email ware@cshl.edu, phone (516) 367-6979

Understanding how genotypes relate to phenotypes continues to be a major challenge in biology. In plants, phenotypes of the greatest interest are associated with crop improvement, such as embryo (seed) size and shape, as well as responses 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 loss? 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. A second area of work is to understand gene regulation in plants, specifically looking at cis-regulatory elements and characterization microRNA genes and their targets. 
 
To study these questions we use multi-disciplinary approaches combining computational analysis, and modeling and prediction, with experimental verification. In addition to understanding basic biological questions my group also participates in the development of bioinformatic tools including public websites, open source software, analysis methods and controlled vocabularies of general value to the larger science community.