Cold Spring Harbor Laboratory  
Contact Us | Faculty & Staff Directory

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

Genomics; genome evolution; genetic diversity; gene regulation; plant biology; computational biology

email This email address is being protected from spambots. You need JavaScript enabled to view it. , phone (516) 367-6979

Understanding how genotypes relate to phenotypes continues to be a major challenge in biology. In plants, phenotypes of greatest interest tend to be complex traits impacting yield, food quality, and responses to the environment, such as drought stress.  Our work focuses on comparative and functional genomics in plants, with emphasis on understanding genome organization and regulation of gene expression.  Prior to the genomics age, genetic mapping in cereals demonstrated that ­– despite large differences in genome size, ploidy level, and chromosome numbers – these grass species still have large blocks of conserved genes that in some cases can span whole chromosomes. This tractability in identifying orthologous regions provides an excellent model system to study how differences in genome organization arise, such as gene gain and loss, and fates of duplicated genes.  Our group also studies natural diversity, with future goals of identifying unique and rare alleles for germplasm enhancement. A third area of work is to understand gene regulation in plants, specifically looking at regulatory networks involving transcription factors and microRNA genes.  To study these questions we use multi-disciplinary approaches combining data integration, computational analysis, and experimental verification. In addition to conducting plant genomics research our group develops genomics resources and discovery tools for the broader research and educational communities. Products of these efforts include, and contributions to two large-scale multi-institutional cyberinfrastructure collaboratives, iPlant and Kbase.


Please visit Doreen's Lab home page.


Selected Publications

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, W.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. and Ware, D. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nat. Gen. 44: 803–807.

Liu, Z., Kumari, S., Zhang, L., Zheng, Y., and Ware, D. Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays. PLoS One. 2012. 7: 6.

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. Gramene database in 2010: updates and extensions. Nucleic Acids Res. 39: D1085–1094.

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

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-Rahman, Ware, D., Westhoff, P., Mayer ,K.F., Messing, J., and Rokhsar, D.S. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature. 457: 551­–556. J., Wei, S., and Ware, D. 2011. Gramenedatabase in 2010: updates and extensions. Nucleic Acids Res. 39: D1085–1094.