Genome Database References

Doug Brutlag

September 26, 2007

  1. The Gene Ontology (GO) project in 2006. (2006). NucleicAcids Res, 34(Database issue), D322-326.

  2. Arnaud, M. B., Costanzo, M. C., Skrzypek, M. S., Shah, P., Binkley, G., Lane, C., et al. (2007). Sequence resources at the Candida Genome Database. Nucleic Acids Res, 35(Database issue), D452-456.

  3. Ball, C. A., Jin, H., Sherlock, G., Weng, S., Matese, J. C., Andrada, R., et al. (2001). Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res, 29(1), 80-81.

  4. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Wheeler, D. L. (2007). GenBank. Nucleic Acids Res, 35(Database issue), D21-25.

  5. Birney, E., Andrews, D., Bevan, P., Caccamo, M., Cameron, G., Chen, Y., et al. (2004). Ensembl 2004. Nucleic Acids Res, 32(Database issue), D468-470.

  6. Crosby, M. A., Goodman, J. L., Strelets, V. B., Zhang, P., & Gelbart, W. M. (2007). FlyBase: genomes by the dozen. Nucleic Acids Res, 35(Database issue), D486-491.

  7. Durand, P., Medigue, C., Morgat, A., Vandenbrouck, Y., Viari, A., & Rechenmann, F. (2003). Integration of data and methods for genome analysis. Curr Opin Drug Discov Devel, 6(3), 346-352.

  8. Eppig, J. T., Blake, J. A., Bult, C. J., Kadin, J. A., & Richardson, J. E. (2007). The mouse genome database (MGD): new features facilitating a model system. Nucleic Acids Res, 35(Database issue), D630-637.

  9. Eyre, T. A., Ducluzeau, F., Sneddon, T. P., Povey, S., Bruford, E. A., & Lush, M. J. (2006). The HUGO Gene Nomenclature Database, 2006 updates. Nucleic Acids Res, 34(Database issue), D319-321.

  10. Gilbert, D. G. (2007). DroSpeGe: rapid access database for new Drosophila species genomes. Nucleic Acids Res, 35(Database issue), D480-485.

  11. Glasner, J. D., Rusch, M., Liss, P., Plunkett, G., 3rd, Cabot, E. L., Darling, A., et al. (2006). ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. Nucleic Acids Res, 34(Database issue), D41-45.

  12. Gregory, T. R., Nicol, J. A., Tamm, H., Kullman, B., Kullman, K., Leitch, I. J., et al. (2007). Eukaryotic genome size databases. Nucleic Acids Res, 35(Database issue), D332-338.

  13. Hammond, M. P., & Birney, E. (2004). Genome information resources - developments at Ensembl. Trends Genet, 20(6), 268-272.

  14. Harris, M. A., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R., et al. (2004). The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res, 32(Database issue), D258-261.

  15. Hubbard, T. J., Aken, B. L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., et al. (2007). Ensembl 2007. Nucleic Acids Res, 35(Database issue), D610-617.

  16. Karolchik, D., Hinrichs, A. S., Furey, T. S., Roskin, K. M., Sugnet, C. W., Haussler, D., et al. (2004). The UCSC Table Browser data retrieval tool. Nucleic Acids Res, 32(Database issue), D493-496.

  17. Karro, J. E., Yan, Y., Zheng, D., Zhang, Z., Carriero, N., Cayting, P., et al. (2007). Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res, 35(Database issue), D55-60.

  18. Kuhn, R. M., Karolchik, D., Zweig, A. S., Trumbower, H., Thomas, D. J., Thakkapallayil, A., et al. (2007). The UCSC genome browser database: update 2007. Nucleic Acids Res, 35(Database issue), D668-673.

  19. Kulikova, T., Akhtar, R., Aldebert, P., Althorpe, N., Andersson, M., Baldwin, A., et al. (2007). EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res, 35(Database issue), D16-20.

  20. Lee, Y., Tsai, J., Sunkara, S., Karamycheva, S., Pertea, G., Sultana, R., et al. (2005). The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res, 33(Database issue), D71-74.

  21. Loveland, J. (2005). VEGA, the genome browser with a difference. Brief Bioinform, 6(2), 189-193.

  22. Maglott, D., Ostell, J., Pruitt, K. D., & Tatusova, T. (2007). Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res, 35(Database issue), D26-31.

  23. Mungall, C. J., Misra, S., Berman, B. P., Carlson, J., Frise, E., Harris, N., et al. (2002). An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol, 3(12), RESEARCH0081.

  24. Nash, R., Weng, S., Hitz, B., Balakrishnan, R., Christie, K. R., Costanzo, M. C., et al. (2007). Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res, 35(Database issue), D468-471.

  25. Ouzounis, C. A., & Karp, P. D. (2002). The past, present and future of genome-wide re-annotation. Genome Biol, 3(2), COMMENT2001.

  26. Reed, J. L., Famili, I., Thiele, I., & Palsson, B. O. (2006). Towards multidimensional genome annotation. Nat Rev Genet, 7(2), 130-141.

  27. Riley, M. L., Schmidt, T., Artamonova, II, Wagner, C., Volz, A., Heumann, K., et al. (2007). PEDANT genome database: 10 years online. Nucleic Acids Res, 35(Database issue), D354-357.

  28. Schattner, P. (2007). Automated querying of genome databases. PLoS Comput Biol, 3(1), e1.

  29. Schneider, K. L., Pollard, K. S., Baertsch, R., Pohl, A., & Lowe, T. M. (2006). The UCSC Archaeal Genome Browser. Nucleic Acids Res, 34(Database issue), D407-410.

  30. Selengut, J. D., Haft, D. H., Davidsen, T., Ganapathy, A., Gwinn-Giglio, M., Nelson, W. C., et al. (2007). TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res, 35(Database issue), D260-264.

  31. Stothard, P., & Wishart, D. S. (2006). Automated bacterial genome analysis and annotation. Curr Opin Microbiol, 9(5), 505-510.

  32. Strausberg, R. L., Greenhut, S. F., Grouse, L. H., Schaefer, C. F., & Buetow, K. H. (2001). In silico analysis of cancer through the Cancer Genome Anatomy Project. Trends Cell Biol, 11(11), S66-71.

  33. Sugawara, H., Abe, T., Gojobori, T., & Tateno, Y. (2007). DDBJ working on evaluation and classification of bacterial genes in INSDC. Nucleic Acids Res, 35(Database issue), D13-15.

  34. Twigger, S. N., Shimoyama, M., Bromberg, S., Kwitek, A. E., & Jacob, H. J. (2007). The Rat Genome Database, update 2007--easing the path from disease to data and back again. Nucleic Acids Res, 35(Database issue), D658-662.

  35. Uchiyama, I. (2007). MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucleic Acids Res, 35(Database issue), D343-346.

  36. Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., et al. (2007). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res, 35(Database issue), D5-12.

** Last Updated September 23, 2007**