Browse by CSHL Author

Paper

Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel MD, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong (July 2018) KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology, 36 (7). pp. 566-569. ISSN 1087-0156

Seaver, S. M., Gerdes, S., Frelin, O., Lerma-Ortiz, C., Bradbury, L. M., Zallot, R., Hasnain, G., Niehaus, T. D., El Yacoubi, B., Pasternak, S., Olson, R., Pusch, G., Overbeek, R., Stevens, R., de Crecy-Lagard, V., Ware, D., Hanson, A. D., Henry, C. S. (June 2014) High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proceedings of the National Academy of Sciences of the United States of America, 111 (26). pp. 9645-9650. ISSN 0027-8424

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

Luo, M. C., Gu, Y. Q., You, F. M., Deal, K. R., Ma, Y., Hu, Y., Huo, N., Wang, Y., Wang, J., Chen, S., Jorgensen, C. M., Zhang, Y., McGuire, P. E., Pasternak, S., Stein, J. C., Ware, D., Kramer, M., McCombie, W. R., Kianian, S. F., Martis, M. M., Mayer, K. F. X., Sehgal, S. K., Li, W., Gill, B. S., Bevan, M. W., Šimková, H., Doležel, J., Weining, S., Lazo, G. R., Anderson, O. D., Dvorak, J. (May 2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences of the United States of America, 110 (19). pp. 7940-7945. ISSN 00278424

The Tomato Genome Consortium (May 2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485 (7400). pp. 635-41. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S. M., Belter, E., Du, F., Kim, K., Abbott, R. M., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S. M., Gillam, B., Chen, W., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L., Wei, S., Kumari, S., Faga, B., Levy, M. J., McMahan, L., Van Buren, P., Vaughn, M. W. (November 2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326 (5956). pp. 1112-5. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Wei, F., Stein, J. C., Liang, C., Zhang, J., Fulton, R. S., Baucom, R. S., De Paoli, E., Zhou, S., Yang, L., Han, Y., Pasternak, S., Narechania, A., Zhang, L., Yeh, C. T., Ying, K., Nagel, D. H., Collura, K., Kudrna, D., Currie, J., Lin, J., Kim, H., Angelova, A., Scara, G., Wissotski, M., Golser, W., Courtney, L., Kruchowski, S., Graves, T. A., Rock, S. M., Adams, S., Fulton, L. A., Fronick, C., Courtney, W., Kramer, M., Spiegel, L., Nascimento, L., Kalyanaraman, A., Chaparro, C., Deragon, J. M., Miguel, P. S., Jiang, N., Wessler, S. R., Green, P. J., Yu, Y., Schwartz, D. C., Meyers, B. C., Bennetzen, J. L., Martienssen, R. A., McCombie, W. R., Aluru, S., Clifton, S. W., Schnable, P. S., Ware, D., Wilson, R. K., Wing, R. A. (November 2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS genetics, 5 (11). e1000728. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M. R., Churas, C., Pasternak, S., Forrest, D. K., Wise, R., Ware, D. H., Wing, R. A., Waterman, M. S., Livny, M., Schwartz, D. C. (November 2009) A single molecule scaffold for the maize genome. PLoS Genet, 5 (11). e1000711. ISSN 1553-7404 (Electronic)

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