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- MetaCrop: a detailed database of crop plant metabolism

  1. Grusak MA, DellaPenna D. Improving the nutrient composition of plants to enhance human nutrition and health. Annu. Rev. Plant Physiol. Plant Mol. Biol. (1999) 50:133–161

  2. Metzger JO, Bornscheuer U. Lipids as renewable resources: current state of chemical and biotechnological conversion and diversification. Appl. Microbiol. Biotechnol. (2006) 71:13–22

  3. Tilman D, Hill J, Lehman C. Carbon-negative biofuels from low-input high-diversity grassland biomass. Science (2006) 314:1598–1600

  4. Jenner HL. Transgenesis and yield: what are our targets? Trends Biotechnol. (2003) 21:190–192.

  5. Carrari F, Urbanczyk-Wochniak E, Willmitzer L, Fernie AR. Engineering central metabolism in crop species: learning the system. Metab. Eng. (2003) 5:191–200

  6. Yu J, Hu S, Wang J, Wong G.K.-S, Li S, Liu B, Deng Y, Dai L, Zhou Y, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 296:79–92.

  7. Goff SA, Ricke D, Lan T.-H, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 296:92–100

  8. Jaiswal P, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, et al. Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. Comp. Funct. Genomics (2005) 6:388–397

  9. Gene Ontology Consertium. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. (2006) 34(Suppl. 1):D322–D326

  10. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (2003) 19:524–531

  11. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes PU, et al. COPASI—a complex pathway simulator. Bioinformatics (2006) 22:3067–3074

  12. Alves R, Antunes F, Salvador A. Tools for kinetic modeling of biochemical networks. Nat. Biotechnol. (2006) 24:667–672

  13. Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker BH. Meta-All: a system for managing metabolic pathway information. BMC Bioinformatics (2006) 7:e465

  14. Buchanan BB, Gruissem W, Russel LJ. Biochemistry & Molecular Biology of Plants. (2000) Rockeville, MD: American Society of Plant Physiologists.

  15. Bewley JD, Black M. Seeds: Physiology of Development and Germination (1994) 2nd. New York, USA: Plenum Press.

  16. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita K, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. (2006) 34(Suppl. 1):D354–D357

  17. Masoudi-Nejad A, Goto S, Jauregui R, Ito M, Kawashima S, Moriya Y, Endo T, Kanehisa M. EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG. Plant Physiol. (2007) 144:857–866

  18. Rhee SY, Zhang P, Foerster H, Tissier C. AraCyc: overview of an Arabidopsis metabolism database and its applications for plant research. In: Plant Metabolomics.—Saito K, Dixon RA, Willmitzer L, eds. (2006) Heidelberg: Springer Berlin. 141–154.

  19. Caspi R, Foerster H, Fulcher C, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, et al. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. (2006) 34(Suppl. 1):D511–D516

  20. Vastrik I, D’Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biol. (2007) 8:R39

  21. Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D. BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res. (2007) 35(Suppl. 1):D511–D514

  22. Bairoch A. The ENZYME database in 2000. Nucleic Acids Res. (2000) 28:304–305.

  23. Boeckmann B, Bairoch A, Apweiler R, Blatter M.-C, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O’Donovan C, et al. The SWISS-PROT protein knowledgebase and its supplement trEMBL in 2003. Nucleic Acids Res. (2003) 31:365–370.

  24. Schwacke R, Schneider A, van der Graaff E, Fischer K, Catoni E, Desimone M, Frommer WB, Flügge U.-I, Kunze R. ARAMEMNON: a novel database for Arabidopsis integral membrane proteins. Plant Physiol. (2003) 131:16–26

  25. Klamt S, Saez-Rodriguez J, Gilles ED. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. (2007) 1:e2.

  26. Junker BH, Klukas C, Schreiber F. VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics (2006) 7:e109.

  27. Wurtele ES, Li J, Diao L, Zhang H, Foster CM, Fatland B, Dickerson J, Brown A, Cox Z, et al. MetNet: software to build and model the biogenetic lattice of Arabidopsis. Comp. Funct. Genomics (2003) 4:239–245.

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