Projects

IDENTIFICATION OF FUNCTIONAL SEQUENCE IN PLANT GENOMES THROUGH BIOINFORMATIC, GENOMIC, AND GENETIC APPROACHES Appropriated (D)   Accession Number: 413089

BEST OF BREED II: COMPUTATIONAL RESOURCES FOR PLANT GENOMES Specific Cooperative Agreement (S)   Accession Number: 414476

USE OF GENETIC AND GENOMICS TOOLS TO ENHANCE OUR UNDERSTANDING OF DEVELOPMENTAL PROCESSES LIMITING YIELD AND/OR QUALITY IN MAIZE Specific Cooperative Agreement (S)   Accession Number: 418141

IMPROVING CEREAL AND GRAPE GENOME RESOURCES FOR CROP IMPROVEMENT Specific Cooperative Agreement (S)   Accession Number: 408934

USE OF GENETIC AND GENOMIC TOOLS IN SORGHUM TO ENHANCE OUR UNDERSTANDING OF DEVELOPMENTAL PROCESSES LIMITING YIELD AND/OR QUALITY IN GRASSES Specific Cooperative Agreement (S)   Accession Number: 418047

IMPROVING SORGHUM GENOME RESOURCES FOR CEREAL CROP IMPROVEMENT Specific Cooperative Agreement (S)   Accession Number: 408935

IMPROVING MAIZE GENOME RESOURCES FOR CEREAL CROP IMPROVEMENT Specific Cooperative Agreement (S)   Accession Number: 408936

CHARACTERIZING PLANT GENOMES FOR AGRICULTURE IMPROVEMENT Specific Cooperative Agreement (S)   Accession Number: 418046

Publications

Genetic Properties of the Maize Nested Association Mapping Population - (Peer Reviewed Journal)

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

The Genetic Architecture of Maize Flowering Time - (Peer Reviewed Journal)

Buckler Iv, E.S., Holland, J.B., Mcmullen, M.D., Kresovich, S., Acharya, C., Bradbury, P., Brown, P., Browne, C.J., Eller, M.S., Ersoz, E., Flint Garcia, S.A., Garcia, A., Glaubitz, J.C., Goodman, M., Haries, C., Guill, K.E., Kroon, D., Larsson, S., Lepak, N.K., Li, H., Mitchell, S.E., Pressoir, G., Peiffer, J., Oropeza Rosas, M., Rocheford, T., Romay, C., Romero, S., Salvo, S.A., Sanchez Villeda, H., Sun, Q., Tian, F., Upadyayula, N., Ware, D., Yates, H., Yu, J., Zhang, Z. 2009. The Genetic Architecture of Maize Flowering Time. Science. 325(5941):714-718.

Large-scale enrichment and discovery of gene-associated SNPs - (Peer Reviewed Journal)

Buckler Iv, E.S., Gore, M., Wright, M., Ersoz, E., Bouffard, P., Jarvie, T., Hurwitz, B., Narechania, A., Harkins, T., Grills, G., Ware, D. 2009. Large-scale enrichment and discovery of gene-associated SNPs. Nature Methods. 2 (2):121-133.

Panzea: An Update on New Content and Features - (Peer Reviewed Journal)

Canaran, P., Buckler Iv, E.S., Glaubitz, J., Stein, L., Sun, Q., Zhao, W., Ware, D. 2009. Panzea: An Update on New Content and Features. Nucleic Acids Research. 36:D1041-D1043.

Genome-wide analysis for discovery of new rice miRNA reveals natural antisense miRNA (nat-miRNAs) - (Peer Reviewed Journal)

Lu, C., Jeong, D., Kulkarni, K., Pillay, M., Nobuta, K., German, R., Thatcher, D., Maher, C., Zhang, L., Ware, D., Liu, B., Cao, X., Meyers, B., Green, P. 2008. Genome-wide analysis for discovery of new rice miRNA reveals natural antisense miRNA (nat-miRNAs). Proceedings of the National Academy of Sciences. 105(12):4951-4956.

The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza - (Peer Reviewed Journal)

Kim, H., Hurwitz, B., Yu, Y., Collura, K., Gill, N., Miguel, P.S., Mullikin, J., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goicoechea, J.L., Stein, L., Ware, D., Jackson, S., Soderlund, C., Wing, R. 2008. The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza. Genome Research. 9:R45.1-R45.15.

Gramene: a growing plant comparative genomics resource - (Peer Reviewed Journal)

Jaiswal, P., Avraham, S., Buckler Iv, E.S., Casstevens, T., Hebbard, C., Liang, C., Ni, J., Ravenscroft, D., Ren, L., Stein, L., Spooner, W., Tecle, I., Thomason, J., Wei Xuehong, Ware, D., Youens-Clark, K., Yap, I., Mccouch, S., Tung, C. 2008. Gramene: a growing plant comparative genomics resource. Nucleic Acids Research. 36:D947-D953.

The Plant Ontology Database: A community resource for plant structure and developmental stages controlled vocabulary and annotations - (Peer Reviewed Journal)

Avraham, S., Tung, C., Jaiswal, P., Ilic, K., Kellogg, E., Mccouch, S., Pujar, A., Reiser, L., Rhee, S., Sachs, M.M., Schaeffer, M.L., Stein, L., Stevens, P., Vincent, L., Zapata, F., Ware, D. 2008. The Plant Ontology Database: A community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research. 36:D449-D454.

The Plant Ontology Database: A Community Resource for Plant Structure and Developmental Stages Controlled Vocabulary and Annotations - (Peer Reviewed Journal)

Avraham, S., Tung, C., Jaiswal, P., Ilic, K., Kellogg, E.A., Mccouch, S.R., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M., Schaeffer, M.L., Stein, L.D., Stevens, P.F., Vincent, L.P., Zapata, F., Ware, D. 2007. The Plant Ontology Database: A Community Resource for Plant Structure and Developmental Stages Controlled Vocabulary and Annotations. Nucleic Acids Research 36: Database issue D449-D454

Databases and data mining - (Book/Chapter)

Lawrence, C.J., Ware, D. 2009. Databases and data mining. In: Bennetzen, J.L., Hake, S., editors. Handbook of Maize. Vol. 2, Genetics and Genomics. 1st edition. New York, NY: Springer Science and Business Media, LLC. p. 659-672.

Plant Structure Ontology, Unified Vocabulary of Anatomy and Morphology of a Flowering Plant - (Peer Reviewed Journal)

Ilic, K., Kellogg, E., Jaiswal, P., Zapata, F., Stevens, P., Vincent, L., Avraham, S., Reiser, L., Pujar, A., Sachs, M.M., Whitman, N., Mccouch, S., Schaeffer, M.L., Ware, D., Stein, L., Rhee, S. 2007. Plant Structure Ontology, Unified Vocabulary of Anatomy and Morphology of a Flowering Plant. Plant Physiology. 143:587-599.

Gramene: a bird's eye view of cereal genomes - (Peer Reviewed Journal)

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, T., Buckler Iv, E.S., Stein, L., Mccouch, S. 2007. Gramene: a bird's eye view of cereal genomes. Nucleic Acids Research. 34:D717-D723. Available: http://nar.oxfordjournals.org/

Tissue-specific expression of maize domestication and crop improvement loci - (Peer Reviewed Journal)

Hufford, K., Canaran, P., Ware, D., Mcmullen, M.D., Gaut, B. 2007. Tissue-specific expression of maize domestication and crop improvement loci. Plant Physiology. 144:1642-1653.

Evolution of Arabidopsis microRNA families through duplication events - (Peer Reviewed Journal)

Maher, C., Stein, L., Ware, D. 2007. Evolution of Arabidopsis microRNA families through duplication events. Genome Research. 16:510-519.

Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum - (Peer Reviewed Journal)

Hass-Jacobus, B., Futrell-Griggs, M., Abernathy, B., Westerman, R., Goicoechea, J., Stein, J., Ware, D. 2007. Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum. Biomed Central (BMC) Genomics. 7:199.

Panzea: A Database and Resource for Molecular and Functional Diversity in the Maize Genome - (Peer Reviewed Journal)

Zhao, W., Canaran, P., Jurkuta, R., Fulton, T., Glaubitz, J., Buckler Iv, E.S., Doebley, J., Gaut, B., Goodman, M., Holland, J.B., Kresovich, S., Mcmullen, M.D., Stein, L., Ware, D. 2007. Panzea: A Database and Resource for Molecular and Functional Diversity in the Maize Genome. Nucleic Acids Research. 34:D752-D757.

Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support - (Peer Reviewed Journal)

Canaran, P., Stein, L., Ware, D. 2007. Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics. 22(7):885-886.

Plant Structure Ontology. Unified Vocabulary of Anatomy and Morphology of a Flowering Plant - (Peer Reviewed Journal)

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., Stein, L.D., Rhee, S.Y. 2006. Plant Structure Ontology. Unified Vocabulary of Anatomy and Morphology of a Flowering Plant. Plant Physiology 143:587-599

Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology - (Peer Reviewed Journal)

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

Plant Ontology (Po): a Controlled Vocabulary of Plant Structures and Growth Stages - (Peer Reviewed Journal)

Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E.A., Mccouch, S., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M., Schaeffer, M.L., Stein, L., Stevens, P., Vincent, L., Ware, D., Zapata, F. 2005. Plant ontology (po): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics. 6:388-397.

Molecular and Functional Diversity in the Maize Genome - (Abstract)

Briggs, W., Buckler Iv, E.S., Canaran, P., Doebley, J., Fulton, T., Gaut, B., Goodman, M., Holland, J.B., Kresovich, S., Mcmullen, M.D., Stein, L., Ware, D., Wright, S., Zhao, W. 2005. Molecular and functional diversity in the maize genome [abstract]. Maize Genetics Conference. Paper No. 177. p. 126.