca mendes modelling used-gepasi by pmendes on 2008-02-29 17:29:00 as
	Quantifying gene networks with regulatory strengths. [My Copy] Mol Biol Rep, Vol. 29, No. 1-2. (2002), pp. 73-77. by A. de la Fuente, P. Mendes posted to gene-networks mendes reverse-engineering systems-biology transcriptomics by pmendes on 2008-02-29 17:27:21 as
	Gene networks: how to put the function in genomics. [My Copy] Trends in biotechnology, Vol. 20, No. 11. (November 2002), pp. 467-472. by Paul Brazhnik, Alberto de la Fuente, Pedro Mendes posted to gene-networks mendes review systems-biology transcriptomics by pmendes on 2008-02-29 17:26:27 as along with 1 person frohike
	Plant metabolomics: large-scale phytochemistry in the functional genomics era. [My Copy] Phytochemistry, Vol. 62, No. 6. (March 2003), pp. 817-836. by L. W. Sumner, P. Mendes, R. A. Dixon posted to mendes metabolomics review by pmendes on 2008-02-29 17:25:25 as along with 2 people and 1 group ajaymalik irenas dbk-lab
	The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models [My Copy] Bioinformatics, Vol. 19, No. 4. (1 March 2003), pp. 524-531. by M. Hucka, A. Finney, H. M. Sauro, et al.H. Bolouri, J. C. Doyle, H. Kitano, and the rest of the SBML Forum:, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J. H. Hofmeyr, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, J. Wang posted to mendes modelling sbml simulation standards by pmendes on 2008-02-29 17:22:13 as along with 20 people and 2 groups jporternj daforerog whitead antonkratz michaelbarton allysonlister rh020 shikin subhacom irenas husain easr balajis wnpx jbchang lenov nicholasflann csanford AlexanderPico dullhunk Jiang Research Group dbk-lab
	Artificial gene networks for objective comparison of analysis algorithms [My Copy] Bioinformatics In Bioinformatics, Vol. 19, No. suppl_2. (27 September 2003), pp. ii122-129. by Pedro Mendes, Wei Sha, Keying Ye posted to gene-networks mendes modelling reverse-engineering simulation transcriptomics by pmendes on 2008-02-29 17:21:30 as along with 9 people and 2 groups meanerelk fastjoe23 poirel tonamswish kaarsinogen camster tmmurali dragonrez lfriedl dbk-lab kdl
	Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods [My Copy] Genome Research, Vol. 13, No. 11. (1 November 2003), pp. 2467-2474. by Carmen G. Moles, Pedro Mendes, Julio R. Banga posted to mendes modelling parameter-estimation simulation by pmendes on 2008-02-29 17:18:15 as along with 10 people and 3 groups yuansong78 kentz peterli cannin Borelli os252 nojhan jrbanga petrposik lord_weldaan EvolutionaryComputation Metaheuristics Optimization
	myo-inositol oxygenase offers a possible entry point into plant ascorbate biosynthesis. [My Copy] Plant Physiol, Vol. 134, No. 3. (March 2004), pp. 1200-1205. by A. Lorence, B. I. Chevone, P. Mendes, C. L. Nessler posted to ascorbate mendes metabolism by pmendes on 2008-02-29 17:17:30 as
	Integrative modelling of gene expression and cell metabolism. [My Copy] Appl Bioinformatics, Vol. 2, No. 2. (2003), pp. 79-90. by A. de la Fuente, P. Mendes posted to mendes metabolism modelling review transcription by pmendes on 2008-02-29 17:15:05 as
	Discovery of meaningful associations in genomic data using partial correlation coefficients. [My Copy] Bioinformatics, Vol. 20, No. 18. (12 December 2004), pp. 3565-3574. by A. de la Fuente, N. Bing, I. Hoeschele, P. Mendes posted to mendes partial-correlation reverse-engineering transcriptomics by pmendes on 2008-02-29 17:14:00 as along with 1 person dragonrez
	Potential of metabolomics as a functional genomics tool. [My Copy] Trends Plant Sci, Vol. 9, No. 9. (September 2004), pp. 418-425. by R. J. Bino, R. D. Hall, O. Fiehn, et al.J. Kopka, K. Saito, J. Draper, B. J. Nikolau, P. Mendes, U. Roessner-Tunali, M. H. Beale, R. N. Trethewey, B. M. Lange, E. S. Wurtele, L. W. Sumner posted to mendes metabolomics standards by pmendes on 2008-02-29 17:12:15 as along with 3 people and 1 group katerinakal irenas BIBLIOma dbk-lab
	A proposed framework for the description of plant metabolomics experiments and their results [My Copy] Nature Biotechnology, Vol. 22, No. 12. (06 December 2004), 1601. by Helen Jenkins, Nigel Hardy, Manfred Beckmann, et al.John Draper, Aileen R. Smith, Janet Taylor, Oliver Fiehn, Royston Goodacre, Raoul J. Bino, Robert Hall, Joachim Kopka, Geoffrey A. Lane, B. Markus Lange, Jang R. Liu, Pedro Mendes, Basil J. Nikolau, Stephen G. Oliver, Norman W. Paton, Sue Rhee, Ute Roessner-Tunali, Kazuki Saito, Jørn Smedsgaard, Lloyd W. Sumner, Trevor Wang, Sean Walsh, Eve S. Wurtele, Douglas B. Kell posted to mendes metabolomics standards by pmendes on 2008-02-29 17:11:24 as along with 9 people and 2 groups dbk irenas betainverse LeightonP andytseng agileproteomics BIBLIOma dullhunk katerinakal streptomyces dbk-lab
	Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. [My Copy] J Exp Bot, Vol. 56, No. 410. (January 2005), pp. 323-336. by C. D. Broeckling, D. V. Huhman, M. A. Farag, et al.J. T. Smith, G. D. May, P. Mendes, R. A. Dixon, L. W. Sumner posted to medicago mendes metabolomics by pmendes on 2008-02-29 17:10:45 as
	Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula. [My Copy] Planta, Vol. 220, No. 5. (March 2005), pp. 696-707. by H. Suzuki, M. S. Reddy, M. Naoumkina, et al.N. Aziz, G. D. May, D. V. Huhman, L. W. Sumner, J. W. Blount, P. Mendes, R. A. Dixon posted to medicago mendes metabolomics proteomics transcriptomics by pmendes on 2008-02-29 17:09:23 as
	A two-dimensional electrophoresis proteomic reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula. [My Copy] Mol Cell Proteomics, Vol. 4, No. 11. (November 2005), pp. 1812-1825. by Z. Lei, A. M. Elmer, B. S. Watson, R. A. Dixon, P. J. Mendes, L. W. Sumner posted to medicago mendes proteomics by pmendes on 2008-02-29 17:08:03 as
	A hybrid approach for efficient and robust parameter estimation in biochemical pathways. [My Copy] Biosystems, Vol. 83, No. 2-3. (r 2006), pp. 248-265. by M. Rodriguez-Fernandez, P. Mendes, J. R. Banga posted to mendes modelling parameter-estimation simulation by pmendes on 2008-02-29 17:04:17 as along with 2 people and 1 group julius jrbanga SysbioMPI-TCells
	Modelling and simulation for metabolomics data analysis. [My Copy] Biochem Soc Trans, Vol. 33, No. Pt 6. (December 2005), pp. 1427-1429. by P. Mendes, D. Camacho, A. de la Fuente posted to mendes metabolomics modelling simulation by pmendes on 2008-02-29 17:02:40 as
	Minimum information requested in the annotation of biochemical models (MIRIAM) [My Copy] Nature Biotechnology, Vol. 23, No. 12. (06 December 2005), pp. 1509-1515. by Nicolas L. Novere, Andrew Finney, Michael Hucka, et al.Upinder S. Bhalla, Fabien Campagne, Julio Collado-Vides, Edmund J. Crampin, Matt Halstead, Edda Klipp, Pedro Mendes, Poul Nielsen, Herbert Sauro, Bruce Shapiro, Jacky L. Snoep, Hugh D. Spence, Barry L. Wanner posted to mendes modelling simulation standards by pmendes on 2008-02-29 17:00:22 as along with 16 people and 2 groups mtaschuk perkeo irenas jmuhlich bertelsen moonhouse schwartzjmc tjtaylor Vincent_Rouilly allysonlister michaelbarton subhacom dullhunk dagmar lenov leilaperie dIEMoSIRIS compneur
	Metabolomics and the challenges ahead. [My Copy] Brief Bioinform, Vol. 7, No. 2. (June 2006) by P. Mendes posted to editorial mendes metabolomics by pmendes on 2008-02-29 16:58:23 as along with 1 person katerinakal
	COPASI: a COmplex PAthway SImulator [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 24. (15 December 2006), pp. 3067-3074. by Stefan Hoops, Sven Sahle, Christine Lee, et al.Jurgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer posted to copasi kinetics mendes simulation software stochastic systems-biology by pmendes on 2008-02-29 16:56:05 as along with 11 people and 3 groups dadiamah jvb yujiangwang schwartzjmc tonamswish peterli agomez guhjy dragonrez carmaus dagmar dIEMoSIRIS MoSi-Rostock compneur
	Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae. [My Copy] Yeast, Vol. 24, No. 3. (March 2007), pp. 181-188. by A. M. Martins, W. Sha, C. Evans, S. Martino-Catt, P. Mendes, V. Shulaev posted to mendes metabolomics transcriptomics yeast by pmendes on 2008-02-29 16:54:06 as
	Metabolic footprinting: a new approach to identify physiological changes in complex microbial communities upon exposure to toxic chemicals. [My Copy] Environ Sci Technol, Vol. 41, No. 11. (1 June 2007), pp. 3945-3951. by I. D. Henriques, D. S. Aga, P. Mendes, S. K. O'Connor, N. G. Love posted to mendes metabolomics by pmendes on 2008-02-29 16:52:12 as
	The metabolomics standards initiative. [My Copy] Nat Biotechnol, Vol. 25, No. 8. (August 2007), pp. 846-848. by , S. A. Sansone, T. Fan, et al.R. Goodacre, J. L. Griffin, N. W. Hardy, R. Kaddurah-Daouk, B. S. Kristal, J. Lindon, P. Mendes, N. Morrison, B. Nikolau, D. Robertson, L. W. Sumner, C. Taylor, M. van der Werf, B. van Ommen, O. Fiehn posted to mendes metabolomics msi standards by pmendes on 2008-02-29 16:49:40 as along with 2 people guhjy katerinakal
	Comparison of Reverse-Engineering Methods Using an in Silico Network [My Copy] Annals of the New York Academy of Sciences, Vol. 1115, No. 1. (December 2007), pp. 73-89. by Diogo Camacho, Paola Vera-Licona, Pedro Mendes, Reinhard Laubenbacher posted to mendes reverse-engineering used-copasi by pmendes on 2008-02-29 16:47:59 as along with 2 people bertelsen guhjy
	The markup is the model: Reasoning about systems biology models in the Semantic Web era [My Copy] Journal of Theoretical Biology, Vol. 252, No. 3. (07 June 2008), pp. 538-543. by Douglas B. Kell, Pedro Mendes posted to semantics mendes mcisb heinrich by pmendes on 2008-02-29 16:43:01 as along with 5 people dagmar guhjy dullhunk fisherp alanrw

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