Items where Community is "CSHL labs > Ware lab"

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
Number of items at this level: 138.

Paper

Gaudinier, A., Rodriguez-Medina, J., Zhang, L., Olson, A., Liseron-Monfils, C., Bagman, A. M., Foret, J., Abbitt, S., Tang, M., Li, B., Runcie, D. E., Kliebenstein, D. J., Shen, B., Frank, M. J., Ware, D., Brady, S. M. (October 2018) Transcriptional regulation of nitrogen-associated metabolism and growth. Nature, 563 (7730). pp. 259-264. ISSN 0028-0836

Lee, Y. K., Kim, I. J. (October 2018) Functional conservation of Arabidopsis LNG1 in tobacco relating to leaf shape change by increasing longitudinal cell elongation by overexpression. Genes Genomics, 40 (10). pp. 1053-1062. ISSN 1976-9571

Chougule, K. M., Wang, L., Stein, J. C., Wang, X., Devisetty, U. K., Klein, R. R., Ware, D. (August 2018) Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure. Curr Protoc Bioinformatics. e53. ISSN 1934-3396

Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., Liu, H., Ma, X., Jiao, Y., Wang, B., Wei, X., Stein, J. C., Glaubitz, J. C., Lu, F., Yu, G., Liang, C., Fengler, K., Li, B., Rafalski, A., Schnable, P. S., Ware, D. H., Buckler, E. S., Lai, J. (July 2018) Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet. ISSN 1061-4036

Springer, N. M., Anderson, S. N., Andorf, C. M., Ahern, K. R., Bai, F., Barad, O., Barbazuk, W. B., Bass, H. W., Baruch, K., Ben-Zvi, G., Buckler, E. S., Bukowski, R., Campbell, M. S., Cannon, E. K. S., Chomet, P., Dawe, R. K., Davenport, R., Dooner, H. K., Du, L. H., Du, C., Easterling, K. A., Gault, C., Guan, J. C., Hunter, C. T., Jander, G., Jiao, Y., Koch, K. E., Kol, G., Kollner, T. G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D. R., Noshay, J. M., Portwood, J. L., Ronen, G., Settles, A. M., Shem-Tov, D., Shi, J., Soifer, I., Stein, J. C., Stitzer, M. C., Suzuki, M., Vera, D. L., Vollbrecht, E., Vrebalov, J. T., Ware, D., Wei, S., Wimalanathan, K., Woodhouse, M. R., Xiong, W., Brutnell, T. P. (July 2018) The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet. ISSN 1061-4036

Wang, L., Lu, Z., Van Buren, P., Ware, D. (June 2018) SciApps: A cloud-based platform for reproducible bioinformatics workflows. Bioinformatics. ISSN 1367-4803

Wang, B., Regulski, M., Tseng, E., Olson, A., Goodwin, S., McCombie, W. R., Ware, D. (June 2018) A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Res, 28 (6). pp. 921-932. ISSN 1088-9051

Holt, C., Campbell, M., Keays, D. A., Edelman, N., Kapusta, A., Maclary, E., Domyan, E. T., Suh, A., Warren, W. C., Yandell, M., Gilbert, M. T. P., Shapiro, M. D. (May 2018) Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia). G3-Genes Genomes Genetics, 8 (5). pp. 1391-1398. ISSN 2160-1836

Xin, Z., Chen, J., Jiao, Y., Gladman, N., Hayes, C., Burow, G., Emendack, Y., Burke, J. J. (May 2018) Registration of BTx623ms8, a new and easily identifiable nuclear male sterile mutant in sorghum. Journal of Plant Registrations, 12 (2). pp. 278-281. ISSN 1936-5209

Majoros, W. H., Holt, C., Campbell, M. S., Ware, D., Yandell, M., Reddy, T. E. (April 2018) Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features. Bioinformatics, 34 (21). pp. 3616-3623. ISSN 1367-4803

Bukowski, R., Guo, X., Lu, Y., Zou, C., He, B., Rong, Z., Wang, B., Xu, D., Yang, B., Xie, C., Fan, L., Gao, S., Xu, X., Zhang, G., Li, Y., Jiao, Y., Doebley, J. F., Ross-Ibarra, J., Lorant, A., Buffalo, V., Romay, M. C., Buckler, E. S., Ware, D., Lai, J., Sun, Q., Xu, Y. (April 2018) Construction of the third generation Zea mays haplotype map. Gigascience, 7 (4). pp. 1-12. ISSN 2047-217x

Jiao, Y., Lee, Y. K., Gladman, N., Chopra, R., Christensen, S. A., Regulski, M., Burow, G., Hayes, C., Burke, J., Ware, D., Xin, Z. (February 2018) MSD1 regulates pedicellate spikelet fertility in sorghum through the jasmonic acid pathway. Nat Commun, 9 (1). p. 822. ISSN 2041-1723

Evans, K. C., Benomar, S., Camuy-Velez, L. A., Nasseri, E. B., Wang, X., Neuenswander, B., Chandler, J. R. (January 2018) Quorum-sensing control of antibiotic resistance stabilizes cooperation in Chromobacterium violaceum. The ISME Journal. ISSN 1751-7362

Stein, J. C., Yu, Y., Copetti, D., Zwickl, D. J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J. L., Wei, S., Wang, J., Liao, Y., Wang, M., Jacquemin, J., Becker, C., Kudrna, D., Zhang, J., Londono, C. E. M., Song, X., Lee, S., Sanchez, P., Zuccolo, A., Ammiraju, J. S. S., Talag, J., Danowitz, A., Rivera, L. F., Gschwend, A. R., Noutsos, C., Wu, C. C., Kao, S. M., Zeng, J. W., Wei, F. J., Zhao, Q., Feng, Q., El Baidouri, M., Carpentier, M. C., Lasserre, E., Cooke, R., Rosa Farias, D. D., da Maia, L. C., Dos Santos, R. S., Nyberg, K. G., McNally, K. L., Mauleon, R., Alexandrov, N., Schmutz, J., Flowers, D., Fan, C., Weigel, D., Jena, K. K., Wicker, T., Chen, M., Han, B., Henry, R., Hsing, Y. C., Kurata, N., de Oliveira, A. C., Panaud, O., Jackson, S. A., Machado, C. A., Sanderson, M. J., Long, M., Ware, D., Wing, R. A. (January 2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet. ISSN 1061-4036

Jiao, Y. P., Burow, G., Gladman, N., Acosta-Martinez, V., Chen, J. P., Burke, J., Ware, D., Xin, Z. G. (January 2018) Efficient Identification of Causal Mutations through Sequencing of Bulked F-2 from Two Allelic Bloomless Mutants of Sorghum bicolor. Frontiers in Plant Science, 8. p. 2267. ISSN 1664-462X

Kersey, P. J., Allen, J. E., Allot, A., Barba, M., Boddu, S., Bolt, B. J., Carvalho-Silva, D., Christensen, M., Davis, P., Grabmueller, C., Kumar, N., Liu, Z., Maurel, T., Moore, B., McDowall, M. D., Maheswari, U., Naamati, G., Newman, V., Ong, C. K., Paulini, M., Pedro, H., Perry, E., Russell, M., Sparrow, H., Tapanari, E., Taylor, K., Vullo, A., Williams, G., Zadissia, A., Olson, A., Stein, J., Wei, S., Tello-Ruiz, M., Ware, D., Luciani, A., Potter, S., Finn, R. D., Urban, M., Hammond-Kosack, K. E., Bolser, D. M., De Silva, N., Howe, K. L., Langridge, N., Maslen, G., Staines, D. M., Yates, A. (January 2018) Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res, 46 (D1). D802-D808. ISSN 0305-1048

Tello-Ruiz, M. K., Naithani, S., Stein, J. C., Gupta, P., Campbell, M., Olson, A., Wei, S., Preece, J., Geniza, M. J., Jiao, Y., Lee, Y. K., Wang, B., Mulvaney, J., Chougule, K., Elser, J., Al-Bader, N., Kumari, S., Thomason, J., Kumar, V., Bolser, D. M., Naamati, G., Tapanari, E., Fonseca, N., Huerta, L., Iqbal, H., Keays, M., Munoz-Pomer Fuentes, A., Tang, A., Fabregat, A., D'Eustachio, P., Weiser, J., Stein, L. D., Petryszak, R., Papatheodorou, I., Kersey, P. J., Lockhart, P., Taylor, C., Jaiswal, P., Ware, D. (January 2018) Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res, 46 (D1). D1181-D1189. ISSN 0305-1048

Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., Andorf, C., Arnaud, E., Berardini, T. Z., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C. G., Farmer, A., Ficklin, S. P., Grant, D., Grau, E., Herndon, N., Hu, Z. L., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M. A., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C. J., Munoz-Torres, M. C., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L. A., Sen, T. Z., Staton, M., Subramaniam, S., Tello-Ruiz, M. K., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M., Yu, J., Main, D. (January 2018) AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database (Oxford), 2018. ISSN 1758-0463

Friesner, J., Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., Buell, C. R., Bucksch, A., Busch, W., Demura, T., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Falter-Braun, P., Gehan, M. A., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., Krouk, G., Ma, S., Markelz, R. J. C., Megraw, M., Meyers, B. C., Murray, J. A. H., Provart, N. J., Rhee, S., Smith, R., Spalding, E. P., Taylor, C., Teal, T. K., Torii, K. U., Town, C., Vaughn, M., Vierstra, R., Ware, D., Wilkins, O., Williams, C., Brady, S. M. (December 2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol, 175 (4). pp. 1499-1509. ISSN 0032-0889

Majsec, K., Bhuiyan, N. H., Sun, Q., Kumari, S., Kumar, V., Ware, D., van Wijk, K. J. (November 2017) The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis. Plant Cell, 29 (11). pp. 2687-2710. ISSN 1040-4651

Hwang, G., Zhu, J. Y., Lee, Y. K., Kim, S., Nguyen, T. T., Kim, J., Oh, E. (July 2017) PIF4 promotes expression of LNG1 and LNG2 to induce thermomorphogenic growth in arabidopsis. Frontiers in Plant Science, 8.

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

Majoros, W. H., Campbell, M. S., Holt, C., DeNardo, E., Ware, D., Allen, A. S., Yandell, M., Reddy, T. E. (May 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. (May 2017) DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor. New Phytol, 214 (3). pp. 1213-1229. ISSN 0028-646x (Public Dataset)

Eroh, G. D., Clayton, F. C., Florell, S. R., Cassidy, P. B., Chirife, A., Maron, C. F., Valenzuela, L. O., Campbell, M. S., Seger, J., Rowntree, V. J., Leachman, S. A. (February 2017) Cellular and ultrastructural characterization of the grey-morph phenotype in southern right whales (Eubalaena australis). PLoS One, 12 (2). e0171449. ISSN 1932-6203

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. (November 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 (November 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. (October 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. (July 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. (June 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)

Campbell, Michael, Oakeson, Kelly F., Yandell, Mark, Halpert, James R., Dearing, Denise (June 2016) The draft genome sequence and annotation of the desert woodrat Neotoma lepida. Genomics Data, 9. pp. 58-59. ISSN 2213-5960

He, F., Yoo, S., Wang, D., Kumari, S., Gerstein, M., Ware, D., Maslov, S. (June 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)

Braasch, I., Gehrke, A. R., Smith, J. J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A. M., Campbell, M. S., Barrell, D., Martin, K. J., Mulley, J. F., Ravi, V., Lee, A. P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Canestro, C., Sydes, J., Beaudry, F. E., Sun, Y., Hertel, J., Beam, M. J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J. H., Litman, G. W., Litman, R. T., Mikami, M., Ota, T., Saha, N. R., Williams, L., Stadler, P. F., Wang, H., Taylor, J. S., Fontenot, Q., Ferrara, A., Searle, S. M., Aken, B., Yandell, M., Schneider, I., Yoder, J. A., Volff, J. N., Meyer, A., Amemiya, C. T., Venkatesh, B., Holland, P. W., Guiguen, Y., Bobe, J., Shubin, N. H., Di Palma, F., Alfoldi, J., Lindblad-Toh, K., Postlethwait, J. H. (April 2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet, 48 (4). pp. 427-37. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Wang, L., Van Buren, P., Ware, D. (March 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.

Herrero, J., Muffato, M., Beal, K., Fitzgerald, S., Gordon, L., Pignatelli, M., Vilella, A. J., Searle, S. M., Amode, R., Brent, S., Spooner, W., Kulesha, E., Yates, A., Flicek, P. (February 2016) Ensembl comparative genomics resources. Database : the journal of biological databases and curation, 2016. ISSN 17580463 (ISSN)

Merchant, N., Lyons, E., Goff, S., Vaughn, M., Ware, D., Micklos, D., Antin, P. (January 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)

Song, Seung Yeob, Lee, Young Koung, Kim, In-Jung (January 2016) Sugar and acid content of Citrus prediction modeling using FT-IR fingerprinting in combination with multivariate statistical analysis. Food Chemistry, 190. pp. 1027-1032. ISSN 0308-8146

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. (January 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. (January 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. (January 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. (December 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 (December 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. (May 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. (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)

Wang, L., Ware, D., Lushbough, C., Merchant, N., Stein, L. (February 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. (January 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. (January 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. (December 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. (November 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

Noutsos, C., Borevitz, J. O., Hodges, S. A. (November 2014) Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens. Molecular Ecology, 23 (22). pp. 5589-98. ISSN 0962-1083

Zwickl, D. J., Stein, J. C., Wing, R. A., Ware, D., Sanderson, M. J. (September 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. (July 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. (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

Downs, G. S., Liseron-Monfils, C., Lukens, L. N. (March 2014) Regulatory motifs identified from a maize developmental coexpression network. Genome, 57 (3). pp. 181-184. ISSN 0831-2796

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. (February 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. (January 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. (January 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

Moreau, M., Westlake, T., Zampogna, G., Popescu, G., Tian, M., Noutsos, C., Popescu, S. (November 2013) The Arabidopsis oligopeptidases TOP1 and TOP2 are salicylic acid targets that modulate SA-mediated signaling and the immune response. Plant Journal, 76 (4). pp. 603-614. ISSN 09607412

Kumari, S., Ware, D. (October 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

Lam, T. H., Shen, M., Chia, J. M., Chan, S. H., Ren, E. C. (August 2013) Population-specific recombination sites within the human MHC region. Heredity, 111 (2). pp. 131-138. ISSN 0018067X

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. (June 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. (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

Dharmawardhana, P., Ren, L. Y., Amarasinghe, V., Monaco, M., Thomason, J., Ravenscroft, D., McCouch, S., Ware, D., Jaiswal, P. (May 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. (March 2013) Maize Metabolic Network Construction and Transcriptome Analysis. Plant Genome, 6 (1). ISSN 1940-3372

Boyle, B., Hopkins, N., Lu, Z. Y., Garay, J. A. R., Mozzherin, D., Rees, T., Matasci, N., Narro, M. L., Piel, W. H., McKay, S. J., Lowry, S., Freeland, C., Peet, R. K., Enquist, B. J. (January 2013) The taxonomic name resolution service: an online tool for automated standardization of plant names. BMC Bioinformatics, 14. ISSN 1471-2105

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. (July 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. (July 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. (June 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. (June 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 (June 2012) Taking the Next Step: Building an Arabidopsis Information Portal. Plant Cell, 24 (6). pp. 2248-2256. ISSN 1040-4651

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)

Xie, W. W., Liang, C. Z., Birchler, J. A. (August 2011) Inhibition of RNA Interference and Modulation of Transposable Element Expression by Cell Death in Drosophila. Genetics, 188 (4). pp. 823-834. ISSN 0016-6731

Consortium, Arabidopsis Interactome Mapping (July 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. (March 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. (February 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. (January 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. (January 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. (January 2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res, 39. D1085-D1094. ISSN 1362-4962 (Electronic) 0305-1048 (Linking)

Guberman, J. M., Ai, J., Arnaiz, O., Baran, J., Blake, A., Baldock, R., Chelala, C., Croft, D., Cros, A., Cutts, R. J., Di Génova, A., Forbes, S., Fujisawa, T., Gadaleta, E., Goodstein, D. M., Gundem, G., Haggarty, B., Haider, S., Hall, M., Harris, T., Haw, R., Hu, S., Hubbard, S., Hsu, J., Iyer, V., Jones, P., Katayama, T., Kinsella, R., Kong, L., Lawson, D., Liang, Y., Lopez-Bigas, N., Luo, J., Lush, M., Mason, J., Moreews, F., Ndegwa, N., Oakley, D., Perez-Llamas, C., Primig, M., Rivkin, E., Rosanoff, S., Shepherd, R., Simon, R., Skarnes, B., Smedley, D., Sperling, L., Spooner, W., Stevenson, P., Stone, K., Teague, J., Wang, J., Whitty, B., Wong, D. T., Wong-Erasmus, M., Yao, L., Youens-Clark, K., Yung, C., Zhang, J., Kasprzyk, A. (2011) BioMart Central Portal: an open database network for the biological community. Database : the journal of biological databases and curation, 2011. ISSN 17580463 (ISSN)

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. (December 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. (December 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. (September 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. (January 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. (November 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. (November 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. (November 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. (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)

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. (November 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. (November 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. (November 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. (October 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. (October 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. (August 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. (August 2009) The genetic architecture of maize flowering time. Science, 325 (5941). pp. 714-8. ISSN 1095-9203 (Electronic)

Wang, L., Markley, J. L. (May 2009) Empirical correlation between protein backbone (15)N and (13)C secondary chemical shifts and its application to nitrogen chemical shift re-referencing. J Biomol NMR, 44 (2). p. 95. ISSN 1573-5001 (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. (May 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. (May 2009) Microdissection of shoot meristem functional domains. PLoS Genet, 5 (5). e1000476.

Wang, L., Uilecan, I. V., Assadi, A. H., Kozmik, C. A., Spalding, E. P. (April 2009) HYPOTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape Demonstrated on Arabidopsis Seedlings Undergoing Photomorphogenesis. Plant Physiol., 149 (4). pp. 1632-1637.

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. (January 2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457 (7229). pp. 551-556.

Ding, D., Zhang, L., Wang, H., Liu, Z., Zhang, Z., Zheng, Y. (January 2009) Differential expression of miRNAs in response to salt stress in maize roots. Ann Bot, 103 (1). pp. 29-38.

Wicker, T., Narechania, A., Sabot, F., Stein, J. C., Vu, G. T. H., Graner, A., Ware, D. H., Stein, N. (October 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. (October 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. (February 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. (January 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. (January 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.

Ray, S. S., Tejero, J., Wang, Z. Q., Dutta, T., Bhattacharjee, A., Regulski, M. R., Tully, T., Ghosh, S., Stuehr, D. J. (October 2007) Oxygenase Domain of Drosophila melanogaster Nitric Oxide Synthase: Unique Kinetic Parameters Enable a More Efficient NO Release. Biochemistry, 46 (42). pp. 11857-11864. ISSN 0006-2960 (Print)

Ray, S. S., Sengupta, R., Tiso, M., Haque, M. M., Sahoo, R., Konas, D. W., Aulak, K., Regulski, M. R., Tully, T., Stuehr, D. J., Ghosh, S. (October 2007) Reductase Domain of Drosophila melanogaster Nitric-Oxide Synthase: Redox Transformations, Regulation, and Similarity to Mammalian Homologues. Biochemistry, 46 (42). pp. 11865-11873. ISSN 0006-2960 (Print)

Hufford, K. M., Canaran, P., Ware, D. H., McMullen, M. D., Gaut, B. S. (July 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

Hladish, T., Gopalan, V., Liang, C., Qiu, W., Yang, P., Stoltzfus, A. (June 2007) Bio :: NEXUS: a Perl API for the NEXUS format for comparative biological data. Bmc Bioinformatics, 8. p. 191. ISSN 1471-2105

Price, A. L., Patterson, N., Yu, F., Cox, D. R., Waliszewska, A., McDonald, G. J., Tandon, A., Schirmer, C., Neubauer, J., Bedoya, G., Duque, C., Villegas, A., Bortolini, M. C., Salzano, F. M., Gallo, C., Mazzotti, G., Tello-Ruiz, M., Riba, L., Aguilar-Salinas, C. A., Canizales-Quinteros, S., Menjivar, M., Klitz, W., Henderson, B., Haiman, C. A., Winkler, C., Tusie-Luna, T., Ruiz-Linares, A., Reich, D. (June 2007) A genomewide admixture map for Latino populations. American Journal of Human Genetics, 80 (6). pp. 1024-1036. ISSN 0002-9297

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. (February 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. (October 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. (April 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. (April 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. (January 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. (April 2003) Comparison of genes among cereals. Current Opinion in Plant Biology, 6 (2). pp. 121-7. ISSN 1369-5266

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. (December 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. (April 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. (April 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. (January 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. (October 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. (January 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, L., Van Buren, P., Lu, Z., Ware, D. (August 2018) SciApps: A bioinformatics workflow platform powered by XSEDE and cyverse. Association for Computing Machinery, p. 138224. ISBN 9781450364461 (ISBN)

Wang, D., Pan, E., Fang, G., Kumari, S., He, F., Ware, D., Maslov, S., Gerstein, M. (September 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. (November 2011) Talk from Doreen Ware at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

This list was generated on Sat Dec 15 21:28:24 2018 EST.
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving