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Doreen Ware
USDA ARS
Cold Spring Harbor Lab
1 Bungtown Rd.
Williams #5
Cold Spring Harbor, NY
11724

Publications

  • 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)

  • 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.)

  • Gramene: a growing plant comparative genomics resource
    Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard, Shuly Avraham, Edward S. Buckler, Terry Casstevens, Bonnie Hurwitz, Susan McCouch, Junjian Ni, Anuradha Pujar, Dean Ravenscroft, Liya Ren, William Spooner, Lincoln Stein, Isaak Tecle, Jim Thomason, Chih-wei Tung, Doreen Ware, Xuehong Wei, Immanuel Yap, Ken Youens-Clark (Nucleic Acid Research published on-line 2007, Nov 4, 1-7)

  • 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)

  • 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.)

  • 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.)

  • 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)

  • 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)

  • 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. PMID: 17142475)

  • 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. PMID: 16905665)

  • 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. PMID: 16895597)

  • Evolution of Arabidopsis microRNA families through duplication events.
    Maher C, Stein L, Ware D. (Genome Res. 2006 Mar 6; [Epub ahead of print])

  • 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.)

  • 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)

  • Panzea: a database and resource for molecular and functional diversity in the maize genome
    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., and Ware D. (Nucleic Acids Res. 2006 Jan 1;34(Database issue):D752-7.)

  • 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])

  • 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.

  • Identifying microRNAs in plant genomes.
    Maher, C., Timmermans, M., Stein, L., and Ware D. (2004) (Proc. IEEE, CBS: 718-723)

  • 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)

  • Rice chromosome 10 reveals a high degree of heterchromatin and collinearity with cereals.
    The Rice Chromosome 10 Sequencing Consortium. (2003) Science June 300 (5629) 1566-15

  • Comparison of genes among cereals.
    Ware, D. and L. Stein. (2003) (Curr Opin Plant Biol 6: 121-127)

  • 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. (2002) (Plant Physiology. Dec. 130 (4) 1606-13)

  • Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) (supplement).
    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):257-79. No abstract available. PMID: 12597280)

  • 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. PMID: 12597276)

  • 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. (2002), (Nucleic Acids Res., Jan 1;30(1):103-5.)

  • Gramene: development and integration of trait and gene ontologies for rice.
    Pankaj Jaiswal, Doreen Ware, Junjian Ni, Kuan Chang, Wei Zhao, Steven Schmidt, Xiaokang Pan, Kenneth Clark, Leonid Teytelman, Samuel Cartinhour, Lincoln Stein, Susan McCouch, (2002) (Comparative and Functional Genomics, Vol. 3 (2))

  • Gramene: a resource for comparative grass genomics, Ware et al. (Nucleic Acids Res. 2002 Jan 1;30(1):103-5.)

  • Gramene, a tool for grass genomics., Ware et al. (Plant Physiol. 2002 Dec;130(4):1606-13.)

  • Seed and molecular resources for Arabidopsis.
    Scholl, RL, May ST, Ware DH. (2000) (Plant Physiol. Dec;124(4):1477-80)

  • Handling and preservation of clones in a DNA stock center.
    Scholl, R, Ware, D. and Davis, K. (1999), In: Wilson, Z. ed. A Practical Approach: Arabidopsis. Oxford Univ. Press. pp 29-50. (Book chapter)