Items where Subject is "bioinformatics > genomics and proteomics > databases > database optimization"

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Number of items at this level: 41.

B

Benfey, P., Carpenter, A., Waterston, W., Ohler, U. (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. (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. (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. (2005) EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics, 6. p. 143. ISSN 1471-2164

C

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. (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. (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. (2010) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res, 39 (Suppl ). D691. 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.

d'Alencon, E., Negre, N., Stanojcic, S., Alassoeur, B., Gimenez, S., Leger, A., Abd-Alla, A., Juliant, S., Fournier, P. (2011) Characterization of a CENP-B homolog in the holocentric Lepidoptera Spodoptera frugiperda. Gene, 485 (2). pp. 91-101. ISSN 0378-1119

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. (2005) The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Research, 33. D485-D491. ISSN 0305-1048

F

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. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449 (7164). 851-U3. ISSN 0028-0836

G

Girard, L. R., Fiedler, T. J., Harris, T. W., Carvalho, F., Antoshechkin, I., Han, M., Sternberg, P.l W., Stein, L. D., Chalfie, M. (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. In: C. elegans: methods and applications. Methods Mol Biol, 351 . Humana Press, Totowa, NJ, pp. 31-50. ISBN 1064-3745 (Print)

Haw, R., Hermjakob, H., D'Eustachio, P., Stein, L. D. (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. (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. (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

L

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. (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. (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. (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). Plos Biology, 9 (4). ISSN 1544-9173

O

Olson, A., Sheth, N., Lee, J., Hannon, G. J., Sachidanandam, R. (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. (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. (2006) WormBase: better software, richer content. Nucl. Acids Res., 34 (suppl_). D475-478.

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

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

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

Stein, L. D. (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. (2005) DWE: discriminating word enumerator. Bioinformatics, 21 (1). pp. 31-8. ISSN 1367-4803 (Print)

T

Thorisson, G. A., Smith, A. V., Krishnan, L., Stein, L. D. (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. (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. (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)

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