Archives

2017
2016
2015
  • Liu, H., Niu, Y., Gonzalez-Portilla, P. J., Zhou, H., Wang, L., Zuo, T., Qin, C., Tai, S., Jansen, C., Shen, Y., Lin, H., Lee, M., Ware, D., Zhang, Z., Lubberstedt, T., Pan, G. (2015) An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize. BMC Genomics, 16 (1). p. 1078. ISSN 1471-2164 (Electronic)1471-2164 (Linking)
  • Liseron-Monfils, Christophe, Ware, Doreen (2015) Revealing gene regulation and associations through biological networks. Current Plant Biology, 3-4. pp. 30-39. ISSN 2214-6628
  • Noutsos, C., Perera, A. M., Nikolau, B. J., Seaver, S. M., Ware, D. H. (2015) Metabolomic Profiling of the Nectars of Aquilegia pubescens and A. Canadensis. PLoS One, 10 (5). e0124501. ISSN 1932-6203 (Electronic)1932-6203 (Linking)
  • 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. (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)
  • Wang, L., Ware, D., Lushbough, C., Merchant, N., Stein, L. (2015) A genome-wide association study platform built on iPlant cyber-infrastructure. Concurrency Computation, 27 (2). pp. 420-432. ISSN 15320626
  • Taylor-Teeples, M., Lin, L., de Lucas, M., Turco, G., Toal, T. W., Gaudinier, A., Young, N. F., Trabucco, G. M., Veling, M. T., Lamothe, R., Handakumbura, P. P., Xiong, G., Wang, C., Corwin, J., Tsoukalas, A., Zhang, L., Ware, D., Pauly, M., Kliebenstein, D. J., Dehesh, K., Tagkopoulos, I., Breton, G., Pruneda-Paz, J. L., Ahnert, S. E., Kay, S. A., Hazen, S. P., Brady, S. M. (2015) An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature, 517 (7536). pp. 571-575. ISSN 0028-0836
  • Law, M., Childs, K. L., Campbell, M. S., Stein, J. C., Olson, A. J., Holt, C., Panchy, N., Lei, J., Jiao, D., Andorf, C. M., Lawrence, C. J., Ware, D., Shiu, S. H., Sun, Y., Jiang, N., Yandell, M. (2015) Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes. Plant Physiol, 167 (1). pp. 25-39. ISSN 0032-0889
2014
2013
2012
2011
2010
2009
  • Zhou, S., F. Wei, J. Nguyen, M. Bechner, K. Potamousis, S. Goldstein, L. Pape, M. R. Mehan, C. Churas, S. Pasternak, D. K. Forrest, R. Wise, D. Ware, R. A. Wing, M. S. Waterman, M. Livny and D. C. Schwartz (2009). “A single molecule scaffold for the maize genome.” PLoS Genet 5(11): e1000711.
  • Zhang, L., J. M. Chia, S. Kumari, J. C. Stein, Z. Liu, A. Narechania, C. A. Maher, K. Guill, M. D. McMullen and D. Ware (2009). “A genome-wide characterization of microRNA genes in maize.” PLoS Genet 5(11): e1000716.
  • Youens-Clark, K., B. Faga, I. V. Yap, L. Stein and D. Ware (2009). “CMap 1.01: a comparative mapping application for the Internet.” Bioinformatics 25(22): 3040-3042.
  • Wei, F., J. Zhang, S. Zhou, R. He, M. Schaeffer, K. Collura, D. Kudrna, B. P. Faga, M. Wissotski, W. Golser, S. M. Rock, T. A. Graves, R. S. Fulton, E. Coe, P. S. Schnable, D. C. Schwartz, D. Ware, S. W. Clifton, R. K. Wilson and R. A. Wing (2009). “The physical and genetic framework of the maize B73 genome.” PLoS Genet 5(11): e1000715.
  • Wei, F., J. C. Stein, C. Liang, J. Zhang, R. S. Fulton, R. S. Baucom, E. De Paoli, S. Zhou, L. Yang, Y. Han, S. Pasternak, A. Narechania, L. Zhang, C. T. Yeh, K. Ying, D. H. Nagel, K. Collura, D. Kudrna, J. Currie, J. Lin, H. Kim, A. Angelova, G. Scara, M. Wissotski, W. Golser, L. Courtney, S. Kruchowski, T. A. Graves, S. M. Rock, S. Adams, L. A. Fulton, C. Fronick, W. Courtney, M. Kramer, L. Spiegel, L. Nascimento, A. Kalyanaraman, C. Chaparro, J. M. Deragon, P. S. Miguel, N. Jiang, S. R. Wessler, P. J. Green, Y. Yu, D. C. Schwartz, B. C. Meyers, J. L. Bennetzen, R. A. Martienssen, W. R. McCombie, S. Aluru, S. W. Clifton, P. S. Schnable, D. Ware, R. K. Wilson and R. A. Wing (2009). “Detailed analysis of a contiguous 22-Mb region of the maize genome.” PLoS Genet 5(11): e1000728.
  • Schnable, P. S., D. Ware, R. S. Fulton, J. C. Stein, F. Wei, S. Pasternak, C. Liang, J. Zhang, L. Fulton, T. A. Graves, P. Minx, A. D. Reily, L. Courtney, S. S. Kruchowski, C. Tomlinson, C. Strong, K. Delehaunty, C. Fronick, B. Courtney, S. M. Rock, E. Belter, F. Du, K. Kim, R. M. Abbott, M. Cotton, A. Levy, P. Marchetto, K. Ochoa, S. M. Jackson, B. Gillam, W. Chen, L. Yan, J. Higginbotham, M. Cardenas, J. Waligorski, E. Applebaum, L. Phelps, J. Falcone, K. Kanchi, T. Thane, A. Scimone, N. Thane, J. Henke, T. Wang, J. Ruppert, N. Shah, K. Rotter, J. Hodges, E. Ingenthron, M. Cordes, S. Kohlberg, J. Sgro, B. Delgado, K. Mead, A. Chinwalla, S. Leonard, K. Crouse, K. Collura, D. Kudrna, J. Currie, R. He, A. Angelova, S. Rajasekar, T. Mueller, R. Lomeli, G. Scara, A. Ko, K. Delaney, M. Wissotski, G. Lopez, D. Campos, M. Braidotti, E. Ashley, W. Golser, H. Kim, S. Lee, J. Lin, Z. Dujmic, W. Kim, J. Talag, A. Zuccolo, C. Fan, A. Sebastian, M. Kramer, L. Spiegel, L. Nascimento, T. Zutavern, B. Miller, C. Ambroise, S. Muller, W. Spooner, A. Narechania, L. Ren, S. Wei, S. Kumari, B. Faga, M. J. Levy, L. McMahan, P. Van Buren, M. W. Vaughn, K. Ying, C. T. Yeh, S. J. Emrich, Y. Jia, A. Kalyanaraman, A. P. Hsia, W. B. Barbazuk, R. S. Baucom, T. P. Brutnell, N. C. Carpita, C. Chaparro, J. M. Chia, J. M. Deragon, J. C. Estill, Y. Fu, J. A. Jeddeloh, Y. Han, H. Lee, P. Li, D. R. Lisch, S. Liu, Z. Liu, D. H. Nagel, M. C. McCann, P. SanMiguel, A. M. Myers, D. Nettleton, J. Nguyen, B. W. Penning, L. Ponnala, K. L. Schneider, D. C. Schwartz, A. Sharma, C. Soderlund, N. M. Springer, Q. Sun, H. Wang, M. Waterman, R. Westerman, T. K. Wolfgruber, L. Yang, Y. Yu, L. Zhang, S. Zhou, Q. Zhu, J. L. Bennetzen, R. K. Dawe, J. Jiang, N. Jiang, G. G. Presting, S. R. Wessler, S. Aluru, R. A. Martienssen, S. W. Clifton, W. R. McCombie, R. A. Wing and R. K. Wilson (2009). “The B73 maize genome: complexity, diversity, and dynamics.” Science 326(5956): 1112-1115.
  • Paterson, A. H., J. E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood, H. Gundlach, G. Haberer, U. Hellsten, T. Mitros, A. Poliakov, J. Schmutz, M. Spannagl, H. Tang, X. Wang, T. Wicker, A. K. Bharti, J. Chapman, F. A. Feltus, U. Gowik, I. V. Grigoriev, E. Lyons, C. A. Maher, M. Martis, A. Narechania, R. P. Otillar, B. W. Penning, A. A. Salamov, Y. Wang, L. Zhang, N. C. Carpita, M. Freeling, A. R. Gingle, C. T. Hash, B. Keller, P. Klein, S. Kresovich, M. C. McCann, R. Ming, D. G. Peterson, Mehboob-ur-Rahman, D. Ware, P. Westhoff, K. F. Mayer, J. Messing and D. S. Rokhsar (2009). “The Sorghum bicolor genome and the diversification of grasses.” Nature 457(7229): 551-556.
  • Ni, J., A. Pujar, K. Youens-Clark, I. Yap, P. Jaiswal, I. Tecle, C. W. Tung, L. Ren, W. Spooner, X. Wei, S. Avraham, D. Ware, L. Stein and S. McCouch (2009). “Gramene QTL database: development, content and applications.” Database (Oxford) 2009: bap005.
  • McMullen, M. D., S. Kresovich, H. S. Villeda, P. Bradbury, H. Li, Q. Sun, S. Flint-Garcia, J. Thornsberry, C. Acharya, C. Bottoms, P. Brown, C. Browne, M. Eller, K. Guill, C. Harjes, D. Kroon, N. Lepak, S. E. Mitchell, B. Peterson, G. Pressoir, S. Romero, M. Oropeza Rosas, S. Salvo, H. Yates, M. Hanson, E. Jones, S. Smith, J. C. Glaubitz, M. Goodman, D. Ware, J. B. Holland and E. S. Buckler (2009). “Genetic properties of the maize nested association mapping population.” Science 325(5941): 737-740.
  • Liang, C., L. Mao, D. Ware and L. Stein (2009). “Evidence-based gene predictions in plant genomes.” Genome Res 19(10): 1912-1923.
  • Gore, M. A., J. M. Chia, R. J. Elshire, Q. Sun, E. S. Ersoz, B. L. Hurwitz, J. A. Peiffer, M. D. McMullen, G. S. Grills, J. Ross-Ibarra, D. H. Ware and E. S. Buckler (2009). “A first-generation haplotype map of maize.” Science 326(5956): 1115-1117.
  • Cranston, K. A., B. Hurwitz, D. Ware, L. Stein and R. A. Wing (2009). “Species trees from highly incongruent gene trees in rice.” Syst Biol 58(5): 489-500.
  • Buckler, E. S., J. B. Holland, P. J. Bradbury, C. B. Acharya, P. J. Brown, C. Browne, E. Ersoz, S. Flint-Garcia, A. Garcia, J. C. Glaubitz, M. M. Goodman, C. Harjes, K. Guill, D. E. Kroon, S. Larsson, N. K. Lepak, H. Li, S. E. Mitchell, G. Pressoir, J. A. Peiffer, M. O. Rosas, T. R. Rocheford, M. C. Romay, S. Romero, S. Salvo, H. Sanchez Villeda, H. S. da Silva, Q. Sun, F. Tian, N. Upadyayula, D. Ware, H. Yates, J. Yu, Z. Zhang, S. Kresovich and M. D. McMullen (2009). “The genetic architecture of maize flowering time.” Science 325(5941): 714-718.
  • Brooks, L., J. Strable, X. Zhang, K. Ohtsu, R. Zhou, A. Sarkar, S. Hargreaves, R. J. Elshire, D. Eudy, T. Pawlowska, D. Ware, D. Janick-Buckner, B. Buckner, M. C. Timmermans, P. S. Schnable, D. Nettleton and M. J. Scanlon (2009). “Microdissection of shoot meristem functional domains.” PLoS Genet 5(5): e1000476.
2008
2007
2006
2005

Jaiswal, P., S. Avraham, K. Ilic, E. A. Kellogg, S. McCouch, A. Pujar, L. Reiser, S. Y. Rhee, M. M. Sachs, M. Schaeffer, L. Stein, P. Stevens, L. Vincent, D. Ware and F. Zapata (2005). “Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.” Comp Funct Genomics 6(7-8): 388-397.

2003
2002
2000

Scholl, R. L., S. T. May and D. H. Ware (2000). “Seed and molecular resources for Arabidopsis.” Plant Physiol 124(4): 1477-1480.

RSS Current publications

  • Improved maize reference genome with single-molecule technologies
    Jiao, Y., Peluso, P., Shi, J., Liang, T., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C. S., Guill, K., Regulski, M., Kumari, S., Olson, A., Gent, J., Schneider, K. L., Wolfgruber, T. K., May, M. R., Springer, N. M., Antoniou, E., McCombie, W. R., Presting, G. G., McMullen, M., Ross-Ibarra, J., Dawe, R. K., Hastie, A., Rank, D. R. […]
  • DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor
    Turco, G. M., Kajala, K., Kunde-Ramamoorthy, G., Ngan, C. Y., Olson, A., Deshphande, S., Tolkunov, D., Waring, B., Stelpflug, S., Klein, P., Schmutz, J., Kaeppler, S., Ware, D., Wei, C. L., Etchells, J. P., Brady, S. M. (2017) DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor. New Phytol, 214 (3). pp. 1213-1229 […]
  • Gramene Database: Navigating Plant Comparative Genomics Resources
    Gupta, Parul, Naithani, Sushma, Tello-Ruiz, Marcela Karey, Chougule, Kapeel, D’Eustachio, Peter, Fabregat, Antonio, Jiao, Yinping, Keays, Maria, Lee, Young Koung, Kumari, Sunita, Mulvaney, Joseph, Olson, Andrew, Preece, Justin, Stein, Joshua, Wei, Sharon, Weiser, Joel, Huerta, Laura, Petryszak, Robert, Kersey, Paul, Stein, Lincoln D., Ware, Doreen, Jaiswal, […]
  • High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE
    Majoros, W. H., Campbell, M. S., Holt, C., DeNardo, E., Ware, D., Allen, A. S., Yandell, M., Reddy, T. E. (2016) High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. Bioinformatics. ISSN 1367-4811 (Electronic)1367-4803 (Linking) […]
  • Towards an open grapevine information system
    Adam-Blondon, A. F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z. M., Cramer, G. R., Davies, C., Delrot, S., Deluc, L., Di Gaspero, G., Grimplet, J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M. A., Ware, D., Quesneville, H. (2016) Towards an open grapevine info […]