Items where Subject is "database optimization"

B

Benfey, P., Carpenter, A., Waterston, W., Ohler, U. (December 2010) AUTOMATED IMAGING & HIGH-THROUGHPUT PHENOTYPING. In: 2010 meeting on Automated Imaging and high througput phenotyping, December 5–December 8, 2010, Cold Spring Harbor Laboratory.

Bieri, T., Blasiar, D., Ozersky, P., Antoshechkin, I., Bastiani, C., Canaran, P., Chan, J., Chen, N., Chen, W. J., Davis, P., Fiedler, T. J., Girard, L. R., Han, M., Harris, T. W., Kishore, R., Lee, R., McKay, S. J., Müller, H- M., Nakamura, C., Petcherski, A., Rangarajan, A., Rogers, A., Schindelman, G., Schwarz, E. M., Spooner, W., Tuli, M. A., Van Auken, K., Wang, D., Wang, X., Williams, G., Durbin, R., Stein, L. D., Sternberg, P. W., Spieth, J. (January 2007) WormBase: new content and better access. Nucleic Acids Res, 35 (Databa). D506-D510. ISSN 0305-1048

Boyle, B., Hopkins, N., Lu, Z. Y., Garay, J. A. R., Mozzherin, D., Rees, T., Matasci, N., Narro, M. L., Piel, W. H., McKay, S. J., Lowry, S., Freeland, C., Peet, R. K., Enquist, B. J. (January 2013) The taxonomic name resolution service: an online tool for automated standardization of plant names. BMC Bioinformatics, 14. ISSN 1471-2105

Brenner, E. D., Katari, M. S., Stevenson, D. W., Rudd, S. A., Douglas, A. W., Moss, W. N., Twigg, R. W., Runko, S. J., Stellari, G. M., McCombie, W. R., Coruzzi, G. M. (October 2005) EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics, 6. p. 143. ISSN 1471-2164

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Canaran, P., Buckler, E. S., Glaubitz, J. C., Stein, L. D., Sun, Q., Zhao, W., Ware, D. H. (2008) Panzea: an update on new content and features. Nucleic Acids Res, 36 (Databa). D1041-3.

Canaran, P., Stein, L. D., Ware, D. H. (April 2006) Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics, 22 (7). pp. 885-6. ISSN 1367-4803 (Print)

Chen, N., Harris, T. W., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Bradnam, K., Canaran, P., Chan, J., Chen, C.-K., Chen, W. J., Cunningham, F., Davis, P., Kenny, E., Kishore, Ra.., Lawson, D., Lee, R., Muller, H. M., Nakamura, Ce., Pai, S., Ozersky, P., Petcherski, A., Rogers, An., Sabo, A., Schwarz, Er. M., Van Auken, K., Wang, Q., Durbin, R., Spieth, J., Sternberg, P. W., Stein, L. D. (January 2005) WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res, 33 (Databa). D383-9. ISSN 1362-4962 (Electronic)

Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., Jupe, S., Kataskaya, I., Mahajan, S., May, B., Ndegwa, N., Schmidt, E., Shamovsky, V., Yung, C., Birney, E., Hermjakob, H., D'Eustachio, P., Stein, L. D. (January 2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res, 39 (Suppl ). D691-7. ISSN 1362-4962 (Electronic) 0305-1048 (Linking)

D

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, Ö, Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., Van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K. H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L. , Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novère, N. L., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C., Bader, G. D. (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnology, 28 (9). pp. 935-942.

de la Cruz, N., Bromberg, S., Pasko, D., Shimoyama, M., Twigger, S., Chen, J. L., Chen, C. F., Fan, C., Foote, C., Gopinath, G. R., Harris, G., Hughes, A., Ji, Y., Jin, W. H., Li, D. W., Mathis, J., Nenasheva, N., Nie, J., Nigam, R., Petri, V., Reilly, D., Wang, W. Y., Wu, W. H., Zuniga-Meyer, A., Zhao, L., Kwitek, A., Tonellato, P., Jacob, H. (January 2005) The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Research, 33. D485-D491. ISSN 0305-1048

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Frazer, K. A., Ballinger, D. G., Cox, D. R., Hinds, D. A., Stuve, L. L., Gibbs, R. A., Belmont, J. W., Boudreau, A., Hardenbol, P., Leal, S. M., Pasternak, S., Wheeler, D. A., Willis, T. D., Yu, F. L., Yang, H. M., Zeng, C. Q., Gao, Y., Hu, H. R., Hu, W. T., Li, C. H., Lin, W., Liu, S. Q., Pan, H., Tang, X. L., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q. R., Zhao, H. B., Zhao, H., Zhou, J., Gabriel, S. B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Nguyen, H., Onofrio, R. C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z. J., Huang, W., Chu, X., He, Y. G., Jin, L., Liu, Y. F., Shen, Y. Y., Sun, W. W., Wang, H. F., Wang, Y., Wang, Y., Xiong, X. Y., Xu, L., Waye, M. M. Y., Tsui, S. K. W., Wong, J. T. F., Galver, L. M., Fan, J. B., Gunderson, K., Murray, S. S., Oliphant, A. R., Chee, M. S., Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Olivier, J. F., Phillips, M. S., Roumy, S., Sallee, C., Verner, A., Hudson, T. J., Kwok, P. Y., Cai, D. M., Koboldt, D. C., Miller, R. D., Pawlikowska, L., Taillon-Miller, P., Xiao, M., Tsui, L. C., Mak, W., Song, Y. Q., Tam, P. K. H., Nakamura, Y., Kawaguchi, T., Kitamoto, T., Morizono, T., Nagashima, A., Ohnishi, Y., Sekine, A. (October 2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449 (7164). 851-U3. ISSN 0028-0836

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Girard, L. R., Fiedler, T. J., Harris, T. W., Carvalho, F., Antoshechkin, I., Han, M., Sternberg, P.l W., Stein, L. D., Chalfie, M. (January 2007) WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res, 35 (Databa). D472-D475. ISSN 0305-1048

H

Harris, T. W., Stein, L. D. (2006) WormBase: methods for data mining and comparative genomics. Methods Mol Biol, 351. pp. 31-50. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Haw, R., Hermjakob, H., D'Eustachio, P., Stein, L. D. (September 2011) Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics, 11 (18). pp. 3598-3613. ISSN 16159853 (ISSN)

J

Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L. D., Ware, D. H., Zapata, F. (2005) Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comp Funct Genomics, 6 (7-8). pp. 388-97. ISSN 1531-6912 (Print)

Jiang, C., Xuan, Z. Y., Zhao, F., Zhang, M. Q. (January 2007) TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res, 35 (Databa). D137-D140. ISSN 0305-1048

Jordan, C., Stanzione, D., Ware, D. H., Lu, J., Noutsos, C. (2010) Comprehensive data infrastructure for plant bioinformatics. 2010 IEEE International Conference on Cluster Computing Workshops and Posters.

Joshi-Tope, G., Gillespie, M., Vastrik, I., D'Eustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G. R., Wu, G. R., Matthews, L., Lewis, S., Birney, E., Stein, L. D. (January 2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res, 33 (Databa). D428-32. ISSN 1362-4962 (Electronic)

Joshi-Tope, G., Vastrik, I., Gopinath, G. R., Matthews, L., Schmidt, E., Gillespie, M., D'Eustachio, P., Jassal, B., Lewis, S., Wu, G., Birney, E., Stein, L. (2003) The genome knowledgebase: A resource for biologists and bioinformaticists. Cold Spring Harbor Symposia on Quantitative Biology, 68. pp. 237-243. ISSN 0091-7451

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Lawrence, Carolyn J., Ware, Doreen (2008) Databases and data mining. In: Handbook of Maize: History and Practice of Genetics and Genomics. Springer Science + Business Media LLC, pp. 659-672. ISBN 978-0-387-77862-4

Li, J., Zhang, M. Q., Zhang, X. (2006) A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. American Journal of Human Genetics, 79 (4). pp. 628-639. ISSN 00029297

M

Martin, L., Cook, C., Matasci, N., Williams, J., Bastow, R. (2015) Data mining with iPlant: A meeting report from the 2013 GARNet workshop, Data mining with iPlant. Journal of Experimental Botany, 66 (1). pp. 1-6. ISSN 0022-0957

McKay, S. J., Vergara, I. A., Stajich, J. E. (September 2010) Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics, Chapte. Unit 9 12. ISSN 1934-340X (Electronic) 1934-3396 (Linking)

Miller, R. D., Phillips, M. S., Jo, I., Donaldson, M. A., Studebaker, J. F., Addleman, N., Alfisi, S. V., Ankener, W. M., Bhatti, H. A., Callahan, C. E., Carey, B. J., Conley, C. L., Cyr, J. M., Derohannessian, V., Donaldson, R. A., Elosua, C., Ford, S. E., Forman, A. M., Gelfand, C. A., Grecco, N. M., Gutendorf, S. M., Hock, C. R., Hozza, M. J., Hur, S., In, S. M., Jackson, D. L., Jo, S. A., Jung, S. C., Kim, S., Kimm, K., Kloss, E. F., Koboldt, D. C., Kuebler, J. M., Kuo, F. S., Lathrop, J. A., Lee, J. K., Leis, K. L., Livingston, S. A., Lovins, E. G., Lundy, M. L., Maggan, S., Minton, M., Mockler, M. A., Morris, D. W., Nachtman, E. P., Oh, B., Park, C., Park, C. W., Pavelka, N., Perkins, A. B., Restine, S. L., Sachidanandam, R., Reinhart, A. J., Scott, K. E., Restine, S. L., Sachidanandam, R., Reinhart, A. J., Scott, K. E., Shah, G. J., Tate, J. M., Varde, S. A., Walters, A., White, J. R., Yoo, Y. K., Lee, J. E., Boyce-Jacino, M. T., Kwok, P. Y. (August 2005) High-density single-nucleotide polymorphism maps of the human genome. Genomics, 86 (2). pp. 117-126. ISSN 0888-7543

Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., Gingeras, T. R., Kent, W. J., Birney, E., Wold, B., Crawford, G. E., Epstein, C. B., Shoresh, N., Ernst, J., Mikkelsen, T. S., Kheradpour, P., Zhang, X. L., Wang, L., Issner, R., Coyne, M. J., Durham, T., Ku, M. C., Truong, T., Ward, L. D., Altshuler, R. C., Lin, M. F., Kellis, M., Davis, C. A., Kapranov, P., Dobin, A., Zaleski, C., Schlesinger, F., Batut, P., Chakrabortty, S., Jha, S., Lin, W., Drenkow, J., Wang, H. E., Bell, K. G., Gao, H., Bell, I., Dumais, E., Dumais, J., Antonarakis, S. E., Ucla, C., Borel, C., Guigo, R., Djebali, S., Lagarde, J., Kingswood, C., Ribeca, P., Sammeth, M., Alioto, T., Merkel, A., Tilgner, H., Carninci, P., Hayashizaki, Y., Lassmann, T., Takahashi, H., Abdelhamid, R. F., Hannon, G., Fejes-Toth, K., Preall, J., Gordon, A., Sotirova, V., Reymond, A., Howald, C., Graison, E. A. Y., Chrast, J., Ruan, Y. J., Ruan, X. A., Shahab, A., Poh, W. T., Wei, C. L., Furey, T. S., Boyle, A. P., Sheffield, N. C., Song, L. Y., Shibata, Y., Vales, T., Winter, D., Zhang, Z. C., London, D., Wang, T. Y., Keefe, D., Iyer, V. R., Lee, B. K., McDaniell, R. M., Liu, Z., Battenhouse, A., Bhinge, A. A., Lieb, J. D., Grasfeder, L. L., Showers, K. A., Giresi, P. G., Kim, S. K. C., Shestak, C., Pauli, F., Reddy, T. E., Gertz, J. (April 2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). Plos Biology, 9 (4). ISSN 1544-9173 (Public Dataset)

O

Olson, A., Sheth, N., Lee, J., Hannon, G. J., Sachidanandam, R. (March 2005) Rnai codex - a comprehensive RNAi resource. Briefings in Bioinformatics, 6 (1). pp. 104-106. ISSN 1467-5463

Olson, A. J., Tully, T., Sachidanandam, R. (2005) GeneSeer: a sage for gene names and genomic resources. BMC Genomics, 6 (1). p. 134. ISSN 1471-2164 (Electronic)

P

Pan, X. K., Stein, L. D., Brendel, V. (September 2005) SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics, 21 (17). pp. 3461-3468. ISSN 1367-4803

S

Schatz, M. C. (2010) The missing graphical user interface for genomics. Genome Biology, 11 (8). p. 128. ISSN 14656914 (ISSN)

Schwarz, E. M., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Canaran, P., Chan, J., Chen, N., Chen, W. J., Davis, P., Fiedler, T. J., Girard, L., Harris, T. W., Kenny, E. E., Kishore, R., Lawson, D., Lee, R., Muller, H. M., Nakamura, C., Ozersky, P., Petcherski, A., Rogers, A., Spooner, W., Tuli, M. A., Van Auken, K., Wang, D., Durbin, R., Spieth, J., Stein, L. D., Sternberg, P. W. (January 2006) WormBase: better software, richer content. Nucl. Acids Res., 34 (suppl_). D475-478.

Smith, A. D., Sumazin, P., Zhang, M. Q. (January 2007) Tissue-specific regulatory elements in mammalian promoters. Molecular Systems Biology, 3. ISSN 1744-4292

Stein, L. D. (January 2007) Unix survival guide. Curr Protoc Bioinformatics, Append. Appendix 1C.

Stein, L. D. (October 2004) Using the Reactome database. Curr Protoc Bioinformatics, Chapte. Unit 8.7.

Stein, L. D. (March 2007) X Window System survival guide. Curr Protoc Bioinformatics, Append. Appendix 1D.

Sumazin, P., Chen, G., Hata, N., Smith, A. D., Zhang, T., Zhang, M. Q. (January 2005) DWE: discriminating word enumerator. Bioinformatics, 21 (1). pp. 31-8. ISSN 1367-4803 (Print)

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Thorisson, G. A., Smith, A. V., Krishnan, L., Stein, L. D. (November 2005) The International HapMap Project Web site. Genome Res, 15 (11). pp. 1592-3. ISSN 1088-9051 (Print)

V

Vastrik, I., D'Eustachio, P., Schmidt, E., Joshi-Tope, G., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., Matthews, L., Wu, G., Birney, E., Stein, L. D. (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol, 8 (3). R39. ISSN 1474-760X

X

Xuan, Z. Y., Zhao, F., Wang, J., Chen, G., Zhang, M. Q. (2005) Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biology, 6 (8). R72. ISSN 1465-6906

Y

Youens-Clark, K., Buckler, E., Casstevens, T., Chen, C., Declerck, G., Derwent, P., Dharmawardhana, P., Jaiswal, P., Kersey, P., Karthikeyan, A. S., Lu, J., McCouch, S. R., Ren, L., Spooner, W., Stein, J. C., Thomason, J., Wei, S., Ware, D. H. (January 2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res, 39. D1085-D1094. ISSN 1362-4962 (Electronic) 0305-1048 (Linking)

Z

Zhao, W., Canaran, P., Jurkuta, R., Fulton, T., Glaubitz, J., Buckler, E., Doebley, J., Gaut, B., Goodman, M., Holland, J., Kresovich, S., McMullen, M., Stein, L. D., Ware, D. (January 2006) Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res, 34 (Databa). D752-7. ISSN 1362-4962 (Electronic)