Publications
| 2010 |
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Rapid Genomic Characterization of the Genus Vitis Sean Myles, Jer-Ming Chia, Bonnie Hurwitz, Charles Simon, Gan Yuan Zhong, Edward Buckler and Doreen Ware (PLoS One. 2010 Jan 13;5(1):e8219) [PubMed][ Download Datasets ] |
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Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza Hurwitz, B.L., Kudrna, D., Yu, Y., Sebastian, A., Zuccolo, A., Jackson, S.A., Ware, D., Wing, R.A., and Stein, L. (The Plant Journal (In press) DOI: 10.1111/j.1365-313X.2010.04293.x) [PubMed] |
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Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration. Nelson RT, Avraham S, Shoemaker RC, May GD, Ware D, Gessler DD (BioData Min. 2010 Jun 4;3(1):3) [PubMed] |
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Phylogenomic analysis from deep BAC-end sequence libraries of rice Cranston, K.A., Hurwitz, B.L., Sanderson, M.J., Ware, D., Wing, R.A., and Stein, L. (Systematic Botany. In press.) |
| 2009 |
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Evidence-based gene predictions in plant genomes Liang, C, Mao, L., Ware, D. and Stein, L. (Genome Res. 2009 Oct;19(10):1912-23) [PubMed] |
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The Sorghum bicolor genome and the diversification of grasses Paterson AH, Bowers JE, 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 AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (Nature. 2009 Jan 29;457(7229):551-6) [PubMed] |
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Microdissection of Shoot Meristem Functional Domains Brooks, L., Strable, J., Zhang, X., Ohtsu, K., Zhou, R., Sarkar, A., Hargreaves, S., Elshire, R., Eudy, D., Pawlowska, T., Ware, D., Janick-Buckner, D., Buckner, B., Timmermans, M., Schnable, P., Nettleton, D., Scanlon, M. (PLoS Genetics 5(5): e1000476. doi:10.1371/journal.pgen.1000476) |
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Gramene QTL database: development, content and applications Ni, J., Pujar, A., Youens-Clark, K., Yap, I., Jaiswal, J., Tecle, I., Tung, C.W., Ren, L., Spooner, W., Wei, X., Avraham, S., Ware, D., Stein L., and McCouch, S. (Database: The Journal of Biological Databases and Curation Vol. 2009:bap005; doi:10.1093/database/bap005) |
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Large-Scale Discovery of Gene-Enriched SNPs Gore, M., Wright, M., Ersoz, E., Bouffard, P., Szekeres, E., Jarvie, T., Hurwitz, B., Narechania, A., Harkins, T., Grills, G., Ware, D., Buckler, E. (The Plant Genome doi: 10.3835/plantgenome2009.01.0002, vol. 2, no. 2 121-133) |
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CMap 1.01: A comparative mapping application for the Internet Youens-Clark, K., Faga, B., Yap, I., Stein, L., Ware, D. (Bioinformatics, doi:10.1093/bioinformatics/btp458) [PubMed] |
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The genetic architecture of maize flowering time Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Sanchez Villeda H, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD (Science. 2009 Aug 7;325(5941):714-8) [PubMed] |
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Genetic properties of the maize nested association mapping population McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Oropeza Rosas M, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz JC, Goodman M, Ware D, Holland JB, Buckler ES (Science. 2009 Aug 7;325(5941):688-9) [PubMed] |
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The B73 Maize Genome: Complexity, Diversity, and Dynamics Patrick S. Schnable, Doreen Ware, Robert S. Fulton, Joshua C. Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A. Graves, Patrick Minx, Amy Denise Reily, Laura Courtney, Scott S. Kruchowski, Chad Tomlinson, Cindy Strong, Kim Delehaunty, Catrina Fronick, Bill Courtney, Susan M. Rock, Eddie Belter, Feiyu Du, Kyung Kim, Rachel M. Abbott, Marc Cotton, Andy Levy, Pamela Marchetto, Kerri Ochoa, Stephanie M. Jackson, Barbara Gillam, Weizu Chen, Le Yan, Jamey Higginbotham, Marco Cardenas, Jason Waligorski, Elizabeth Applebaum, Lindsey Phelps, Jason Falcone, Krishna Kanchi, Thynn Thane, Adam Scimone, Nay Thane, Jessica Henke, Tom Wang, Jessica Ruppert, Neha Shah, Kelsi Rotter, Jennifer Hodges, Elizabeth Ingenthron, Matt Cordes, Sara Kohlberg, Jennifer Sgro, Brandon Delgado, Kelly Mead, Asif Chinwalla, Shawn Leonard, Kevin Crouse, Kristi Collura, Dave Kudrna, Jennifer Currie, Ruifeng He, Angelina Angelova, Shanmugam Rajasekar, Teri Mueller, Rene Lomeli, Gabriel Scara, Ara Ko, Krista Delaney, Marina Wissotski, Georgina Lopez, David Campos, Michele Braidotti, Elizabeth Ashley, Wolfgang Golser, HyeRan Kim, Seunghee Lee, Jinke Lin, Zeljko Dujmic, Woojin Kim, Jayson Talag, Andrea Zuccolo, Chuanzhu Fan, Aswathy Sebastian, Melissa Kramer, Lori Spiegel, Lidia Nascimento, Theresa Zutavern, Beth Miller, Claude Ambroise, Stephanie Muller, Will Spooner, Apurva Narechania, Liya Ren, Sharon Wei, Sunita Kumari, Ben Faga, Michael J. Levy, Linda McMahan, Peter Van Buren, Matthew W. Vaughn, Kai Ying, Cheng-Ting Yeh, Scott J. Emrich, Yi Jia, Ananth Kalyanaraman, An-Ping Hsia, W. Brad Barbazuk, Regina S. Baucom, Thomas P. Brutnell, Nicholas C. Carpita, Cristian Chaparro, Jer-Ming Chia, Jean-Marc Deragon, James C. Estill, Yan Fu, Jeffrey A. Jeddeloh, Yujun Han, Hyeran Lee, Pinghua Li, Damon R. Lisch, Sanzhen Liu, Zhijie Liu, Dawn Holligan Nagel, Maureen C. McCann, Phillip SanMiguel, Alan M. Myers, Dan Nettleton, John Nguyen, Bryan W. Penning, Lalit Ponnala, Kevin L. Schneider, David C. Schwartz, Anupma Sharma, Carol Soderlund, Nathan M. Springer, Qi Sun, Hao Wang, Michael Waterman, Richard Westerman, Thomas K. Wolfgruber, Lixing Yang, Yeisoo Yu, Lifang Zhang, Shiguo Zhou, Qihui Zhu, Jeffrey L. Bennetzen, R. Kelly Dawe, Jiming Jiang, Ning Jiang, Gernot G. Presting, Susan R. Wessler, Srinivas Aluru, Robert A. Martienssen, Sandra W. Clifton, W. Richard McCombie, Rod A. Wing, and Richard K. Wilson (Science 20 November 2009 326: 1112-1115 [DOI: 10.1126/science.1178534]) |
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A First-Generation Haplotype Map of Maize Michael A. Gore, Jer-Ming Chia, Robert J. Elshire, Qi Sun, Elhan S. Ersoz, Bonnie L. Hurwitz, Jason A. Peiffer, Michael D. McMullen, George S. Grills, Jeffrey Ross-Ibarra, Doreen H. Ware, and Edward S. Buckler (Science 20 November 2009 326: 1115-1117 [DOI: 10.1126/science.1177837]) |
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Detailed analysis of a contiguous 22-Mb region of the maize genome Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, Nagel DH, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves TA, Rock SM, Adams S, Fulton LA, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon JM, Miguel PS, Jiang N, Wessler SR, Green PJ, Yu Y, Schwartz DC, Meyers BC, Bennetzen JL, Martienssen RA, McCombie WR, Aluru S, Clifton SW, Schnable PS, Ware D, Wilson RK, Wing RA (PLoS Genet. 2009 Nov;5(11):e1000728) [PubMed] |
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A genome-wide characterization of microRNA genes in maize Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D (PLoS Genet. 2009 Nov;5(11):e1000716) [PubMed] |
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The physical and genetic framework of the maize b73 genome Wei F, Zhang J, Zhou S, He R, Schaeffer M, Collura K, Kudrna D, Faga BP, Wissotski M, Golser W, Rock SM, Graves TA, Fulton RS, Coe E, Schnable PS, Schwartz DC, Ware D, Clifton SW, Wilson RK, Wing RA (PLoS Genet. 2009 Nov;5(11):e1000715) [PubMed] |
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A single molecule scaffold for the maize genome Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S, Forrest DK, Wise R, Ware D, Wing RA, Waterman MS, Livny M, Schwartz DC (PLoS Genet. 2009 Nov;5(11):e1000711) [PubMed] |
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Species trees from highly incongruent gene trees in rice Cranston, K., Hurwitz, B., Ware, D., Stein, L. and Wing, R. (Systematic Biology 2009 58(5):489-500; doi:10.1093/sysbio/syp054) |
| 2008 |
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Handbook of Maize: History and Practice of Genetics and Genomics Lawrence, C.J. and Ware, D. (In Bennetzen, J.L. and Jake, S.C. (eds.), Springer Science + Business Media LLC, pp. 659-672) |
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Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats Wicker, T., Narechania, A., Sabot, F., Stein, J., Vu, GT., Graner, A., Ware, D. and Stein, N. (BMC Genomics 9:518) [PubMed] |
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A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes Kurtz, S., A. Narechania, J.C. Stein, and D. Ware (BMC Genomics 9: 517) [PubMed] |
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The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Y Rhee, Martin M Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata and Doreen Ware (Nucleic Acids Research 2008 36(Database issue):D449-D454) [PubMed] |
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Construction, alignment and analysis of 12 framework physical maps that represent the 10 genome types of the genus Oryza 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. Goigochia, L. Stein, D. Ware, S.A. Jackson, C. Soderlund, and R.A. Wing (Genome Biol 9: R45. 2008) [PubMed] |
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Genome-wide analysis for discovery of new rice miRNAs reveals natural antisense miRNAs (nat-miRNAs) Lu, C., D.H. Jeong, K. Kulkarni, M. Pillay, K. Nobuta, R. German, S.R. Thatcher, D. Maher, L. Zhang, D. Ware, B. Liu, X. Cao, B.C. Meyers, and P.J. Green (PNAS In press February 2008) [PubMed] |
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Panzea: An Update on New Content and Features Canaran, P., Buckler, E., Glaubitz, J., Stein, L., Sun, Q., Zhao, W., Ware, D. (Nucleic Acid Research (Database issue D1041-1043)) |
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Gramene: a growing plant comparative genomics resource Liang, C., Jaiswal, P. Hebbard, C., Avraham, S., Buckler, E.S., Casstevens, T., Hurwitz, B., McCouch, W., Ni, J., Pujar, A., Ravenscroft, D. Ren, L., Spooner, W., Stein, L., Tecle, I., Thomason, J., Tung, C.W., Ware, D., Wei, X., Yap, I., Youens-Clark, K. (Nucleic Acid Research (Database issue D947-953)) [PubMed] |
| 2007 |
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The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, Rhee SY (Plant Physiol. 2007 Feb;143(2):587-99. Epub 2006 Dec 1.) [PubMed] |
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Patterns of Selection and Tissue-Specific Expression among Maize Domestication and Crop Improvement Loci Kristina M. Hufford, Payan Canaran, Doreen H. Ware, Michael D. McMullen, and Brandon S. Gaut (Plant Physiol. 2007;144 1642-1653 Open Access) [PubMed] |
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Panzea: An Update on New Content and Features Payan Canaran, Edward Buckler Jeffrey Glaubitz, Lincoln Stein, Qi Sun, Wei Zhao, Doreen Ware (Nucleic Acid Research Advance Access published November 19, 2007, 1-3) [PubMed] |
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The Oryza map alignment project (OMAP): A new resource for comparative genomics studies within Oryza Wing, R., Kim, H., Goicoechea, J.L., Yu, Y., Kudrna, D., Zuccolo, A., Ammiraju, J.S., Luo, M., Nelson, W., Soderlund, C., San Miguel, P., Gill, N., Walling, J.G., Jackson, S., Hurwitz, B., Ware, D., Stein, L., Brar, D., and Mackill, D. (Rice Genetics V: Proceedings of the Fifth International Rice Genetics Symposium, D.a.H. Brar, B., Editor. 2007, IRRI: Manila) |
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The Oryza Map Alignment Project (OMAP): A New Resource for Comparative Genome Studies within the Oryza Wing, R., Kim, H., Goicoechea, J., Yu, Y., Kudrna, D., Zuccolo, A., Ammiraju, J., Luo, M., Nelson, W., Ma, J., SanMiguel, P., Hurwitz, B., Ware, D., Brar, D., Mackill, D., Soderlund, C., Stein, L., and Jackson, S. (Rice Functional Genomics: Challenges, Progress and Prospects, N.M. Upadhyaya, Editor. 2007, Springer) |
| 2006 |
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Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support Canaran P, Stein L, Ware D. (Bioinformatics. 2006 Feb 10; [Epub ahead of print]) [PubMed] |
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Panzea: a database and resource for molecular and functional diversity in the maize genome 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 (Nucleic Acids Res 34: D752-757) [PubMed] |
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Plant Ontology (PO): A Controlled Vocabulary of Plant Structures and Growth Stages Jaiswal, P., Avraham, A., Ilic, K., Kellogg, E., McCouch, S., Pujar, A., Reiser, L., Rhee, S., Sachs, M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L., Ware, D., and Zapata, F. (Comparative and Functional Genomics 2006 Volume 6 Issue 7-8, pg 388-397) [PubMed] |
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Gramene: a bird's eye view of cereal genomes Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S. (Nucleic Acids Res. 2006 Jan 1;34(Database issue):D717-23) [PubMed] |
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Evolution of Arabidopsis microRNA families through duplication events Maher C, Stein L, Ware D. (Genome Res. 2006 Apr;16(4):510-9. Epub 2006 Mar 6) [PubMed] |
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Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum Hass-Jacobus BL, Futrell-Griggs M, Abernathy B, Westerman R, Goicoechea JL, Stein J, Klein P, Hurwitz B, Zhou B, Rakhshan F, Sanyal A, Gill N, Lin JY, Walling JG, Luo MZ, Ammiraju JS, Kudrna D, Kim HR, Ware D, Wing RA, San Miguel P, Jackson SA (BMC Genomics. 2006 Aug 8;7:199.) [PubMed] |
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Whole-plant growth stage ontology for angiosperms and its application in plant biology Pujar A, Jaiswal P, Kellogg EA, Ilic K, Vincent L, Avraham S, Stevens P, Zapata F, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Ware D, McCouch S. (Plant Physiol. 2006 Oct;142(2):414-28. Epub 2006 Aug 11.) [PubMed] |
| 2005 |
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Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages Jaiswal, P., S. Avraham, K. Ilic, E.A. Kellogg, S. McCouch, A. Pujar, L. Reiser, S.Y. Rhee, M.M. Sachs, M. Schaeffer, L. Stein, P. Stevens, L. Vincent, D. Ware, and F. Zapata (Comparative and Functional Genomics 6: 388-397) [PubMed] |
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Toward Sequencing the Sorghum Genome Sorghum Genomics Planning Workshop Participants. (2005) A U.S. National Science Foundation-Sponsored Workshop Report (Plant Physiol. Aug; 138: 1898-1902) [PubMed] |
| 2004 |
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Identifying microRNAs in plant genomes Maher, C., Timmermans, M., Stein, L., and Ware D. (Proc. IEEE, CBS: 718-723) |
| 2003 |
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Comparison of genes among cereals Ware, D. and L. Stein (Curr Opin Plant Biol 6: 121-127) [PubMed] |
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Rice chromosome 10 reveals a high degree of heterchromatin and collinearity with cereals The Rice Chromosome 10 Sequencing Consortium (Science June 300 (5629) 1566-15) |
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Maintaining Collections of Mutants for Plant Functional Genomics Scholl, R., Sachs, M. M. and Ware, D. (Humana Press, Methods Mol Biol., 2003; 236:311-26) [PubMed] |
| 2002 |
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Gramene: a resource for comparative grass genomics Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L. (Nucleic Acids Res., Jan 1;30(1):103-5.) [PubMed] |
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Gramene: development and integration of trait and gene ontologies for rice Jaiswal, P., D. Ware, J.J. Ni, K. Chang, W. Zhao, S. Schmidt, X.K. Pan, K. Clark, L. Teytelman, S. Cartinhour, L. Stein, and S. McCouch (Comparative and Functional Genomics 3: 132-136) [PubMed] |
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Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L. (DNA Res. 2002 Dec 31;9(6):199-207) [PubMed] |
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Gramene a tool for Grass Genomics Ware D, Jaiswal P, Ni J, Yap I, Pan X, Clark K, Teytelman L, Schmidt S, Zhao W, Chang K, Cartinhour S, Stein L, McCouch S (Plant Physiology. Dec. 130 (4) 1606-13) [PubMed] |
| 2000 |
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Seed and molecular resources for Arabidopsis Scholl, RL, May ST, Ware DH. (Plant Physiol. Dec;124(4):1477-80) [PubMed] |
| 1999 |
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Handling and preservation of clones in a DNA stock center Scholl, R, Ware, D. and Davis, K. (Wilson, Z. ed. A Practical Approach: Arabidopsis. Oxford Univ. Press. pp 29-50. (Book chapter)) |
| 1998 |
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Arabidopsis Rho-related GTPases: Differential gene expression in pollen and polar localization in fission yeast Li, H., G. Wu, D. Ware, K.R. Davis, and Z.B. Yang (Plant Physiology 118: 407-417) [PubMed] |
| 1995 |
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The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana Wanner, L.A., G. Li, D. Ware, I.E. Somssich, and K.R. Davis (Plant Mol Biol 27: 327-38) [PubMed] |
| 1992 |
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Primary structure, chromosomal localization, and functional expression of a voltage-gated sodium channel from human brain. Ahmed, C.M., D.H. Ware, S.C. Lee, C.D. Patten, A.V. Ferrer-Montiel, A.F. Schinder, J.D. McPherson, C.B. Wagner-McPherson, J.J. Wasmuth, G.A. Evans, and et al. (Proc Natl Acad Sci U S A 89: 8220-8224) [PubMed] |
| 1989 |
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Assessment of the number of free cysteines and isolation and identification of cystine-containing peptides from acetylcholine receptor Kellaris, K.V., D.K. Ware, S. Smith, and J. Kyte (Biochemistry 28: 3469-82) [PubMed] |