Items where Subject is "datasets"

B

Barash, Carol Isaacson, Lyon, Gholson (November 2014) Open access and data sharing: Easier said than done. Applied & Translational Genomics. ISSN 2212-0661

Birney, E., Hudson, T. J., Green, E. D., Gunter, C., Eddy, S., Rogers, J., Harris, J. R., Ehrlich, S. D., Apweiler, R., Austin, C. P., Berglund, L., Bobrow, M., Bountra, C., Brookes, A. J., Cambon-Thomsen, A., Carter, N. P., Chisholm, R. L., Contreras, J. L., Cooke, R. M., Crosby, W. L., Dewar, K., Durbin, R., Dyke, S. O., Ecker, J. R., El Emam, K., Feuk, L., Gabriel, S. B., Gallacher, J., Gelbart, W. M., Granell, A., Guarner, F., Hubbard, T., Jackson, S. A., Jennings, J. L., Joly, Y., Jones, S. M., Kaye, J., Kennedy, K. L., Knoppers, B. M., Kyrpides, N. C., Lowrance, W. W., Luo, J., MacKay, J. J., Martin-Rivera, L., McCombie, W. R., McPherson, J. D., Miller, L., Miller, W., Moerman, D., Mooser, V., Morton, C. C., Ostell, J. M., Ouellette, B. F., Parkhill, J., Raina, P. S., Rawlings, C., Scherer, S. E., Scherer, S. W., Schofield, P. N., Sensen, C. W., Stodden, V. C., Sussman, M. R., Tanaka, T., Thornton, J., Tsunoda, T., Valle, D., Vuorio, E. I., Walker, N. M., Wallace, S., Weinstock, G., Whitman, W. B., Worley, K. C., Wu, C., Wu, J., Yu, J. (September 2009) Prepublication data sharing. Nature, 461 (7261). pp. 168-70. ISSN 0028-0836

C

Cokol, M., Weinstein, Z. B., Yilancioglu, K., Tasan, M., Doak, A., Cansever, D., Mutlu, B., Li, S., Rodriguez-Esteban, R., Akhmedov, M., Guvenek, A., Cokol, M., Cetiner, S., Giaever, G., Iossifov, I., Nislow, C., Shoichet, B., Roth, F. P. (April 2014) Large-Scale Identification and Analysis of Suppressive Drug Interactions. Chemistry & Biology, 21 (4). pp. 541-551. ISSN 1074-5521

Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R., Jassal, B., Jupe, S., Matthews, L., May, B., Palatnik, S., Rothfels, K., Shamovsky, V., Song, H., Williams, M., Birney, E., Hermjakob, H., Stein, L., D'Eustachio, P. (January 2014) The Reactome pathway knowledgebase. Nucleic Acids Research, 42 (Databa). D472-7. ISSN 0305-1048

F

Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., Matthews, L., May, B., Milacic, M., Rothfels, K., Shamovsky, V., Webber, M., Weiser, J., Williams, M., Wu, G., Stein, L., Hermjakob, H., D'Eustachio, P. (January 2016) The Reactome pathway Knowledgebase. Nucleic Acids Res, 44 (D1). D481-487. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Feng, X., Grossman, R., Stein, L. D. (May 2011) PeakRanger: A cloud-enabled peak caller for ChIP-seq data. Bmc Bioinformatics, 12. p. 139. ISSN 1471-2105

G

Gerhard, D. S., Clemons, P. A., Shamji, A. F., Hon, C., Wagner, B. K., Schreiber, S. L., Krasnitz, A., Sordella, R., Sander, C., Lowe, S. W., Powers, S., Smith, K., Aburi, M., Iavarone, A., Lasorella, A., Silva, J., Stockwell, B. R., Califano, A., Boehm, J. S., Vazquez, F., Weir, B. A., Hahn, W. C., Khuri, F. R., Moreno, C. S., Johns, M., Fu, H., Nikolova, O., Mendez, E., Gadi, V. K., Margolin, A. A., Grandori, C., Kemp, C. J., Warren, E. H., Riddell, S. R., McIntosh, M. W., Gevaert, O., Kuo, C. J., Ji, H. P., Dhruv, H., Finlay, D., Kiefer, J., Kim, S., Vuori, K., Berens, M. E., Hangauer, M., Boettcher, M., Weissman, J. S., Bivona, T. G., Bandyopadhyay, S., McManus, M. T., McCormick, F., Aksoy, O., Simonds, E. F., Zheng, T., Chen, J., An, Z., Balmain, A., Weiss, W. A., Chen, K., Liang, H., Scott, K. L., Mills, G. B., Posner, B. A., MacMillan, J., Minna, J., White, M., Roth, M. G., Jagu, S., Mazerik, J. (July 2016) Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance. Mol Cancer Res. ISSN 1557-3125 (Electronic)1541-7786 (Linking)

H

Hicks, J. B. (2006) Data file sw.dip.amps.txt for deletions. [Dataset] (Unpublished)

K

Kersey, P. J., Allen, J. E., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Hughes, D. S., Humphrey, J., Kerhornou, A., Khobova, J., Langridge, N., McDowall, M. D., Maheswari, U., Maslen, G., Nuhn, M., Ong, C. K., Paulini, M., Pedro, H., Toneva, I., Tuli, M. A., Walts, B., Williams, G., Wilson, D., Youens-Clark, K., Monaco, M. K., Stein, J., Wei, X., Ware, D., Bolser, D. M., Howe, K. L., Kulesha, E., Lawson, D., Staines, D. M. (January 2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Research, 42 (Databa). D546-52. ISSN 0305-1048

Kinney, J. B., Atwal, G. S. (March 2014) Equitability, mutual information, and the maximal information coefficient. Proceedings of the National Academy of Sciences of the United States of America, 111 (9). pp. 3354-9. ISSN 0027-8424

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

Monaco, M. K., Stein, J., Naithani, S., Wei, S., Dharmawardhana, P., Kumari, S., Amarasinghe, V., Youens-Clark, K., Thomason, J., Preece, J., Pasternak, S., Olson, A., Jiao, Y., Lu, Z., Bolser, D., Kerhornou, A., Staines, D., Walts, B., Wu, G., D'Eustachio, P., Haw, R., Croft, D., Kersey, P. J., Stein, L., Jaiswal, P., Ware, D. (January 2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Research, 42 (Databa). D1193-9. ISSN 0305-1048

R

Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboue, P. A., Weng, W., Wilbur, W. J., Hatzivassiloglou, V., Friedman, C. (February 2004) GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform, 37 (1). pp. 43-53. ISSN 1532-0464 (Print)1532-0464 (Linking)

S

Schatz, M. C. (November 2012) Computational thinking in the era of big data biology. Genome Biology, 13 (11). p. 177. ISSN 1465-6906

Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., Arnaiz, O., Awedh, M. H., Baldock, R., Barbiera, G., Bardou, P., Beck, T., Blake, A., Bonierbale, M., Brookes, A. J., Bucci, G., Buetti, I., Burge, S., Cabau, C., Carlson, J. W., Chelala, C., Chrysostomou, C., Cittaro, D., Collin, O., Cordova, R., Cutts, R. J., Dassi, E., Genova, A. D., Djari, A., Esposito, A., Estrella, H., Eyras, E., Fernandez-Banet, J., Forbes, S., Free, R. C., Fujisawa, T., Gadaleta, E., Garcia-Manteiga, J. M., Goodstein, D., Gray, K., Guerra-Assuncao, J. A., Haggarty, B., Han, D. J., Han, B. W., Harris, T., Harshbarger, J., Hastings, R. K., Hayes, R. D., Hoede, C., Hu, S., Hu, Z. L., Hutchins, L., Kan, Z., Kawaji, H., Keliet, A., Kerhornou, A., Kim, S., Kinsella, R., Klopp, C., Kong, L., Lawson, D., Lazarevic, D., Lee, J. H., Letellier, T., Li, C. Y., Lio, P., Liu, C. J., Luo, J., Maass, A., Mariette, J., Maurel, T., Merella, S., Mohamed, A. M., Moreews, F., Nabihoudine, I., Ndegwa, N., Noirot, C., Perez-Llamas, C., Primig, M., Quattrone, A., Quesneville, H., Rambaldi, D., Reecy, J., Riba, M., Rosanoff, S., Saddiq, A. A., Salas, E., Sallou, O., Shepherd, R., Simon, R., Sperling, L., Spooner, W., Staines, D. M., Steinbach, D., Stone, K., Stupka, E., Teague, J. W., Dayem Ullah, A. Z., Wang, J., Ware, D. (April 2015) The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res, 43 (W1). W589-W598. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Smith, A. D., Sumazin, P., Das, D., Zhang, M. Q. (June 2005) Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics, 21 Sup. i403-12. ISSN 1367-4803 (Print)

Stephens, Z. D., Lee, S. Y., Faghri, F., Campbell, R. H., Zhai, C., Efron, M. J., Iyer, R., Schatz, M. C., Sinha, S., Robinson, G. E. (July 2015) Big Data: Astronomical or Genomical? PLoS Biol, 13 (7). e1002195. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

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)