Publications - Ware Lab

Archives

2017

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. ISSN 0028-646x

2016

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)
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, Pankaj (2016) Gramene Database: Navigating Plant Comparative Genomics Resources. Current Plant Biology. ISSN 2214-6628
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 information system. Horticulture Research, 3. p. 16056. ISSN 2052-7276 (Linking)
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, Pankaj (2016) Gramene Database: Navigating Plant Comparative Genomics Resources. Current Plant Biology, 7-8. pp. 10-15. ISSN 2214-6628
Naithani, S., Preece, J., D’Eustachio, P., Gupta, P., Amarasinghe, V., Dharmawardhana, P. D., Wu, G., Fabregat, A., Elser, J. L., Weiser, J., Keays, M., Fuentes, A. M., Petryszak, R., Stein, L. D., Ware, D., Jaiswal, P. (2016) Plant Reactome: a resource for plant pathways and comparative analysis. Nucleic Acids Res. ISSN 1362-4962 (Electronic)0305-1048
Jiao, Y., Burke, J. J., Chopra, R., Burow, G., Chen, J., Wang, B., Hayes, C., Emendack, Y., Ware, D., Xin, Z. (2016) A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. Plant Cell. ISSN 1532-298X (Electronic)1040-4651 (Linking)
Wang, B., Tseng, E., Regulski, M., Clark, T. A., Hon, T., Jiao, Y., Lu, Z., Olson, A., Stein, J. C., Ware, D. (2016) Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun, 7. p. 11708. ISSN 2041-1723 (Electronic)2041-1723 (Linking)
He, F., Yoo, S., Wang, D., Kumari, S., Gerstein, M., Ware, D., Maslov, S. (2016) Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis. Plant J, 86 (6). pp. 472-80. ISSN 1365-313X (Electronic)0960-7412 (Linking)
Wang, L., Van Buren, P., Ware, D. (2016) Architecting a distributed bioinformatics platform with iRODS and iPlant agave API. 2015 International Conference on Computational Science and Computational Intelligence (CSCI). pp. 420-423.
Merchant, N., Lyons, E., Goff, S., Vaughn, M., Ware, D., Micklos, D., Antin, P. (2016) The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences. PLoS Biol, 14 (1). e1002342. ISSN 1545-7885 (Electronic)1544-9173 (Linking)
Kersey, P. J., Allen, J. E., Armean, I., Boddu, S., Bolt, B. J., Carvalho-Silva, D., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Humphrey, J., Kerhornou, A., Khobova, J., Aranganathan, N. K., Langridge, N., Lowy, E., McDowall, M. D., Maheswari, U., Nuhn, M., Ong, C. K., Overduin, B., Paulini, M., Pedro, H., Perry, E., Spudich, G., Tapanari, E., Walts, B., Williams, G., Tello-Ruiz, M., Stein, J., Wei, S., Ware, D., Bolser, D. M., Howe, K. L., Kulesha, E., Lawson, D., Maslen, G., Staines, D. M. (2016) Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res, 44 (D1). D574-80. ISSN 1362-4962 (Electronic)0305-1048 (Linking)
Tello-Ruiz, M. K., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarasinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D. M., Kerhornou, A., Walts, B., Fonseca, N. A., Huerta, L., Keays, M., Tang, Y. A., Parkinson, H., Fabregat, A., McKay, S., Weiser, J., D’Eustachio, P., Stein, L., Petryszak, R., Kersey, P. J., Jaiswal, P., Ware, D. (2016) Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res, 44 (D1). D1133-40. ISSN 1362-4962 (Electronic)0305-1048 (Linking)
Tello-Ruiz, M. K., Stein, J., Wei, S., Youens-Clark, K., Jaiswal, P., Ware, D. (2016) Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol, 1374. pp. 141-63. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

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

Zwickl, D. J., J. C. Stein, R. A. Wing, D. Ware and M. J. Sanderson (2014). “Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.” Syst Biol 63(5): 645-659.
Wang, L., D. Ware, C. Lushbough, N. Merchant and L. Stein (2014) “A genome-wide association study platform built on iPlant cyber-infrastructure Concurrency and Computation: Practice and Experience Early View.” Concurrency and Computation: Practice and Experience, n/a.
Seaver, S. M., S. Gerdes, O. Frelin, C. Lerma-Ortiz, L. M. Bradbury, R. Zallot, G. Hasnain, T. D. Niehaus, B. El Yacoubi, S. Pasternak, R. Olson, G. Pusch, R. Overbeek, R. Stevens, V. de Crecy-Lagard, D. Ware, A. D. Hanson and C. S. Henry (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): 9645-9650.
Monaco, M. K., J. Stein, S. Naithani, S. Wei, P. Dharmawardhana, S. Kumari, V. Amarasinghe, K. Youens-Clark, J. Thomason, J. Preece, S. Pasternak, A. Olson, Y. Jiao, Z. Lu, D. Bolser, A. Kerhornou, D. Staines, B. Walts, G. Wu, P. D’Eustachio, R. Haw, D. Croft, P. J. Kersey, L. Stein, P. Jaiswal and D. Ware (2014). “Gramene 2013: comparative plant genomics resources.” Nucleic acids research 42(Database issue): D1193-1199.
Law, M., K. L. Childs, M. S. Campbell, J. C. Stein, C. Holt, N. Panchy, J. Lei, D. Jao, C. M. Andorf, C. J. Lawrence, D. Ware, S. H. Shiu, Y. Sun, N. Jiang and M. Yandell (2014). “Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.” Plant Physiol.
Kersey, P. J., J. E. Allen, M. Christensen, P. Davis, L. J. Falin, C. Grabmueller, D. S. Hughes, J. Humphrey, A. Kerhornou, J. Khobova, N. Langridge, M. D. McDowall, U. Maheswari, G. Maslen, M. Nuhn, C. K. Ong, M. Paulini, H. Pedro, I. Toneva, M. A. Tuli, B. Walts, G. Williams, D. Wilson, K. Youens-Clark, M. K. Monaco, J. Stein, X. Wei, D. Ware, D. M. Bolser, K. L. Howe, E. Kulesha, D. Lawson and D. M. Staines (2014). “Ensembl Genomes 2013: scaling up access to genome-wide data.” Nucleic acids research 42(Database issue): D546-552.
Eveland, A. L., A. Goldshmidt, M. Pautler, K. Morohashi, C. Liseron-Monfils, M. W. Lewis, S. Kumari, S. Hiraga, F. Yang, E. Unger-Wallace, A. Olson, S. Hake, E. Vollbrecht, E. Grotewold, D. Ware and D. Jackson (2014). “Regulatory modules controlling maize inflorescence architecture.” Genome Res 24(3): 431-443.
Campbell, M. S., M. Law, C. Holt, J. C. Stein, G. D. Moghe, D. E. Hufnagel, J. Lei, R. Achawanantakun, D. Jiao, C. J. Lawrence, D. Ware, S. H. Shiu, K. L. Childs, Y. Sun, N. Jiang and M. Yandell (2014). “MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.” Plant physiology 164(2): 513-524.
Olson, A., Klein, R. R., Dugas, D. V., Lu, Z. Y., Regulski, M., Klein, P. E., Ware, D. (2014) Expanding and Vetting Sorghum bicolor Gene Annotations through Transcriptome and Methylome Sequencing. Plant Genome, 7 (2). p. 20. ISSN 1940-3372

2013

Regulski, M., Z. Lu, J. Kendall, M. T. Donoghue, J. Reinders, V. Llaca, S. Deschamps, A. Smith, D. Levy, W. R. McCombie, S. Tingey, A. Rafalski, J. Hicks, D. Ware and R. A. Martienssen (2013). “The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.” Genome research 23(10): 1651-1662.
Olson, A., R. R. Klein, D. V. Dugas, Z. Lu, R. Regulski, P. E. Klein and D. Ware (2013). “Expanding and Vetting Sorghum bicolor Gene Annotations through Transcriptome and Methylome.” Plant Genome.
Luo, M. C., Y. Q. Gu, F. M. You, K. R. Deal, Y. Ma, Y. Hu, N. Huo, Y. Wang, J. Wang, S. Chen, C. M. Jorgensen, Y. Zhang, P. E. McGuire, S. Pasternak, J. C. Stein, D. Ware, M. Kramer, W. R. McCombie, S. F. Kianian, M. M. Martis, K. F. Mayer, S. K. Sehgal, W. Li, B. S. Gill, M. W. Bevan, H. Simkov·, J. Dolezel, S. Weining, G. R. Lazo, O. D. Anderson and J. Dvorak (2013). “A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.” Proc Natl Acad Sci U S A 110(19): 7940-7945.
Kumari, S. and D. Ware (2013). “Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots.” PloS one 8(10): e79011.
Dharmawardhana, P., L. Ren, V. Amarasinghe, M. Monaco, J. Thomason, D. Ravenscroft, S. McCouch, D. Ware and P. Jaiswal (2013). “A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress.” Rice 6(1): 15.

2012

Spooner, W., K. Youens-Clark, D. Staines and D. Ware (2012). “GrameneMart: the BioMart data portal for the Gramene project.” Database : the journal of biological databases and curation 2012: bar056.
Liu, Z., S. Kumari, L. Zhang, Y. Zheng and D. Ware (2012). “Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays.” PloS one 7(6): e39786.
Hung, H. Y., L. M. Shannon, F. Tian, P. J. Bradbury, C. Chen, S. A. Flint-Garcia, M. D. McMullen, D. Ware, E. S. Buckler, J. F. Doebley and J. B. Holland (2012). “ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize.” Proc Natl Acad Sci U S A 109(28): E1913-1921.
Hufford, M. B., X. Xu, J. van Heerwaarden, T. Pyhajarvi, J. M. Chia, R. A. Cartwright, R. J. Elshire, J. C. Glaubitz, K. E. Guill, S. M. Kaeppler, J. Lai, P. L. Morrell, L. M. Shannon, C. Song, N. M. Springer, R. A. Swanson-Wagner, P. Tiffin, J. Wang, G. Zhang, J. Doebley, M. D. McMullen, D. Ware, E. S. Buckler, S. Yang and J. Ross-Ibarra (2012). “Comparative population genomics of maize domestication and improvement.” Nature genetics 44(7): 808-811.
Chia, J. M., C. Song, P. J. Bradbury, D. Costich, N. de Leon, J. Doebley, R. J. Elshire, B. Gaut, L. Geller, J. C. Glaubitz, M. Gore, K. E. Guill, J. Holland, M. B. Hufford, J. Lai, M. Li, X. Liu, Y. Lu, R. McCombie, R. Nelson, J. Poland, B. M. Prasanna, T. Pyh‰j‰rvi, T. Rong, R. S. Sekhon, Q. Sun, M. I. Tenaillon, F. Tian, J. Wang, X. Xu, Z. Zhang, S. M. Kaeppler, J. Ross-Ibarra, M. D. McMullen, E. S. Buckler, G. Zhang, Y. Xu and D. Ware (2012). “Maize HapMap2 identifies extant variation from a genome in flux.” Nat Genet 44(7): 803-807.

2011

Youens-Clark, K., E. Buckler, T. Casstevens, C. Chen, G. Declerck, P. Derwent, P. Dharmawardhana, P. Jaiswal, P. Kersey, A. S. Karthikeyan, J. Lu, S. R. McCouch, L. Ren, W. Spooner, J. C. Stein, J. Thomason, S. Wei and D. Ware (2011). “Gramene database in 2010: updates and extensions.” Nucleic acids research 39(Database issue): D1085-1094.
Myles, S., A. R. Boyko, C. L. Owens, P. J. Brown, F. Grassi, M. K. Aradhya, B. Prins, A. Reynolds, J. M. Chia, D. Ware, C. D. Bustamante and E. S. Buckler (2011). “Genetic structure and domestication history of the grape.” Proc Natl Acad Sci U S A 108(9): 3530-3535.
Kump, K. L., P. J. Bradbury, R. J. Wisser, E. S. Buckler, A. R. Belcher, M. A. Oropeza-Rosas, J. C. Zwonitzer, S. Kresovich, M. D. McMullen, D. Ware, P. J. Balint-Kurti and J. B. Holland (2011). “Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population.” Nat Genet 43(2): 163-168.
Goff, S. A., M. Vaughn, S. McKay, E. Lyons, A. E. Stapleton, D. Gessler, N. Matasci, L. Wang, M. Hanlon, A. Lenards, A. Muir, N. Merchant, S. Lowry, S. Mock, M. Helmke, A. Kubach, M. Narro, N. Hopkins, D. Micklos, U. Hilgert, M. Gonzales, C. Jordan, E. Skidmore, R. Dooley, J. Cazes, R. McLay, Z. Lu, S. Pasternak, L. Koesterke, W. H. Piel, R. Grene, C. Noutsos, K. Gendler, X. Feng, C. Tang, M. Lent, S. J. Kim, K. Kvilekval, B. S. Manjunath, V. Tannen, A. Stamatakis, M. Sanderson, S. M. Welch, K. A. Cranston, P. Soltis, D. Soltis, B. O’Meara, C. Ane, T. Brutnell, D. J. Kleibenstein, J. W. White, J. Leebens-Mack, M. J. Donoghue, E. P. Spalding, T. J. Vision, C. R. Myers, D. Lowenthal, B. J. Enquist, B. Boyle, A. Akoglu, G. Andrews, S. Ram, D. Ware, L. Stein and D. Stanzione (2011). “The iPlant Collaborative: Cyberinfrastructure for Plant Biology.” Front Plant Sci 2: 34.
Gaudinier, A., L. Zhang, J. S. Reece-Hoyes, M. Taylor-Teeples, L. Pu, Z. Liu, G. Breton, J. L. Pruneda-Paz, D. Kim, S. A. Kay, A. J. Walhout, D. Ware and S. M. Brady (2011). “Enhanced Y1H assays for Arabidopsis.” Nat Methods 8(12): 1053-1055.
Dugas, D. V., M. K. Monaco, A. Olsen, R. R. Klein, S. Kumari, D. Ware and P. E. Klein (2011). “Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid.” BMC genomics 12: 514.
Consortium, A. I. M. (2011). “Evidence for network evolution in an Arabidopsis interactome map.” Science 333(6042): 601-607.
Brady, S. M., L. Zhang, M. Megraw, N. J. Martinez, E. Jiang, C. S. Yi, W. Liu, A. Zeng, M. Taylor-Teeples, D. Kim, S. Ahnert, U. Ohler, D. Ware, A. J. Walhout and P. N. Benfey (2011). “A stele-enriched gene regulatory network in the Arabidopsis root.” Mol Syst Biol 7: 459.

2010

Swanson-Wagner, R. A., S. R. Eichten, S. Kumari, P. Tiffin, J. C. Stein, D. Ware and N. M. Springer (2010). “Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor.” Genome research 20(12): 1689-1699.
Myles, S., J. M. Chia, B. Hurwitz, C. Simon, G. Y. Zhong, E. Buckler and D. Ware (2010). “Rapid genomic characterization of the genus vitis.” PLoS One 5(1): e8219.
Hurwitz, B. L., D. Kudrna, Y. Yu, A. Sebastian, A. Zuccolo, S. A. Jackson, D. Ware, R. A. Wing and L. Stein (2010). “Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza.” Plant J 63(6): 990-1003.
Gill, N., P. SanMiguel, B. D. S. Dhillon, B. Abernathy, H. Kim, L. Stein, D. Ware, R. Wing and S. A. Jackson (2010). “Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents.” Rice 3(4): 251-269.
Eveland, A. L., N. Satoh-Nagasawa, A. Goldshmidt, S. Meyer, M. Beatty, H. Sakai, D. Ware and D. Jackson (2010). “Digital gene expression signatures for maize development.” Plant Physiol 154(3): 1024-1039.
Consortium, I. A. I. (2010). “An international bioinformatics infrastructure to underpin the Arabidopsis community.” Plant Cell 22(8): 2530-2536.

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

Wicker, T., A. Narechania, F. Sabot, J. Stein, G. T. Vu, A. Graner, D. Ware and N. Stein (2008). “Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats.” BMC Genomics 9: 518.
Liang, C., P. Jaiswal, C. Hebbard, S. Avraham, E. S. Buckler, T. Casstevens, B. Hurwitz, S. McCouch, J. Ni, A. Pujar, D. Ravenscroft, L. Ren, W. Spooner, I. Tecle, J. Thomason, C. W. Tung, X. Wei, I. Yap, K. Youens-Clark, D. Ware and L. Stein (2008). “Gramene: a growing plant comparative genomics resource.” Nucleic Acids Res 36(Database issue): D947-953.
Kurtz, S., A. Narechania, J. C. Stein and D. Ware (2008). “A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.” BMC Genomics 9: 517.
Kim, H., B. Hurwitz, Y. Yu, K. Collura, N. Gill, P. SanMiguel, J. C. Mullikin, C. Maher, W. Nelson, M. Wissotski, M. Braidotti, D. Kudrna, J. L. Goicoechea, L. Stein, D. Ware, S. A. Jackson, C. Soderlund and R. A. Wing (2008). “Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza.” Genome Biol 9(2): R45.
Canaran, P., E. S. Buckler, J. C. Glaubitz, L. Stein, Q. Sun, W. Zhao and D. Ware (2008). “Panzea: an update on new content and features.” Nucleic Acids Res 36(Database issue): D1041-1043.
Avraham, S., C. W. Tung, K. Ilic, P. Jaiswal, E. A. Kellogg, S. McCouch, A. Pujar, L. Reiser, S. Y. Rhee, M. M. Sachs, M. Schaeffer, L. Stein, P. Stevens, L. Vincent, F. Zapata and D. Ware (2008). “The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.” Nucleic Acids Res 36(Database issue): D449-454.

2007

Ilic, K., E. A. Kellogg, P. Jaiswal, F. Zapata, P. F. Stevens, L. P. Vincent, S. Avraham, L. Reiser, A. Pujar, M. M. Sachs, N. T. Whitman, S. R. McCouch, M. L. Schaeffer, D. H. Ware, L. D. Stein and S. Y. Rhee (2007). “The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.” Plant Physiol 143(2): 587-599.
Hufford, K. M., P. Canaran, D. H. Ware, M. D. McMullen and B. S. Gaut (2007). “Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci.” Plant Physiol 144(3): 1642-1653.

2006

Zhao, W., P. Canaran, R. Jurkuta, T. Fulton, J. Glaubitz, E. Buckler, J. Doebley, B. Gaut, M. Goodman, J. Holland, S. Kresovich, M. McMullen, L. Stein and D. Ware (2006). “Panzea: a database and resource for molecular and functional diversity in the maize genome.” Nucleic Acids Res 34(Database issue): D752-757.
Pujar, A., P. Jaiswal, E. A. Kellogg, K. Ilic, L. Vincent, S. Avraham, P. Stevens, F. Zapata, L. Reiser, S. Y. Rhee, M. M. Sachs, M. Schaeffer, L. Stein, D. Ware and S. McCouch (2006). “Whole-plant growth stage ontology for angiosperms and its application in plant biology.” Plant Physiol 142(2): 414-428.
Maher, C., L. Stein and D. Ware (2006). “Evolution of Arabidopsis microRNA families through duplication events.” Genome Res 16(4): 510-519.
Jaiswal, P., J. Ni, I. Yap, D. Ware, W. Spooner, K. Youens-Clark, L. Ren, C. Liang, W. Zhao, K. Ratnapu, B. Faga, P. Canaran, M. Fogleman, C. Hebbard, S. Avraham, S. Schmidt, T. M. Casstevens, E. S. Buckler, L. Stein and S. McCouch (2006). “Gramene: a bird’s eye view of cereal genomes.” Nucleic Acids Res 34(Database issue): D717-723.
Hass-Jacobus, B. L., M. Futrell-Griggs, B. Abernathy, R. Westerman, J. L. Goicoechea, J. Stein, P. Klein, B. Hurwitz, B. Zhou, F. Rakhshan, A. Sanyal, N. Gill, J. Y. Lin, J. G. Walling, M. Z. Luo, J. S. Ammiraju, D. Kudrna, H. R. Kim, D. Ware, R. A. Wing, P. San Miguel and S. A. Jackson (2006). “Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum.” BMC Genomics 7: 199.
Canaran, P., L. Stein and D. Ware (2006). “Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support.” Bioinformatics 22(7): 885-886.

2005

2003

2002

Ware, D. H., P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang, S. Cartinhour, L. D. Stein and S. R. McCouch (2002). “Gramene, a tool for grass genomics.” Plant Physiol 130(4): 1606-1613.
Ware, D., P. Jaiswal, J. Ni, X. Pan, K. Chang, K. Clark, L. Teytelman, S. Schmidt, W. Zhao, S. Cartinhour, S. McCouch and L. Stein (2002). “Gramene: a resource for comparative grass genomics.” Nucleic Acids Res 30(1): 103-105.
McCouch, S. R., L. Teytelman, Y. Xu, K. B. Lobos, K. Clare, M. Walton, B. Fu, R. Maghirang, Z. Li, Y. Xing, Q. Zhang, I. Kono, M. Yano, R. Fjellstrom, G. DeClerck, D. Schneider, S. Cartinhour, D. Ware and L. Stein (2002). “Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.).” DNA Res 9(6): 199-207.

2000