http://w.atwiki.jp/metalmetabo/ Metal Meta-Metabolome Project ja 2010-11-09T20:58:45+09:00 1289303925 https://w.atwiki.jp/metalmetabo/pages/37.html &counter() visitors ＊＊＊＊　　JREC-INで就職した奴　　＊＊＊＊ http://www.unkar.org/read/science6.2ch.net/life/1234855617 2010-11-09T20:58:45+09:00 1289303925 https://w.atwiki.jp/metalmetabo/pages/36.html &counter() visitors ** A metabolic study reveals that plant-based compounds cooperate to overcome dehydration http://www.rikenresearch.riken.jp/eng/research/5806 http://www.rikenresearch.riken.jp/images/figures/hi_3382.jpg ** Comparative systems biology: from bacteria to man http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WSBM74.html http://media.wiley.com/wires/WSBM/WSBM74/nfig002.jpg ** The application of flux balance analysis in systems biology http://wires.wiley.com/WileyCDA/WiresArticle/articles.html?doi=10.1002%2Fwsbm.60 http://media.wiley.com/wires/WSBM/WSBM60/nfig002.jpg ** Comparative systems biology: from bacteria to man http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WSBM74.html http://media.wiley.com/wires/WSBM/WSBM74/nfig003.jpg 2010-10-06T22:01:14+09:00 1286370074 https://w.atwiki.jp/metalmetabo/pages/35.html **74. Comparative metabolic flux analysis of lysine-producing Corynebacterium glutamicum cultured on glucose or fructose nih.gov [HTML]P Kiefer, E Heinzle, O Zelder, C … - Applied and …, 2004 - Am Soc Microbiol >... A comprehensive approach to 13 C tracer studies, labeling measurements by gas chromatography-mass spectrometry, metabolite balancing, and isotopomer modeling, was applied for comparative metabolic network analysis of lysine-producing Corynebacterium glutamicum ... **70. It is all about metabolic fluxes nih.gov [HTML]J Nielsen - Journal of bacteriology, 2003 - Am Soc Microbiol http://scholar.google.com/scholar?q=related:xAvLLrdbbNYJ:scholar.google.com/&hl=ja&as_sdt=2000 >... I. Experimental observations. Biotechnol. Bioeng. 55:305-316.[CrossRef] 21; Thykaer, J., B. Christensen, and J. Nielsen. 2002. [[Metabolic network analysis]] of an adipoyl-7-ADCA producing strain of Penicillium chrysogenum: elucidation of adipate degradation.Metab. Eng. ... **47. In vivo analysis of intracellular amino acid labelings by GC/MS. C Wittmann, M Hans, E Heinzle - Analytical biochemistry, 2002 - mendeley.com >... TBDMS derivatization of amino acids is especially useful in metabolic network analysis, because M-57 fragments containing the entire carbon skeleton of the analyte can be observed by GC/MS with high signal intensities 8. The potential of the method is exemplified for ... 2010-09-28T22:21:47+09:00 1285680107 https://w.atwiki.jp/metalmetabo/pages/34.html &counter() visitors **In vivo analysis of intracellular amino acid labelings by GC/MS. C Wittmann, M Hans, E Heinzle - Analytical biochemistry, 2002 - mendeley.com >... TBDMS derivatization of amino acids is especially useful in metabolic network analysis, because M-57 fragments containing the entire carbon skeleton of the analyte can be observed by GC/MS with high signal intensities 8. The potential of the method is exemplified for ... **Comparative metabolic flux analysis of lysine-producing Corynebacterium glutamicum cultured on glucose or fructose nih.gov [HTML]P Kiefer, E Heinzle, O Zelder, C … - Applied and …, 2004 - Am Soc Microbiol >... A comprehensive approach to 13 C tracer studies, labeling measurements by gas chromatography-mass spectrometry, metabolite balancing, and isotopomer modeling, was applied for comparative metabolic network analysis of lysine-producing Corynebacterium glutamicum ... **It is all about metabolic fluxes nih.gov [HTML]J Nielsen - Journal of bacteriology, 2003 - Am Soc Microbiol http://scholar.google.com/scholar?q=related:xAvLLrdbbNYJ:scholar.google.com/&hl=ja&as_sdt=2000 >... I. Experimental observations. Biotechnol. Bioeng. 55:305-316.[CrossRef] 21; Thykaer, J., B. Christensen, and J. Nielsen. 2002. [[Metabolic network analysis]] of an adipoyl-7-ADCA producing strain of Penicillium chrysogenum: elucidation of adipate degradation.Metab. Eng. ... **Using topology of the metabolic network to predict viability of mutant strains biomedcentral.com [PDF]Z Wunderlich, L Mirny - Genome Biology, 2005 - biomedcentral.com http://scholar.google.com/scholar?q=related:sTavonuje7wJ:scholar.google.com/&hl=ja&as_sdt=2000 >... Ph.D. Thesis. University of Leeds; 1994. 14. Papp B, Pal C, Hurst LD: Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 2004, 429(6992):661-664. 15. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL: The large-scale ... **Novel proteins, putative membrane transporters, and an integrated metabolic network are revealed by quantitative proteomic analysis of Arabidopsis cell … plantphysiol.org [HTML]H Eubel, EH Meyer, NL Taylor, JD Bussell, N O' … - Plant …, 2008 - Am Soc Plant Biol http://scholar.google.com/scholar?q=related:aCgbR-dAtyMJ:scholar.google.com/&hl=ja&as_sdt=2000 >... This is aided by a metabolic network analysis that reveals a tight integration of functions and highlights specific metabolite nodes that most probably represent entry and exit metabolites that could require transport across the peroxisomal membrane. ... **High-throughput phenomics: experimental methods for mapping fluxomes bjmu.cn [PDF]U Sauer - Current opinion in Biotechnology, 2004 - Elsevier http://scholar.google.com/scholar?q=related:XvhSxXXwbn4J:scholar.google.com/&hl=ja&as_sdt=2000 >... From its early days when material fluxes were balanced within assumed reaction networks [7.], metabolic network analysis [6. and 8.] has matured to actually identify the topology of active reactions and pathways and to quantify the molecular flux through them on a variety of ... **Use of genome-scale microbial models for metabolic engineering KR Patil, M Åkesson, J Nielsen - Current opinion in biotechnology, 2004 - Elsevier http://scholar.google.com/scholar?q=related:oAOz5SBTVHAJ:scholar.google.com/&hl=ja&as_sdt=2000 >... incorporate genome-scale biological data. Genome-scale stoichiometric models of microorganisms represent a first step in this direction. FBA, flux balance analysis; MFA, metabolic flux analysis; MNA, metabolic network analysis. ... **Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression nih.gov [HTML]AK Gombert, M Moreira dos Santos, B … - Journal of …, 2001 - Am Soc Microbiol http://scholar.google.com/scholar?q=related:R5V_AodxCrwJ:scholar.google.com/&hl=ja&as_sdt=2000 >... flux estimates. The use of 13 C-labeled substrates enables both identification of the metabolic network structure and quantification of the metabolic fluxes and is therefore referred to as metabolic network analysis (5). This kind ... **Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method freelogy.org [PDF]J Zhao, K Shimizu - Journal of biotechnology, 2003 - Elsevier http://scholar.google.com/scholar?q=related:w1m-5IKYKpsJ:scholar.google.com/&hl=ja&as_sdt=2000 **Structural and functional analysis of cellular networks with CellNetAnalyzer biomedcentral.com [HTML]S Klamt, J Saez-Rodriguez, ED Gilles - BMC Systems Biology, 2007 - biomedcentral.com http://scholar.google.com/scholar?q=related:bzwlVku0FL8J:scholar.google.com/&hl=ja&as_sdt=2000 >... CNA extends its predecessor FluxAnalyzer, originally developed for metabolic network analysis[7], by new methods for signalling and regulatory networks, ie for networks where signal flows are dominating (in contrast to mass flows in metabolic networks). ... 2010-09-28T22:16:14+09:00 1285679774 https://w.atwiki.jp/metalmetabo/pages/33.html &counter() visitors **Metabolic network analysis of Streptomyces tenebrarius, a Streptomyces species with an active Entner-Doudoroff pathway nih.gov [HTML]I Borodina, C Scholler, A Eliasson, J … - Applied and …, 2005 - Am Soc Microbiol http://scholar.google.com/scholar?q=related:vbWz9Ak9HjwJ:scholar.google.com/&hl=ja&as_sdt=2000 >Streptomyces tenebrarius is an industrially important microorganism, producing an antibiotic complex that mainly consists of the aminoglycosides apramycin, tobramycin carbamate, and kanamycin B carbamate. When S. tenebrarius is used for industrial tobramycin ... **Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network J Lee, H Yun, AM Feist, BØ Palsson, SY Lee - Applied microbiology and …, 2008 - Springer http://scholar.google.com/scholar?q=related:6k93cgR0CzwJ:scholar.google.com/&hl=ja&as_sdt=2000 >Page 1. GENOMICS AND PROTEOMICS Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network Joungmin Lee & Hongseok Yun & Adam M. Feist & Bernhard Ø. Palsson & Sang Yup Lee ... **Metabolic networks in motion: 13C-based flux analysis nih.gov [HTML]U Sauer - Molecular systems biology, 2006 - nature.com http://scholar.google.com/scholar?q=related:B0vTesydGZwJ:scholar.google.com/&hl=ja&as_sdt=2000 >... Curr Opin Biotechnol 16: 350–355 | Article | PubMed | ISI | ChemPort |; Borodina I, Schöller C, Eliasson A, Nielsen J (2005) [[Metabolic network analysis]] of Streptomyces tenebrarius, a Streptomyces species with an active Entner–Doudoroff pathway. ... **Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks hindawi.com [PDF]O Fiehn - Comparative and Functional Genomics, 2001 - Wiley Online Library http://scholar.google.com/scholar?q=related:-r0O-RbpfxsJ:scholar.google.com/&hl=ja&as_sdt=2000 >... Metabolomics. The obvious next step in metabolic network analysis is to try to determine metabolic snapshots in a broad and comprehensive way. ... 13 Christensen B, Nielsen J. Metabolic network analysis: a powerful tool in metabolic engineering. ... **A metabolic network analysis & NMR experiment design tool with user interface-driven model construction for depth-first search analysis T Zhu, C Phalakornkule, S Ghosh, IE Grossmann, … - Metabolic …, 2003 - Elsevier http://scholar.google.com/scholar?q=related:Ov3p-3IVXxsJ:scholar.google.com/&hl=ja&as_sdt=2000 >A Windows program for metabolic engineering analysis and experimental design has been developed. A graphical user interface enables the pictorial, “on-screen” construction of a metabolic network. Once a model is composed, balance equations are automatically generated. ... **Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology plos.org [HTML]J Puchałka, MA Oberhardt, M Godinho, A Bielecka, … - PLoS Comput …, 2008 - dx.plos.org PLoS Computational Biology is an open-access. http://scholar.google.com/scholar?q=related:V6wktboEeLMJ:scholar.google.com/&hl=ja&as_sdt=2000 **Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae cshlp.org [HTML]MJ Herrgård, BS Lee, V Portnoy, BØ … - Genome research, 2006 - genome.cshlp.org http://scholar.google.com/scholar?q=related:-IQUN4gFKUgJ:scholar.google.com/&hl=ja&as_sdt=2000 >... biomass composition). The integration of the metabolic network analysis and the transcriptional regulatory network model described above is accomplished using the regulated flux balance analysis approach (Covert et al. 2001). In ... **Validation of a metabolic network for Saccharomyces cerevisiae using mixed substrate studies ulaval.ca [PDF]PA Vanrolleghem, P de Jong-Gubbels, … - Biotechnology …, 1996 - interscience.wiley.com http://scholar.google.com/scholar?q=related:jaCs_pUlSXcJ:scholar.google.com/&hl=ja&as_sdt=2000 >Page 1. ARTICLES Validation of a Metabolic Network for Saccharomyces cerevisiae Using Mixed Substrate Studies Peter A. Vanrolleghem,*,† Patricia de Jong-Gubbels,‡ Walter M. van Gulik,§ Jack T. Pronk,‡ Johannes P. van Dijken,‡ and Sef Heijnen† ... **Metabolic‐flux analysis of Saccharomyces cerevisiae CEN. PK113‐7D based on mass isotopomer measurements of 13C‐labeled primary metabolites WA Winden, JC Dam, C Ras, RJ Kleijn, JL … - FEMS yeast …, 2005 - Wiley Online Library Skip to Main Content. ... http://scholar.google.com/scholar?q=related:fM6Xi9-F_GIJ:scholar.google.com/&hl=ja&as_sdt=2000 **The efficiency of multi-target drugs: the network approach might help drug design arxiv.org [PDF]P Csermely, V Agoston, S Pongor - Trends in pharmacological sciences, 2005 - Elsevier http://scholar.google.com/scholar?q=related:U0rlpj3tgrYJ:scholar.google.com/&hl=ja&as_sdt=2000 >... 6111–6121. Full Text via CrossRef | View Record in Scopus | Cited By in Scopus (53). 8 B. Papp et al., Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast, Nature 429 (2004), pp. 661–664. Full Text via CrossRef | View Record in Scopus |. 2010-09-28T22:05:57+09:00 1285679157 https://w.atwiki.jp/metalmetabo/pages/32.html &counter() visitors **Development of network-based pathway definitions: the need to analyze real metabolic networks nhahocotton.org.vn [PDF]BO Palsson, ND Price, JA Papin - Update, 2003 - nhahocotton.org.vn http://scholar.google.com/scholar?q=related:RJrIZTi52eQJ:scholar.google.com/&hl=ja&as_sdt=2000 >... A recent article [1] addresses the important issue of network-based metabolic pathway analysis. ... References 1 Klamt, S. and Stelling, J. (2003) Two approaches for metabolic pathway analysis? Trends Biotechnol. 21, 64–69 2 Karp, PD et al. ... **PathFinder: reconstruction and dynamic visualization of metabolic pathways oxfordjournals.org [PDF]A Goesmann, M Haubrock, F Meyer, J … - …, 2002 - Oxford Univ Press http://scholar.google.com/scholar?q=related:tN609hXVn9QJ:scholar.google.com/&hl=ja&as_sdt=2000 >... database. Nucleic Acids Res., 26, 43–45. Tohsato,Y., Matsuda,H. and Hashimoto,A.(2000) A multiple align- ment algorithm for metabolic pathway analysis using enzyme hierarchy. Proceedings, ISMB 2000. pp. 376–383. Wackett ... **Toward metabolic phenomics: analysis of genomic data using flux balances dss.go.th [PDF]CH Schilling, JS Edwards, BO … - Biotechnology progress, 1999 - Wiley Online Library http://scholar.google.com/scholar?q=related:5xFNmiGLuFoJ:scholar.google.com/&hl=ja&as_sdt=2000 >... This approach of metabolic pathway analysis accompanied with FBA techniques can allow one to assess the basic structural capabilities and fitness of an organism as a result of the pathways that are theoretically present within the cell. ... **Robustness Analysis of the Escherichiacoli Metabolic Network dss.go.th [PDF]JS Edwards, BO Palsson - Biotechnology Progress, 2000 - interscience.wiley.com http://scholar.google.com/scholar?q=related:F73ImcZpznMJ:scholar.google.com/&hl=ja&as_sdt=2000 >Page 1. Robustness Analysis of the Escherichia coli Metabolic Network Jeremy S.Edwards† and Bernhard O. Palsson* Department of Bioengineering, University of California-San Diego, La Jolla, California 92093-0412 Genomic ... **FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps oxfordjournals.org [PDF]S Klamt, J Stelling, M Ginkel, ED Gilles - Bioinformatics, 2003 - Oxford Univ Press http://scholar.google.com/scholar?q=related:vOydM3d06iMJ:scholar.google.com/&hl=ja&as_sdt=2000 >... additionally reversibility and capacity restrictions for each reaction. Metabolic Pathway Analysis (MPA) searches for meaningful structural and functional units in metabolic networks. The two most promising, very similar ap- proaches ... **Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control JD Young, KL Henne, JA Morgan, AE … - Biotechnology and …, 2008 - interscience.wiley.com http://scholar.google.com/scholar?q=related:SiQjLbrsCw4J:scholar.google.com/&hl=ja&as_sdt=2000 >... biochemical networks. Combining cybernetic control laws with concepts from metabolic pathway analysis has culminated in a sys- tematic strategy for constructing cybernetic models, which was previously lacking. The newly ... **Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae oxfordjournals.org [PDF]S Schuster, T Pfeiffer, F Moldenhauer, I Koch, T … - …, 2002 - Oxford Univ Press http://scholar.google.com/scholar?q=related:o1Qpi78HxmoJ:scholar.google.com/&hl=ja&as_sdt=2000 >Page 1. BIOINFORMATICS Vol. 18 no. 2 2002 Pages 351–361 Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae S. Schuster 1 , T. Pfeiffer 2 , F. Moldenhauer 1 , I. Koch 3 and T. Dandekar 4, 5 ... **The complete genome sequence of the gastric pathogen Helicobacter pylori JF Tomb, O White, AR Kerlavage, RA Clayton, GG … - Nature, 1997 - nature.com http://scholar.google.com/scholar?q=related:Eo36dy8hFLcJ:scholar.google.com/&hl=ja&as_sdt=2000 >... Top of page Metabolism. [[Metabolic pathway analysis]] of the H. pylori genome suggests the following features. H. pylori uses glucose as the only source of carbohydrate and the main source for substrate-level phosphorylation. ... **Deriving phylogenetic trees from the similarity analysis of metabolic pathways oxfordjournals.org [PDF]M Heymans, AK Singh - Bioinformatics, 2003 - Oxford Univ Press http://scholar.google.com/scholar?q=related:Y2vvexN5fz8J:scholar.google.com/&hl=ja&as_sdt=2000 >Page 1. BIOINFORMATICS Vol. 19 Suppl. 1 2003, pages i138–i146 DOI:10.1093/bioinformatics/btg1018 Deriving phylogenetic trees from the similarity analysis of metabolic pathways Maureen Heymans and Ambuj K. Singh ∗ ... **Treatment of multifunctional enzymes in metabolic pathway analysis S Schuster, I Zevedei-Oancea - Biophysical chemistry, 2002 - Elsevier http://scholar.google.com/scholar?q=related:G_O7SiZhvKsJ:scholar.google.com/&hl=ja&as_sdt=2000 >In metabolic pathway analysis, it should be considered that many enzymes operate with low specificity (eg nucleoside diphosphokinase, uridine kinase, transketolase, aldolase), so that various substrates and products can be converted. Here, we analyze the effect of ... 2010-09-28T21:54:44+09:00 1285678484 https://w.atwiki.jp/metalmetabo/pages/31.html &counter() visitors **The small world inside large metabolic networks royalsocietypublishing.org [PDF]A Wagner, DA Fell - … of the Royal Society of London …, 2001 - rspb.royalsocietypublishing.org http://scholar.google.com/scholar?q=related:RzgGd87o6owJ:scholar.google.com/&hl=ja&as_sdt=2000 >Page 1. doi: 10.1098/rspb.2001.1711 , 1803-1810 268 2001 Proc. R. Soc. Lond. B Andreas Wagner and David A. Fell The small world inside large metabolic networks References http://rspb.royalsocietypublishing.org/content/268/1478/1803#related-urls Article cited in: ... **In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data vcu.edu [PDF]JS Edwards, RU Ibarra, BO Palsson - Nature biotechnology, 2001 - nature.com http://scholar.google.com/scholar?q=related:E0x6EPMqz7kJ:scholar.google.com/&hl=ja&as_sdt=2000 >... J. Theor. Biol. 203, 249–83 (2000). | Article | PubMed | ISI | ChemPort |; Schilling, CH, Schuster, S., Palsson, BO & Heinrich, R. [[Metabolic pathway analysis]]: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15, 296–303 (1999). ... **The small world of metabolism stanford.edu [PDF]DA Fell, A Wagner - Nature Biotechnology, 2000 - nature.com http://scholar.google.com/scholar?q=related:vJDOQbOxaVoJ:scholar.google.com/&hl=ja&as_sdt=2000 >... propositions. Top of page References. Schilling, CH, Schuster, S., Palsson, BO & Heinrich, R. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15, 296–303 (1999). ... **Metabolic pathways in the post-genome era psu.edu [PDF]JA Papin, ND Price, SJ Wiback, DA Fell, BO … - Trends in Biochemical …, 2003 - Elsevier http://scholar.google.com/scholar?q=related:yCUSHfucTk8J:scholar.google.com/&hl=ja&as_sdt=2000 >... All possible flux distributions of a metabolic network lie within the 'cone' circumscribed by the pathways. View Within Article. 1. History of network-based metabolic pathway analyses. Network-based metabolic pathway analysis has a relatively short history. ... **The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities pnas.org [HTML]JS Edwards, BO Palsson - … of Sciences of the United States …, 2000 - National Acad Sciences http://scholar.google.com/scholar?q=related:ylmoiEQjy08J:scholar.google.com/&hl=ja&as_sdt=2000 >... These methods include approaches such as metabolic control analysis (3, 4), flux balance analysis (FBA) (5–7), metabolic pathway analysis (8–11, 69), cybernetic modeling (12), biochemical systems theory (13), temporal decomposition (14), and so on. ... **Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices nih.gov [HTML]ND Price, JL Reed, JA Papin, I Famili, BO Palsson - Biophysical journal, 2003 - Elsevier http://scholar.google.com/scholar?q=related:vBbGDsA7avcJ:scholar.google.com/&hl=ja&as_sdt=2000 **Phylogenetic analysis based on genome-scale metabolic pathway reaction content silicobio.com [PDF]SH Hong, TY Kim, SY Lee - Applied microbiology and biotechnology, 2004 - Springer http://scholar.google.com/scholar?q=related:2MW2dxoUfOIJ:scholar.google.com/&hl=ja&as_sdt=2000 >Page 1. Appl Microbiol Biotechnol (2004) 65: 203–210 DOI 10.1007/s00253-004-1641-3 GENOMICS AND PROTEOMICS SH Hong . TY Kim . SY Lee Phylogenetic analysis based on genome-scale metabolic pathway reaction content ... **Extreme pathway lengths and reaction participation in genome-scale metabolic networks cshlp.org [HTML]JA Papin, ND Price, BØ Palsson - Genome research, 2002 - genome.cshlp.org http://scholar.google.com/scholar?q=related:o1ZwGAWEzSUJ:scholar.google.com/&hl=ja&as_sdt=2000 >... Schilling CH,; Schuster S.,; Palsson BO,; Heinrich R. (1999) Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era. Biotech. Prog. 15:296–303. ... **Flux coupling analysis of genome-scale metabolic network reconstructions cshlp.org [HTML]AP Burgard, EV Nikolaev, CH Schilling, CD … - Genome …, 2004 - genome.cshlp.org http://scholar.google.com/scholar?q=related:IXLhT3n9KwQJ:scholar.google.com/&hl=ja&as_sdt=2000 **Metabolic modeling of microbial strains in silico ru.nl [PDF]MW Covert, CH Schilling, I Famili, JS Edwards, … - Trends in Biochemical …, 2001 - Elsevier http://scholar.google.com/scholar?q=related:pjh6sWp3MRMJ:scholar.google.com/&hl=ja&as_sdt=2000 >... References. Schilling, CH et al., Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15, pp. 296–303. Schilling, CH et al., Towards metabolic phenomics: analysis of genomic data using flux balances. Biotechnol. ... 2010-09-28T21:42:52+09:00 1285677772 https://w.atwiki.jp/metalmetabo/pages/25.html &counter() visitors **Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic erapsu.edu [PDF] CH Schilling, S Schuster, BO Palsson, … - Biotechnology …, 1999 - interscience.wiley.com http://scholar.google.com/scholar?q=related:JkHo1UMnlWkJ:scholar.google.com/&hl=ja&as_sdt=2000 >This article reviews the relatively short history of metabolic pathway analysis. Computer-aided algorithms for the synthesis of metabolic pathways are discussed. Important algebraic concepts used in pathway analysis, such as null space and convex cone, are explained. It is ... **Metabolic pathway analysisS Schuster - Information and Simulation Systems for the Analysis of … - Citeseer http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.4013&rep=rep1&type=pdf#page=18 >18 Metabolic pathway analysis Stefan Schuster Max Delbruck Centre for Molecular Medicine D-13092 Berlin-Buch, Germany [[Metabolic network analysis]], alternatively called pathway analysis, has manifold applications in functional genomics, metabolic engineering and ... **Two approaches for metabolic pathway analysis? tkk.fi [PDF]S Klamt, J Stelling - TRENDS in Biotechnology, 2003 - Elsevier http://scholar.google.com/scholar?q=related:Zqc2nsalEsAJ:scholar.google.com/&hl=ja&as_sdt=2000 >Metabolic pathway analysis is becoming increasingly important for assessing inherent network properties in (reconstructed) biochemical reaction networks. Of the two most promising concepts for pathway analysis, one relies on elementary flux modes and the other on extreme ... **Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective CH Schilling, D Letscher, BØ PALSSON - Journal of Theoretical Biology, 2000 - Elsevier http://scholar.google.com/scholar?q=related:5zrGtYrEQUQJ:scholar.google.com/&hl=ja&as_sdt=2000 >... 4193–4198. Full Text via CrossRef | View Record in Scopus | Cited By in Scopus (78). 25. CH SCHILLING, S. SCHUSTER, BO PALSSON and R. HEINRICH, Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. ... **A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy Y Tohsato, H Matsuda, A Hashimoto - Proceedings of the 8th International …, 2000 - aaai.org http://scholar.google.com/scholar?q=related:Gyor1EbInm8J:scholar.google.com/&hl=ja&as_sdt=2000 >In many of the chemical reactions in living cells, enzymes act as catalysts in the conversion of certain compounds (substrates) into other compounds (products). Comparative analyses of the metabolic pathways formed by such reactions give important information on their ... **Metabolic pathway analysis of a recombinant yeast for rational strain development brookes.ac.uk [PDF]R Carlson, D Fell, F Srienc - Biotechnology and …, 2002 - interscience.wiley.com http://scholar.google.com/scholar?q=related:oWtlgoIqVyQJ:scholar.google.com/&hl=ja&as_sdt=2000 >Abstract: Elementary mode analysis has been used to study a metabolic pathway model of a recombinant Saccharomyces cerevisiae system that was genetically engineered to produce the bacterial storage compound poly-b-hydroxybutyrate (PHB). The model includes bio- ... **Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC) oxfordjournals.org [HTML]SA Rahman, P Advani, R Schunk, R Schrader, D … - …, 2005 - Oxford Univ Press http://scholar.google.com/scholar?q=related:MgbBoNOqvX8J:scholar.google.com/&hl=ja&as_sdt=2000 >Motivation: Pathway Hunter Tool (PHT), is a fast, robust and user-friendly tool to analyse the shortest paths in metabolic pathways. The user can perform shortest path analysis for one or more organisms or can build virtual organisms (networks) using enzymes. Using PHT, the ... **Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae tu-harburg.de [PDF]W Wang, J Sun, M Hartlep, WD … - Biotechnology and …, 2003 - interscience.wiley.com http://scholar.google.com/scholar?q=related:OKsyM7nYUH0J:scholar.google.com/&hl=ja&as_sdt=2000 >Abstract: The fed-batch fermentation of glycerol to 1,3- propanediol by Klebsiella pneumoniae displayed an un- usual dynamic behavior that can be clearly divided into four distinct phases according to cell growth and CO2 evolution rate. Metabolism changed significantly during ... **Combinatorial complexity of pathway analysis in metabolic networks u-bordeaux2.fr [PDF]S Klamt, J Stelling - Molecular Biology Reports, 2002 - Springer http://scholar.google.com/scholar?q=related:kLqNimyG924J:scholar.google.com/&hl=ja&as_sdt=2000 >Key words: combinatorial complexity in metabolic networks, elementary flux modes, metabolic pathway analysis, structural network analysis Summary Elementary flux mode analysis is a promising approach for a pathway ... **Comparison of network-based pathway analysis methods cell.com [HTML]JA Papin, J Stelling, ND Price, S Klamt, S … - TRENDS in …, 2004 - Elsevier http://scholar.google.com/scholar?q=related:BYENm_cYtdQJ:scholar.google.com/&hl=ja&as_sdt=2000 >... Recent network-based metabolic pathway analysis has focused on two approaches, those of elementary modes [4] and extreme pathways [5]. Both of these methods use convex analysis [6], a branch of mathematics that enables the analysis of inequalities and systems of linear ... 2010-09-28T21:31:49+09:00 1285677109 https://w.atwiki.jp/metalmetabo/pages/26.html &counter() visitors **Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems slu.edu [PDF]… JS Edwards, D Letscher, BØ Palsson - Biotechnology and …, 2000 - interscience.wiley.com http://scholar.google.com/scholar?q=related:HtFdZ3DFTgMJ:scholar.google.com/&hl=ja&as_sdt=2000 >... dimensional space. From metabolic pathway analysis, the edges of the high-dimensional flux cone are vectors that correspond to sys- temically defined “extreme pathways” spanning the ca- pabilities of the system. The addition ... **Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks T Çakir, B Kirdar, KÖ Ülgen - Biotechnology and …, 2004 - Wiley Online Library http://scholar.google.com/scholar?q=related:cUtrabByB40J:scholar.google.com/&hl=ja&as_sdt=2000 >Abstract: Central carbon metabolism of the yeast Saccha- romyces cerevisiae was analyzed using metabolic pathway analysis tools. Elementary flux modes for three substrates (glucose, galactose, and ethanol) were determined using the catabolic reactions ... **Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum JO Krömer, C Wittmann, H Schröder, E Heinzle - Metabolic engineering, 2006 - Elsevier http://scholar.google.com/scholar?q=related:KSxlsQoF_oIJ:scholar.google.com/&hl=ja&as_sdt=2000 >[[Metabolic pathway analysis]] was carried out to predict the metabolic potential of Corynebacterium glutamicum and Escherichia coli for the production of L-methionine. Based on detailed stoichiometric models for these organisms, this allowed the calculation of the theoretically optimal ... **The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy JA Papin, ND Price, JS Edwards, BØ … - Journal of theoretical …, 2002 - Elsevier http://scholar.google.com/scholar?q=related:KrUkw9kndisJ:scholar.google.com/&hl=ja&as_sdt=2000 >... 229–248. Abstract | PDF (428 K) | View Record in Scopus | Cited By in Scopus (198). 19. CHSCHILLING, S. SCHUSTER, BO PALSSON and R. HEINRICH, Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. ... **Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis psu.edu [PDF]S Anishetty, M Pulimi, G Pennathur - Computational Biology and …, 2005 - Elsevier http://scholar.google.com/scholar?q=related:hEJbAmAPhwkJ:scholar.google.com/&hl=ja&as_sdt=2000 >The emergence of multidrug resistant varieties of Mycobacterium tuberculosis has led to a search for novel drug targets. We have performed an insilico comparative analysis of metabolic pathways of the host Homo sapiens and the pathogen M. tuberculosis. Enzymes from the ... **In silico metabolic pathway analysis and design: succinic acid production by metabolically engineered Escherichia coli as an example jsbi.org [PDF]SY Lee, SH Hong, SY Moon - GENOME INFORMATICS SERIES, 2002 - jsbi.org http://scholar.google.com/scholar?q=related:6Ehoy39R1HUJ:scholar.google.com/&hl=ja&as_sdt=2000 >Abstract The intracellular metabolic fluxes can be calculated by metabolic flux analysis, which uses a stoichiometric model for the intracellular reactions along with mass balances around the intra- cellular metabolites. In this study, we have constructed in silico metabolic pathway ... **Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis cshlp.org [HTML]ND Price, JA Papin, BØ Palsson - Genome Research, 2002 - genome.cshlp.org http://scholar.google.com/scholar?q=related:hyQpOmehsTYJ:scholar.google.com/&hl=ja&as_sdt=2000 **Metabolic pathway analysis in trypanosomes and malaria parasites. nih.gov [PDF]AH Fairlamb - Philosophical Transactions of the Royal Society B: …, 2002 - ncbi.nlm.nih.gov http://scholar.google.com/scholar?q=related:x44FtcJTlQwJ:scholar.google.com/&hl=ja&as_sdt=2000 >Identification of novel drug targets is required for the development of new classes of drugs to overcome drug resistance and replace less efficacious treatments. In theory, knowledge of the entire genome of a pathogen identifies every potential drug target in any given microbe. ... **A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks uni-erlangen.de [PDF]S Schuster, DA Fell, T Dandekar - Nature biotechnology, 2000 - nature.com http://scholar.google.com/scholar?q=related:4GmcRTKIXlwJ:scholar.google.com/&hl=ja&as_sdt=2000 >... Trends Biotechnol. 17, 53–60(1999). | Article | PubMed | ISI | ChemPort |; Schilling, CH, Schuster, S., Palsson, BO & Heinrich R. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15, 296–303 (1999). ... 2010-09-28T21:31:28+09:00 1285677088 https://w.atwiki.jp/metalmetabo/pages/30.html &counter() visitors **Metabolic pathway analysis of enzyme-deficient human red blood cells T ÇakIr, CS Tacer, KÖ Ülgen - Biosystems, 2004 - Elsevier http://scholar.google.com/scholar?q=related:8w1qIgoYqGcJ:scholar.google.com/&hl=ja&as_sdt=2000 >Five enzymopathies (G6PDH, TPI, PGI, DPGM and PGK deficiencies) in the human red blood cells are investigated using a stoichiometric modeling approach, ie, metabolic pathway analysis. Elementary flux modes (EFMs) corresponding to each enzyme deficiency case ... **Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms oxfordjournals.org [PDF]H Ma, AP Zeng - Bioinformatics, 2003 - Oxford Univ Press http://scholar.google.com/scholar?q=related:SuHZgSLeNw8J:scholar.google.com/&hl=ja&as_sdt=2000 >Page 1. BIOINFORMATICS Vol. 19 no. 2 2003 Pages 270–277 Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms Hongwu Ma1, 2 and An-Ping Zeng1,∗ 1GBF ... **Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism CT Trinh, A Wlaschin, F Srienc - Applied microbiology and biotechnology, 2009 - Springer http://scholar.google.com/scholar?q=related:hkaWpJnxK5QJ:scholar.google.com/&hl=ja&as_sdt=2000 >Abstract Elementary mode analysis is a useful metabolic pathway analysis tool to identify the structure of a metabolic network that links the cellular phenotype to the corresponding genotype. The analysis can decompose the intricate metabolic network comprised of ... **Extreme pathway analysis of human red blood cell metabolism nih.gov [PDF]SJ Wiback, BO Palsson - Biophysical Journal, 2002 - Elsevier http://scholar.google.com/scholar?q=related:hVaLEfzPgSEJ:scholar.google.com/&hl=ja&as_sdt=2000 **Constraints-based models: regulation of gene expression reduces the steady-state solution space MW Covert, BO Palsson - Journal of theoretical Biology, 2003 - Elsevier http://scholar.google.com/scholar?q=related:o9VRtN2gAKQJ:scholar.google.com/&hl=ja&as_sdt=2000 >... Biol. 203, 249, 283. 26. CH SCHILLING, S. SCHUSTER, BO PALSSON and R.HEINRICH, [[Metabolic pathway analysis]]: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15 (1999), pp. 296–303. ... **The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis nih.gov [HTML]JA Papin, BO Palsson - Biophysical Journal, 2004 - Elsevier http://scholar.google.com/scholar?q=related:myiNLachV-QJ:scholar.google.com/&hl=ja&as_sdt=2000 **From genome to cellular phenotype—a role for metabolic flux analysis? A Cornish-Bowden, ML Cárdenas - Nature Biotechnology, 2000 - nature.com http://scholar.google.com/scholar?q=related:Q1z877WO_uAJ:scholar.google.com/&hl=ja&as_sdt=2000 >... whether a bypass exists within a complex network. Metabolic pathway analysis aims to identify indispensable enzymes, thus predicting the effects of their deletion or inhibition. Flux analysis should also allow the determination ... **On-line metabolic pathway analysis based on metabolic signal flow diagram H Shi, K Shimizu - Biotechnology and bioengineering, 1998 - interscience.wiley.com http://scholar.google.com/scholar?q=related:wjDdrq_SGcQJ:scholar.google.com/&hl=ja&as_sdt=2000 >Abstract: In this work, an integrated modeling approach based on a metabolic signal flow diagram and cellular energetics was used to model the metabolic pathway analysis for the cultivation of yeast on glucose. This ap- proach enables us to make a clear analysis of the flow ... **Metabolic pathway analysis of recombinant Saccharomyces cerevisiae with a galactose-inducible promoter based on a signal flow modeling approach S Jin, K Ye, K Shimizu - Journal of Fermentation and Bioengineering, 1995 - Elsevier http://scholar.google.com/scholar?q=related:0uzMsbsJrXEJ:scholar.google.com/&hl=ja&as_sdt=2000 >The objective of this work was to develop a signal flow diagram-based modeling approach proposed by Endo et al. (1976) to organize the network of complex metabolic reactions occurring in the living cell, employing directed signal flow diagram in which the enzyme reaction ... **Energy balance for analysis of complex metabolic networks nih.gov [PDF]DA Beard, S Liang, H Qian - Biophysical journal, 2002 - Elsevier http://scholar.google.com/scholar?q=related:wcAvs5fp3FgJ:scholar.google.com/&hl=ja&as_sdt=2000 2010-09-28T21:22:29+09:00 1285676549