Ware, Doreen H. Publications

Up a level
Export as [feed] Atom [feed] RSS 1.0 [feed] RSS 2.0
Group by: Item Type | No Grouping
Jump to: Paper | Book Section | Book | Video

Ware, Doreen H.

http://www.warelab.org/
Number of items at this level: 99.

Paper

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., Ware, D. (2017) Improved maize reference genome with single-molecule technologies. Nature, 546 (7659). pp. 524-527. ISSN 0028-0836

Majoros, W. H., Campbell, M. S., Holt, C., DeNardo, E., Ware, D., Allen, A. S., Yandell, M., Reddy, T. E. (2017) High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. Bioinformatics, 33 (10). pp. 1437-1446. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

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. ISSN 0028-646x

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, 45 (D1). D1029-D1039. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

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, 28 (7). pp. 1551-1562. 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)

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

Schatz, M. C., Maron, L. G., Stein, J. C., Hernandez Wences, A., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., Wright, M. H., Chia, J. M., Ware, D., McCouch, S. R., McCombie, W. R. (2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol, 15 (11). p. 506. ISSN 1465-6906

Law, M., Childs, K. L., Campbell, M. S., Stein, J. C., Holt, C., Panchy, N., Lei, J., Jao, D., Andorf, C. M., Lawrence, C. J., Ware, D., Shiu, S. H., Sun, Y., Jiang, N., Yandell, M. (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 Physiology. ISSN 0032-0889

Zwickl, D. J., Stein, J. C., Wing, R. A., Ware, D., Sanderson, M. J. (2014) Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Systematic Biology, 63 (5). pp. 645-659. ISSN 1076836X (ISSN)

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

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. (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

Campbell, M. S., Law, M., Holt, C., Stein, J. C., Moghe, G. D., Hufnagel, D. E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C. J., Ware, D., Shiu, S. H., Childs, K. L., Sun, Y., Jiang, N., Yandell, M. (2014) MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations. Plant Physiol, 164 (2). pp. 513-24. ISSN 0032-0889

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. (2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Research, 42 (Databa). D546-52. ISSN 0305-1048

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. (2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Research, 42 (Databa). D1193-9. ISSN 0305-1048

Eveland, A. L., Goldshmidt, A., Pautler, M., Morohashi, K., Liseron-Monfils, C., Lewis, M. W., Kumari, S., Hiraga, S., Yang, F., Unger-Wallace, E., Olson, A., Hake, S., Vollbrecht, E., Grotewold, E., Ware, D., Jackson, D. (2014) Regulatory modules controlling maize inflorescence architecture. Genome Research, 24 (3). pp. 431-443. ISSN 1088-9051

Kumari, S., Ware, D. (2013) Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots. PLoS ONE, 8 (10). Art no. e79011. ISSN 1932-6203

Regulski, M., Lu, Z., Kendall, J., Donoghue, M. T., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., McCombie, W. R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., Martienssen, R. (2013) The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research, 23 (10). pp. 1651-1662. ISSN 10889051 (ISSN)

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. (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

Dharmawardhana, P., Ren, L. Y., Amarasinghe, V., Monaco, M., Thomason, J., Ravenscroft, D., McCouch, S., Ware, D., Jaiswal, P. (2013) A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice, 6 (1). pp. 1-15. ISSN 1939-8425

Monaco, M. K., Sen, T. Z., Dharmawardhana, P. D., Ren, L., Schaeffer, M., Naithani, S., Amarasinghe, V., Thomason, J., Harper, L., Gardiner, J., Cannon, E. K. S., Lawrence, C. J., Ware, D., Jaiswal, P. (2013) Maize Metabolic Network Construction and Transcriptome Analysis. Plant Genome, 6 (1). ISSN 1940-3372

Hung, H. Y., Shannon, L. M., Tian, F., Bradbury, P. J., Chen, C., Flint-Garcia, S. A., McMullen, M. D., Ware, D., Buckler, E. S., Doebley, J. F., Holland, J. B. (2012) ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proceedings of the National Academy of Sciences of the United States of America, 109 (28). E1913-E1921. ISSN 0027-8424

Hufford, M. B., Xu, X., van Heerwaarden, J., Pyhajarvi, T., Chia, J. M., Cartwright, R. A., Elshire, R. J., Glaubitz, J. C., Guill, K. E., Kaeppler, S. M., Lai, J. S., Morrell, P. L., Shannon, L. M., Song, C., Springer, N. M., Swanson-Wagner, R. A., Tiffin, P., Wang, J., Zhang, G. Y., Doebley, J., McMullen, M. D., Ware, D., Buckler, E. S., Yang, S., Ross-Ibarra, J. (2012) Comparative population genomics of maize domestication and improvement. Nature Genetics, 44 (7). pp. 808-811. ISSN 1061-4036

Liu, Z. J., Kumari, S., Zhang, L. F., Zheng, Y. L., Ware, D. (2012) Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays. PLoS ONE, 7 (6). e39786. ISSN 1932-6203

Chia, J. M., Song, C., Bradbury, P. J., Costich, D., de Leon, N., Doebley, J., Elshire, R. J., Gaut, B., Geller, L., Glaubitz, J. C., Gore, M., Guill, K. E., Holland, J., Hufford, M. B., Lai, J., Li, M., Liu, X., Lu, Y., McCombie, R., Nelson, R., Poland, J., Prasanna, B. M., Pyhajarvi, T., Rong, T., Sekhon, R. S., Sun, Q., Tenaillon, M. I., Tian, F., Wang, J., Xu, X., Zhang, Z., Kaeppler, S. M., Ross-Ibarra, J., McMullen, M. D., Buckler, E. S., Zhang, G., Xu, Y., Ware, D. (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet, 44 (7). 803-U238. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Baerenfaller, K., Bastow, R., Beynon, J., Brady, S., Brendel, V., Donaldson, S., Dooley, R., Forster, M., Friesner, J., Gifford, D., Grotewold, E., Gutierrez, R., Huala, E., Jaiswal, P., Joshi, H., Kersey, P., Liu, L., Loraine, A., Lyons, E., May, S., Mayer, K., MacLean, D., Meyers, B., Mueller, L., Muller, R., Muller, H. M., Ouellette, F., Pires, J. C., Provart, N., Staiger, D., Stanzione, D., Taylor, J., Taylor, C., Town, C., Toyoda, T., Vaughn, M., Walsh, S., Ware, D., Weckwerth, W., Int Arabidopsis, Informatics (2012) Taking the Next Step: Building an Arabidopsis Information Portal. Plant Cell, 24 (6). pp. 2248-2256. ISSN 1040-4651

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

Spooner, W., Youens-Clark, K., Staines, D., Ware, D. (2012) GrameneMart: the BioMart data portal for the Gramene project. Database (Oxford), 2012. ISSN 1758-0463 (Electronic)

Consortium, Arabidopsis Interactome Mapping (2011) Evidence for Network Evolution in an Arabidopsis Interactome Map. Science, 333 (6042). pp. 601-607.

Myles, S., Boyko, A. R., Owens, C. L., Brown, P. J., Grassi, F., Aradhya, M. K., Prins, B., Reynolds, A., Chia, J. M., Ware, D. H., Bustamante, C. D., Buckler, E. S. (2011) Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences of the United States of America, 108 (9). pp. 3530-3535. ISSN 0027-8424

Chia, J. M., Ware, D. H. (2011) Sequencing for the cream of the crop. Nature Biotechnology, 29 (2). pp. 138-9. ISSN 1546-1696 (Electronic) 1087-0156 (Linking)

Brady, S. M., Zhang, L., Megraw, M., Martinez, N. J., Jiang, E., Yi, C. S., Liu, W., Zeng, A., Taylor-Teeples, M., Kim, D., Ahnert, S., Ohler, U., Ware, D. H., Walhout, A. J. M., Benfey, P. N. (2011) A stele-enriched gene regulatory network in the Arabidopsis root. Molecular Systems Biology, 7. p. 459.

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 Research, 39 (SUPPL.).

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)

Goff, S. A, Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E, Gessler, D. , Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M, Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W. H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S. J., Kvilekval, K., Manjunath, B.S., Tannen, V., Stamatakis, A., Sanderson, M. J., Welch, S. M., Cranston, K. , Soltis, P. , Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D. J., White, J. W., Leebens-Mack, J., Donoghue, M. J., Spalding, E. P., Vision, T. J., Myers, C. R., Lowenthal, D., Enquist, B. J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., Stanzione, D. (2011) The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science, 2. ISSN 1664-462X

Gill, N., SanMiguel, P., Dhillon, B. D. S., Abernathy, B., Kim, H., Stein, L. D., Ware, D. H., Wing, R., Jackson, S. A. (2010) Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents. Rice, 3 (4). pp. 251-269.

Swanson-Wagner, R. A., Eichten, S. R., Kumari, S., Tiffin, P., Stein, J. C., Ware, D. H., Springer, N. M. (2010) Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Research, 20 (12). pp. 1689-1699.

Eveland, A. L., Satoh-Nagasawa, N., Goldschmidt, A., Meyer, S., Beatty, M., Sakai, H., Ware, D. H., Jackson, D. P. (2010) Digital Gene Expression Signatures for Maize Development. Plant Physiology, 154 (3). pp. 1024-1039. ISSN 0032-0889

Myles, S., Chia, J. M., Hurwitz, B. L., Simon, C., Zhong, G. Y., Buckler, E., Ware, D. H. (2010) Rapid Genomic Characterization of the Genus Vitis. PLoS ONE, 5 (1). ISSN 1932-6203

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.

Ammiraju, J. S. S., Song, X., Luo, M., Sisneros, N., Angelova, A., Kudrna, D., Kim, H., Yu, Y., Goicoechea, J. L., Lorieux, M., Kurata, N., Brar, D., Ware, D. H., Jackson, S., Wing, R. A. (2010) The Oryza BAC resource: A genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives. Breeding Science, 60 (5). pp. 536-543. ISSN 13447610 (ISSN)

Cranston, K. A., Hurwitz, B. L., Sanderson, M. J., Ware, D. H., Wing, R. A., Stein, L. D. (2010) Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae). Systematic Botany, 35 (3). pp. 512-523.

Hurwitz, B. L., Kudrna, D., Yu, Y., Sebastian, A., Zuccolo, A., Jackson, S. A., Ware, D. H., Wing, R. A., Stein, L. D. (2010) Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant Journal, 63 (6). pp. 990-1003.

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. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326 (5956). pp. 1112-5. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Gore, M. A., Chia, J. M., Elshire, R. J., Sun, Q., Ersoz, E. S., Hurwitz, B. L., Peiffer, J. A., McMullen, M. D., Grills, G. S., Ross-Ibarra, J., Ware, D. H., Buckler, E. S. (2009) A first-generation haplotype map of maize. Science, 326 (5956). pp. 1115-1117. ISSN 0036-8075

Youens-Clark, K., Faga, B. P., Yap, I. V., Stein, L. D., Ware, D. H. (2009) CMap 1.01: A comparative mapping application for the Internet. Bioinformatics, 25 (22). pp. 3040-3042.

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. (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)

Zhang, L., Chia, J. M., Kumari, S., Stein, J. C., Liu, Z., Narechania, A., Maher, C. A., Guill, K., McMullen, M. D., Ware, D. H. (2009) A Genome-Wide Characterization of MicroRNA Genes in Maize. PLoS Genet, 5 (11). e1000716. ISSN 1553-7404 (Electronic)

Wei, F., Zhang, J., Zhou, S., He, R., Schaeffer, M., Collura, K., Kudrna, D., Faga, B. P., Wissotski, M., Golser, W., Rock, S. M., Graves, T. A., Fulton, R. S., Coe, E., Schnable, P. S., Schwartz, D. C., Ware, D. H., Clifton, S. W., Wilson, R. K., Wing, R. A. (2009) The physical and genetic framework of the maize b73 genome. PLoS Genet, 5 (11). e1000715. ISSN 1553-7404 (Electronic)

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. (2009) A single molecule scaffold for the maize genome. PLoS Genet, 5 (11). e1000711. ISSN 1553-7404 (Electronic)

Liang, C., Mao, L., Ware, D. H., Stein, L. D. (2009) Evidence-based gene predictions in plant genomes. Genome Res, 19 (10). 1912-1923 .

Cranston, K. A., Hurwitz, B. L., Ware, D. H., Stein, L. D., Wing, R. A. (2009) Species Trees from Highly Incongruent Gene Trees in Rice. Systematic Biology, 58 (5). pp. 489-500. ISSN 1063-5157

McMullen, M. D., Kresovich, S., Villeda, Hector S., Bradbury, P. J., Li, H., Sun, Q., Flint-Garcia, S., Thornsberry, J., Acharya, C. B., Bottoms, C., Brown, P. J., Browne, C., Eller, M., Guill, K., Harjes, C., Kroon, D. E., Lepak, N.., Mitchell, S. E., Peterson, B., Pressoir, G., Romero, S., Rosas, M. O., Salvo, S., Yates, H., Hanson, M., Jones, E. G., Smith, S., Glaubitz, J. C., Goodman, M. M., Ware, D. H., Holland, J. B., Buckler, E. S. (2009) Genetic Properties of the Maize Nested Association Mapping Population. Science, 325 (5941). pp. 737-740.

Buckler, E. S., Holland, J. B., Bradbury, P. J., Acharya, C. B., Brown, P. J., Browne, C., Ersoz, E., Flint-Garcia, S., Garcia, A., Glaubitz, J. C., Goodman, M. M., Harjes, C., Guill, K., Kroon, D. E., Larsson, S., Lepak, N. K., Li, H., Mitchell, S. E., Pressoir, G., Peiffer, J. A., Rosas, M. O., Rocheford, T. R., Romay, M. C., Romero, S., Salvo, S., Sanchez Villeda, H., da Silva, H. S., Sun, Q., Tian, F., Upadyayula, N., Ware, D. H., Yates, H., Yu, J., Zhang, Z., Kresovich, S., McMullen, M. D. (2009) The genetic architecture of maize flowering time. Science, 325 (5941). pp. 714-8. ISSN 1095-9203 (Electronic)

Ni, J., Pujar, A., Youens-Clark, K., Yap, I. V., Jaiswal, P., Tecle, I., Tung, C.-W., Ren, L. , Spooner, W., Wei, X, Avraham, S, Ware, D. H., Stein, L. D., McCouch, S. (2009) Gramene QTL database: development, content and applications. Database, 2009. bap005.

Brooks, L., Strable, J., Zhang, X., Ohtsu, K., Zhou, R., Sarkar, A., Hargreaves, S., Elshire, R. J., Eudy, D., Pawlowska, T., Ware, D. H., Janick-Buckner, D., Buckner, B., Timmermans, M. C. P., Schnable, P. S., Nettleton, D., Scanlon, M. J. (2009) Microdissection of shoot meristem functional domains. PLoS Genet, 5 (5). e1000476.

Paterson, A. H., Bowers, J. E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., Schmutz, J., Spannagl, M., Tang, H., Wang, X., Wicker, T., Bharti, A. K., Chapman, J., Feltus, F. A., Gowik, U., Grigoriev, I. V., Lyons, E., Maher, C. A., Martis, M., Narechania, A., Otillar, R. P., Penning, B. W., Salamov, A. A., Wang, Y., Zhang, L., Carpita, N. C., Freeling, M., Gingle, A. R., Hash, C. T., Keller, B., Klein, P., Kresovich, S., McCann, M. C., Ming, R., Peterson, D. G., Mehboob ur, R., Ware, D. H., Westhoff, P., Mayer, K. F. X., Messing, J., Rokhsar, D. S. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457 (7229). pp. 551-556.

Wicker, T., Narechania, A., Sabot, F., Stein, J. C., Vu, G. T. H., Graner, A., Ware, D. H., Stein, N. (2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics, 9. p. 518.

Kurtz, S., Narechania, A., Stein, J. C., Ware, D. H. (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics, 9. p. 517.

Kim, H. R., Hurwitz, B. L., Yu, Y., Collura, K., Gill, N., SanMiguel, P., Mullikin, J. C., Maher, C., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goigochia, J. L., Stein, L. D., Ware, D. H., Jackson, S., Soderlund, C., Wing, R. (2008) Construction, alignment and analysis of 12 framework physical maps that represent the 10 genome types of the genus Oryza. Genome Biology, 9 (2). R45. ISSN 1465-6906

Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E. S., Casstevens, T., Hurwitz, B. L., McCouch, S., Ni, J., Pujar, A., Ravenscroft, D., Ren, L., Spooner, W., Tecle, I., Thomason, J., Tung, C. W., Wei, X., Yap, I., Youens-Clark, K., Ware, D. H., Stein, L. D. (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res, 36 (Databa). D947-53.

Avraham, S., Tung, C. W., Ilic, K., Jaiswal, P., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L. D., Stevens, P., Vincent, L., Zapata, F., Ware, D. H. (2008) The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res, 36 (Databa). D449-54.

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.

Hufford, K. M., Canaran, P., Ware, D. H., McMullen, M. D., Gaut, B. S. (2007) Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci. Plant Physiology, 144 (3). pp. 1642-1653. ISSN 0032-0889

Ilic, K., Kellogg, E. A., Jaiswal, P., Zapata, F., Stevens, P. F., Vincent, L. P., Avraham, S., Reiser, L., Pujar, A., Sachs, M. M., Whitman, N. T., McCouch, S. R., Schaeffer, M. L., Ware, D. H., Stein, L. D., Rhee, S. Y. (2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiology, 143 (2). pp. 587-599. ISSN 0032-0889

Ware, D. H. (2007) Gramene. Methods Mol Biol, 406. pp. 315-329. ISSN 1064-3745 (Print)

Pujar, An., Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, Sh., Stevens, P., Zapata, F., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L. D., Ware, D. H., McCouch, S. (2006) Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology, 142 (2). pp. 414-428. ISSN 00320889

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)

Maher, C., Stein, L. D., Ware, D. (2006) Evolution of Arabidopsis microRNA families through duplication events. Genome Res, 16 (4). pp. 510-9. ISSN 1088-9051 (Print)

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)

Hass-Jacobus, B. L., Futrell-Griggs, M., Abernathy, B., Westerman, R., Goicoechea, J. L., Stein, J., Klein, P., Hurwitz, B., Zhou, B., Rakhshan, F., Sanyal, A., Gill, N., Lin, J. Y., Walling, J. G., Luo, M. Z., Ammiraju, J. S. S., Kudrna, D., Kim, H. R., Ware, D., Wing, Rod A., San Miguel, P., Jackson, S. A. (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. p. 199. ISSN 14712164

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)

Kresovich, S., Barbazuk, B., Bedell, J. A., Borrell, A., Buell, C. R., Burke, J., Clifton, S., Cordonnier-Pratt, M. M., Cox, S., Dahlberg, J., Erpelding, J., Fulton, T. M., Fulton, B., Fulton, L., Gingle, A. R., Hash, C. T., Huang, Y., Jordan, D., Klein, P. E., Klein, R. R., Magalhaes, J., McCombie, R., Moore, P., Mullet, J. E., Ozias-Akins, P., Paterson, A. H., Porter, K., Pratt, L., Roe, B., Rooney, W., Schnable, P. S., Stelly, D. M., Tuinstra, M., Ware, D., Warek, U. (2005) Toward sequencing the sorghum genome. A U.S. National Science Foundation-sponsored workshop report. Plant Physiology, 138 (4). pp. 1898-1902. ISSN 00320889 (ISSN)

Ware, D., Stein, L. (2003) Comparison of genes among cereals. Current Opinion in Plant Biology, 6 (2). pp. 121-7. ISSN 1369-5266

Yu, Y., Rambo, T., Currie, J., Saski, C., Kim, H. R., Collura, K., Thompson, S., Simmons, J., Yang, T. J., Nah, G., Patel, A. J., Thurmond, S., Henry, D., Oates, R., Palmer, M., Pries, G., Gibson, J., Anderson, H., Paradkar, M., Crane, L., Dale, J., Carver, M. B., Wood, T., Frisch, D., Engler, F., Soderlund, C., Palmer, L. E., Tetylman, L., Nascimento, L., de la Bastide, M., Spiegel, L., Ware, D., O'Shaughnessy, A., Dike, S., Dedhia, N., Preston, R., Huang, E., Ferraro, K., Kuit, K., Miller, B., Zutavern, T., Katzenberger, F., Muller, S., Balija, V., Martienssen, R. A., Stein, L., Minx, P., Johnson, D., Cordum, H., Mardis, E., Cheng, Z., Jiang, J., Wilson, R., McCombie, W. R., Wing, R. A., Yuan, Q., Ouyang, S., Liu, J., Jones, K. M., Gansberger, K., Moffat, K., Hill, J., Tsitrin, T., Overton, L., Bera, J., Kim, M., Jin, S., Tallon, L., Ciecko, A., Pai, G., van Aken, S., Utterback, T., Reidmuller, S., Bormann, J., Feldblyum, T., Hsiao, J., Zismann, V., Blunt, S., de Vazeilles, A., Shaffer, T., Koo, H., Suh, B., Yang, Q., Haas, B., Peterson, J., Pertea, M., Volfovsky, N., Wortman, J., White, O., Salzberg, S. L., Fraser, C. M., Robin Buell, C., Messing, J., Song, R., Fuks, G., Llaca, V., Kovchak, S., Young, S., Bowers, J. E., Paterson, A. H. (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science, 300 (5625). pp. 1566-1569. ISSN 00368075 (ISSN)

Scholl, R., Sachs, M. M., Ware, D. (2003) Maintaining collections of mutants for plant functional genomics. Methods in Molecular Biology, 236. pp. 311-26. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Ware, D. H., Jaiswal, P. J., Ni, J. J., Yap, I., Pan, X. K., Clark, K. Y., Teytelman, L., Schmidt, S. C., Zhao, W., Chang, K., Cartinhour, S., Stein, L. D., McCouch, S. R. (2002) Gramene, a tool for grass Genomics. Plant Physiology, 130 (4). pp. 1606-1613. ISSN 0032-0889

Jaiswal, P., Ware, D., Ni, J. J., Chang, K., Zhao, W., Schmidt, S., Pan, X. K., Clark, K., Teytelman, L., Cartinhour, S., Stein, L., McCouch, S. (2002) Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics, 3 (2). pp. 132-136. ISSN 1531-6912

Bruskiewich, R., Coe, E. H., Jaiswal, P., McCouch, S., Polacco, M., Stein, L., Vincent, L., Ware, D. (2002) The Plant Ontology (TM) Consortium and plant ontologies. Comparative and Functional Genomics, 3 (2). pp. 137-142. ISSN 1531-6912

Ware, D., Jaiswal, P., Ni, J. J., Pan, X. K., Chang, K., Clark, K., Teytelman, L., Schmidt, S., Zhao, W., Cartinhour, S., McCouch, S., Stein, L. (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Research, 30 (1). pp. 103-105. ISSN 0305-1048

Li, H., Wu, G., Ware, D., Davis, K. R., Yang, Z. (1998) Arabidopsis Rho-related GTPases: differential gene expression in pollen and polar localization in fission yeast. Plant Physiology, 118 (2). pp. 407-17. ISSN 0032-0889 (Print)

Wanner, L. A., Li, G., Ware, D., Somssich, I. E., Davis, K. R. (1995) The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana. Plant Mol Biol, 27 (2). pp. 327-38. ISSN 0167-4412 (Print)

Book Section

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

Book

Wang, D., Pan, E., Fang, G., Kumari, S., He, F., Ware, D., Maslov, S., Gerstein, M. (2013) Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between arabidopsis and poplar. 2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 . ACM, pp. 689-690. ISBN 9781450324342 (ISBN)

Video

Ware, D. H. (2011) Talk from Doreen Ware at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

This list was generated on Sat Sep 23 05:09:26 2017 EDT.
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving