Article thumbnail

MEMOSys: Bioinformatics platform for genome-scale metabolic models

By Stephan Pabinger, Robert Rader, Rasmus Agren, Jens Nielsen and Zlatko Trajanoski
Topics: Software
Publisher: BioMed Central
OAI identifier:
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles


  1. (2010). Alper H: Systems metabolic engineering: Genome-scale models and beyond.
  2. (2008). Analysis of Aspergillus nidulans metabolism at the genome-scale. BMC Genomics
  3. (2008). Bhumiratana S: The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism.
  4. (2010). BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.
  5. (2005). BL: Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol
  6. (2008). ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res
  7. (2008). DB: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol
  8. (2005). Enhancement of the chemical semantic web through the use of InChI identifiers. Org Biomol Chem
  9. (2010). Envers.
  10. (2005). G: The Java(TM) Language Specification. 3 edition.
  11. (2009). Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens.
  12. (2010). Genome-scale modeling and in silico analysis of mouse cell metabolic network. Mol Biosyst
  13. (2009). Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev
  14. (2003). Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res
  15. (2007). Herrgard MJ: Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc
  16. (2010). Hibernate Persistence Framework.
  17. (2005). I: The Unified Modeling Language User Guide. 2 edition.
  18. (2008). Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae.
  19. (2008). Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae.
  20. (2008). JBoss Group: JBoss Application Server.
  21. (2003). Kitano H: Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS
  22. (2005). Kriete A: Computational Systems Biology
  23. (2010). Laibe C: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
  24. (2008). LibSBML: an API library for SBML. Bioinformatics
  25. (2010). Liebermeister W: Annotation and merging of SBML models with semanticSBML. Bioinformatics
  26. (2002). LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res
  27. (2005). Lopez-Bigas N: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res
  28. (2008). Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol
  29. (2009). Metabolic systems biology.
  30. (2010). Middleware, LLC: The Seam framework.
  31. (2002). Nakaya A: The KEGG databases at GenomeNet. Nucleic Acids Res
  32. (2010). Nucleic Acids Res
  33. (2010). Oracle Corporation: JSF Reference Implementation.
  34. (2011). Oracle Corporation: Oracle Database.
  35. (2003). Palsson BO: Metabolic pathways in the post-genome era. Trends Biochem Sci
  36. (2004). Palsson BO: The evolution of molecular biology into systems biology. Nat Biotechnol
  37. (2010). Pathway Tools version 13.0: integrated software for pathway/ genome informatics and systems biology. Brief Bioinform
  38. (2010). RichFaces.
  39. (2010). Roberto Olivares-Hernández, Agren Rasmus, Dahr Niklas, Vongsangnak Wanwipa, Nookaew Intawat, Kiran Raosaheb Patil, Nielsen Jens: BioMet Toolbox: genome-wide analysis of metabolism. Nucl Acids Res
  40. (2006). Schilling CH: Use of constraint-based modeling for the prediction and validation of antimicrobial targets. Biochem Pharmacol
  41. (2005). Siezen RJ: In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. Appl Environ Microbiol
  42. (2006). Systems Biology: Properties of Reconstructed Networks
  43. (2005). Systems biotechnology for strain improvement. Trends Biotechnol
  44. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics
  45. The UniProt Consortium: The Universal Protein Resource (UniProt)
  46. (2005). Trajanoski Z: MARS: microarray analysis, retrieval, and storage system.
  47. (2006). U: COPASI–a COmplex PAthway SImulator. Bioinformatics
  48. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science
  49. (2009). Wren BW: Recent advances in systems microbiology. Curr Opin Microbiol