Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance

Database

Volumn 2013, Issue , 2013, Pages

  Heavner, Benjamin D ^a   Smallbone, Kieran ^b   Price, Nathan D ^a   Walker, Larry P ^c  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AEROBIC METABOLISM; ANAEROBIC GROWTH; ARTICLE; BIOLOGICAL MODEL; DATA BASE; FUNGAL GENE; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; MUTATION; SACCHAROMYCES CEREVISIAE;

AEROBIOSIS; ANAEROBIOSIS; DATABASES AS TOPIC; GENES, FUNGAL; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE ANNOTATION; MUTATION; SACCHAROMYCES CEREVISIAE;

EID: 84885911432     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat059     Document Type: Article

References (23)

1. Mo,M.L., Palsson,B.Ø. and Herrgård,M.J. (2009) Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst. Biol., 3, 37.
2. Kuepfer,L., Sauer,U. and Blank,L.M. (2005) Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res., 15, 1421-1430.
3. Herrgard,M.J., Swainston,N., Dobson,P. et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat. Biotech., 26, 1155-1160.
4. Dobson,P.D., Jameson,D., Simeonidis,E. et al. (2010) Further developments towards a genome-scale metabolic model of yeast. BMC Syst. Biol., 4, 145.
5. Heavner,B.D., Smallbone,K., Barker,B. et al. (2012) Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst. Biol., 6, 55.
6. Schellenberger,J., Que,R., Fleming,R.M.T. et al. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc., 6, 1290-1307.
7. Price,N.D., Reed,J.L. and Palsson,B.O. (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat. Rev. Microbiol., 2, 886-897.
8. Zomorrodi,A.R. and Maranas,C.D. (2010) Improving the iMM 904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst. Biol., 4, 178.
9. Andreasen,A.A. and Stier,T.J. (1954) Anaerobic nutrition of Saccharomyces cerevisiae. II. Unsaturated fatty acid requirement for growth in a defined medium. J. Cell. Physiol., 43, 271-281.
10. Andreasen,A.A. and Stier,T.J.B. (1953) Anaerobic nutrition of Saccharomyces cerevisiae. I. Ergosterol requirement for growth in a defined medium. J. Cell. Physiol., 41, 23-36.
11. Hucka,M., Finney,A., Sauro,H.M. et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531.
12. Novère,N.L., Finney,A., Hucka,M. et al. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol., 23, 1509-1515.
13. The UniProt Consortium. (2012) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
14. Hastings,J., De Matos,P., Dekker,A. et al. (2012) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res., 41, D456-D463.
15. Winzeler,E.A., Shoemaker,D.D., Astromoff,A. et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science, 285, 901-906.
16. Alberg,A.J., Park,J.W., Hager,B.W. et al. (2004) The use of "overall accuracy" to evaluate the validity of screening or diagnostic tests. J. Gen. Intern. Med., 19, 460-465.
17. Kubat,M., Holte,R.C. and Matwin,S. (1998) Machine learning for the detection of oil spills in satellite radar images. Mach. Learn., 30, 195-215.
18. Baldi,P., Brunak,S., Chauvin,Y. et al. (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics, 16, 412-424.
19. Cherry,J.M., Hong,E.L., Amundsen,C. et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res., 40, D700-D705.
20. Brooks,J.P., Burns,W.P., Fong,S.S. et al. (2012) Gap detection for genome-scale constraint-based models. Adv. Bioinformatics, 2012, 1-10.
21. Blazier,A.S. and Papin,J.A. (2012) Integration of expression data in genome-scale metabolic network reconstructions. Front. Physiol., 3, 299.
22. Chandrasekaran,S. and Price,N.D. (2010) Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA, 107, 17845-17850.
23. Ghosh,A., Zhao,H. and Price,N.D. (2011) Genome-Scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae. PLoS One, 6, e27316.