Saccharomyces Genome Database: The genomics resource of budding yeast

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Cherry, J Michael ^a   Hong, Eurie L ^a   Amundsen, Craig ^a   Balakrishnan, Rama ^a   Binkley, Gail ^a   Chan, Esther T ^a   Christie, Karen R ^a   Costanzo, Maria C ^a   Dwight, Selina S ^a   Engel, Stacia R ^a   Fisk, Dianna G ^a   Hirschman, Jodi E ^a   Hitz, Benjamin C ^a   Karra, Kalpana ^a   Krieger, Cynthia J ^a   Miyasato, Stuart R ^a   Nash, Rob S ^a   Park, Julie ^a   Skrzypek, Marek S ^a   Simison, Matt ^a   Weng, Shuai ^a   Wong, Edith D ^a   more..

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; CHROMOSOME; COMPUTER INTERFACE; DATA PROCESSING; FUNGAL GENOME; GENE FUNCTION; GENE INTERACTION; GENETIC DATABASE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES GENOME DATABASE; SEARCH ENGINE; WEB BROWSER;

DATABASES, GENETIC; GENES, FUNGAL; GENOME, FUNGAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; PHENOTYPE; SACCHAROMYCES CEREVISIAE; SOFTWARE; TERMINOLOGY AS TOPIC;

EID: 84858588614     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1029     Document Type: Article

References (27)

1. Petranovic,D., Tyo,K., Vemuri,G.N. and Nielsen,J. (2010) Prospects of yeast systems biology for human health: integrating lipid, protein and energy metabolism. FEMS Yeast Res., 10, 1046-1059.
2. Goeckeler,J.L. and Brodsky,J.L. (2010) Molecular chaperones and substrate ubiquitination control the efficiency of endoplasmic reticulum-associated degradation. Diabetes Obes. Metab., 12(Suppl.), 32-38.
3. Rinaldi,T., Dallabona,C., Ferrero,I., Frontali,L. and Bolotin-Fukuhara,M. (2010) Mitochondrial diseases and the role of the yeast models. FEMS Yeast Res., 10, 1006-1022.
4. Bharadwaj,P., Martins,R. and Macreadie,I. (2010) Yeast as a model for studying Alzheimer's disease. FEMS Yeast Res., 10, 961-969.
5. Barros,M.H., da Cunha,F.M., Oliveira,G.A., Tahara,E.B. and Kowaltowski,A.J. (2010) Yeast as a model to study mitochondrial mechanisms in ageing. Mech. Ageing Dev., 131, 494-502.
6. Costanzo,M.C., Park,J., Balakrishnan,R., Cherry,J.M. and Hong,E.L. (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database, 2011, bar004.
7. Barrell,D., Dimmer,E., Huntley,R.P., Binns,D., O'Donovan,C. and Apweiler,R. (2009) The GOA database in 2009 - an integrated Gene Ontology Annotation resource. Nucleic Acids Res., 37, D396-D403.
8. Hong,E.L., Balakrishnan,R., Dong,Q., Christie,K.R., Park,J., Binkley,G., Costanzo,M.C., Dwight,S.S., Engel,S.R., Fisk,D.G. et al. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res., 36, D577-D581. (Pubitemid 351149788)
9. Gaudet,P., Livstone,M.S., Lewis,S.E. and Thomas,P.D. (2011) Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief. Bioinform., doi: 10.1093/bio/bbr042.
10. Reference Genome Group of the Gene Ontology Consortium. (2001) The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput. Biol., 5, e1000431.
11. de Matos,P., Alcantara,R., Dekker,A., Ennis,M., Hastings,J., Haug,K., Spiteri,I., Turner,S. and Steinbeck,C. (2009) Chemical Entities of Biological Interest: an update. Nucleic Acids Res., 38, D249-D254.
12. Costanzo,M.C., Skrzypek,M.S., Nash,R., Wong,E., Binkley,G., Engel,S.R., Hitz,B., Hong,E.L. and Cherry,J.M. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database, doi: 10.1093/database/ bap001.
13. Karp,P.D., Paley,S.M., Krummenacker,M., Latendresse,M., Dale,J.M., Lee,T.J., Kaipa,P., Gilham,F., Spaulding,A., Popescu,L. et al. (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinform., 11, 40-79.
14. Goffeau,A., Barrell,B.G., Bussey,H., Davis,R.W., Dujon,B., Feldmann,H., Galibert,F., Hoheisel,J.D., Jacq,C., Johnston,M. et al. (1996) Life with 6000 genes. Science, 274, 546, 563-567.
15. Mortimer,R.K. and Johnston,J.R. (1986) Genealogy of principal strains of the yeast genetic stock center. Genetics, 113, 35-43. (Pubitemid 16042668)
16. Fan,H.Y., Cheng,K.K. and Klein,H.L. (1996) Mutations in the RNA polymerase II transcription machinery suppress the hyper-recombination mutant hpr1 delta of Saccharomyces cerevisiae. Genetics, 142, 749-759.
17. Kane,S.M. and Roth,R. (1974) Carbohydrate metabolism during ascospore development in yeast. J. Bacteriol., 118, 8-14.
18. Carlson,M. and Botstein,D. (1983) Organization of the SUC gene family in Saccharomyces. Mol. Cell Biol., 3, 351-359. (Pubitemid 13165200)
19. Naumov,G., Turakainen,H., Naumova,E., Aho,S. and Korhola,M. (1990) A new family of polymorphic genes in Saccharomyces cerevisiae: alpha-galactosidase genes MEL1-MEL7. Mol. Gen. Genet., 224, 119-128. (Pubitemid 20364643)
20. Hall,C. and Dietrich,F.S. (2007) The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering. Genetics, 177, 2293-2307. (Pubitemid 350277006)
21. Novo,M., Bigey,F., Beyne,E., Galeote,V., Gavory,F., Mallet,S., Cambon,B., Legras,J.L., Wincker,P., Casaregola,S. et al. (2009) Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc. Natl Acad. Sci. USA, 106, 16333-16338.
22. Borneman,A.R., Forgan,A.H., Pretorius,I.S. and Chambers,P.J. (2008) Comparative genome analysis of a Saccharomyces cerevisiae wine strain. FEMS Yeast Res., 8, 1185-1195.
23. Hibbs,M.A., Hess,D.C., Myers,C.L., Huttenhower,C., Li,K. and Troyanskaya,O.G. (2007) Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics, 23, 2692-2699. (Pubitemid 350048333)
24. Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A., Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610. (Pubitemid 35175099)
25. Lyne,R., Smith,R., Rutherford,K., Wakeling,M., Varley,A., Guillier,F., Janssens,H., Ji,W., Mclaren,P., North,P. et al. (2007) FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol., 8, R129.
26. Celniker,S.E., Dillon,L.A.L., Gerstein,M.B., Gunsalus,K.C., Henikoff,S., Karpen,G.H., Kellis,M., Lai,E.C., Lieb,J.D., MacAlpine,D.M. et al. (2009) Unlocking the secrets of the genome. Nature, 459, 927-930.
27. Muller,H.M., Kenny,E.E. and Sternberg,P.W. (2004) Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol., 2, e309.