Adjunct Associate Professor
Ph.D., Ohio State University, 2000

Computational biology; comparative genomics; genome evolution; diversity; gene regulation; plant biology

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Understanding how genotypes relate to phenotypes continues to be a major challenge in biology. In plants, phenotypes of greatest interest are associated with crop improvement, such as flowering-time, embryo (seed) size, and response to the environment, such as drought tolerance. Our work focuses on using comparative and functional genomics in plants, with an emphasis on understanding genome organization and gene regulation and expression.

Previous genetic work in cereals using genetic markers based on genes demonstrated that — despite large changes in genome size, polyploidy events, and differences in chromosome numbers — these species still have large blocks of conserved genes that in many cases span whole chromosomes. One aspect of our research studies this conserved organization at the sequence level to better understand questions such as: How are genes conserved and lost? What are the fates of duplicated genes? In addition to understanding sequence conservation, we are also interested in studying natural diversity, which holds the hope of identifying unique and rare alleles for germplasm enhancement. For this work we are actively making use of next-generation sequencing technologies. A second area of work is to understand gene regulation in plants, specifically looking at regulatory networks enriched for microRNA genes.

To study these questions we use multi-disciplinary approaches combining data integration, computational analysis, and experimental verification. In addition to understanding basic biological questions my group also participates in the development of bioinformatic resources including public websites, open-source software, analysis methods and controlled vocabularies of general value to the science community.

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., Walhout, .J. and Benfey, P.N. 2011. A stele-enriched gene regulatory network in the Arabidopsis root. Mol. Syst. Biol. 7:459.

Myles, S., Chia, J.M., Hurwitz, B., Simon, C., Zhong, G.Y., Buckler, E., and Ware, D. 2010. Rapid genomic characterization of the genus vitis. PLoS One 5: e8219.

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., and Ware, D. 2011. Gramenedatabase in 2010: updates and extensions. Nucleic Acids Res. 39: D1085–1094.

Schnable, P.S., Ware, D., et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112–1115.

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., and Buckler, E.S. 2009. A first-generation haplotype map of maize. Science 326: 1115–1117.