Welcome to the Ware Lab
Welcome to the website for Doreen Ware's lab at Cold Spring Harbor Laboratories in Cold Spring Harbor, NY. Research in my group focuses on understanding genome organization and evolution in plants. We use multi-disciplinary approaches that combine computational analysis, modeling and prediction with experimental verification. The research supports the implementation and development of bioinformatic tools including public websites, software, analysis methods and controlled vocabularies of general value to the larger bioinformatics, genomics and agronomic communities. The plant genomes studied include agronomically important grass genomes, as well as the model plant arabidopsis. Grasses are responsible for a large part of the world's caloric intake, as either animal feed or human consumption, and more recently have become commodities for renewable energy production. Research in my laboratory contributes to a foundation of knowledge for future agricultural security.
Updated August 22, 2008
We have several new positions available with the group. Please visit our jobs page for more information.
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RiceCyc is a database developed as a new module within Gramene for the annotation of metabolic pathways in rice. It provides information on all the known and putative biochemical pathways with a useful mapping of the rice peptides from TIGR's rice genome assembly of the IRGSP sequence and the Swissprot(SP)-Trembl. An interactive overview diagram presents the users with an option to view the summary of all metabolic pathways in the RiceCyc database. The pathways can be viewed graphically with a multilevel 'zoom in' feature allowing the user to traverse from an overall of pathway reactions down to the molecular structures of compounds and co-factors. RiceCyc can be used to compare datasets with E.Coli (EcoCyc) and Arabidopsis (AraCyc) for reactions, pathways, compounds etc. It also allows users to upload their own gene expression data on the pathways to visualize an overview of the cellular level expression profile. RiceCyc is based on the Pathway Tools software developed at SRI International. The software compares the rice gene functions and EC numbers to the built in reference database MataCyc, to predict the rice metabolic network. In addition to the automated content provided by the Pathway tools software, Interpro annotations, orthlog genes sets using the Ensembl Compara software to Arabidopsis gene models, SP-Trembl rice peptides against the TIGR-rice peptides, Interpro to Gene Ontology (GO), MetaCyc to GO, and EC to GO mappings are available for the rice gene models. To enhance the quality of the computationally derived information, manual curation of pathways is an ongoing process at Gramene. |