3110
Gramene Project

The Gramene database (http://www.gramene.org) is an integrated resource for comparative genome and functional analysis in plants. The database provides agricultural researchers and plant breeders with valuable biological information on genomes and plant pathways of numerous crops and model species, thus enabling powerful comparisons across species. During this workshop, we will demonstrate how to navigate the website and review the available resources at Gramene, including the newly curated pathways and orthologous pathway projections in the Plant Reactome, and the capabilities of the independent Expression Atlas resource for gene expression. In addition, we will introduce a new search tool and web interface that helps users search, interpret and explore our data. Finally, we will showcase the use of long-read sequencing technology to improve reference genome resources. This workshop is open to the community of plant researchers and breeders; beginners, as well as frequent users of the Gramene database alike are welcome and encouraged to join. Attendees may bring their own data to work with during the workshop. The current data release of Gramene contains 39 reference genomes including rice, maize, wheat, barley, soybean, Arabidopsis, Brassicas, poplar, medicago, tomato, potato, banana, cocoa, peach, grapevine, Amborella, spikemoss and algae. In addition to curated rice pathways, the Plant Reactome incorporates pathway projections to 58 plant species, including 2 wild peanut ancestors and the common bean.
Date: Tuesday, January 12, 2016
Time: 1:30 PM-3:40 PM
Room: California
Organizers:
Doreen Ware and Marcela Karey Tello-Ruiz
1:30 PM
Introduction
Marcela Karey Tello-Ruiz, Cold Spring Harbor Laboratory

1:50 PM
Exploring and Comparing Plant Genomes Using the Gramene/Ensembl Plants Browser
Joshua Stein, Cold Spring Harbor Laboratory; Sharon Wei, Cold Spring Harbor Laboratory; Marcela Karey Tello-Ruiz, Cold Spring Harbor Laboratory; Andrew Olson, Cold Spring Harbor Laboratory; Sunita Kumari, Cold Spring Harbor Laboratory; Joseph Mulvaney, Cold Spring Harbor Laboratory; Jim Thomason, Cold Spring Harbor Laboratory; Dan Bolser, EMBL - The European Bioinformatics Institute; Arnaud Kerhornou, EMBL - The European Bioinformatics Institute; Paul J. Kersey, EMBL - The European Bioinformatics Institute; Doreen Ware, Cold Spring Harbor Laboratory/USDA-ARS

2:10 PM
Plant Reactome: A Resource for Comparative Plant Pathway Analysis
Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University

2:30 PM
Exploring Gramene’s Comparative Genomics Datasets Using New Search Tools
Joseph Mulvaney, Cold Spring Harbor Laboratory; Andrew Olson, Cold Spring Harbor Laboratory; Jim Thomason, Cold Spring Harbor Laboratory; Doreen Ware, Cold Spring Harbor Laboratory/USDA-ARS

3:10 PM
Developments for Plant Data in Expression Atlas
Robert Petryszak, EMBL - The European Bioinformatics Institute

3:30 PM
Improving Reference Genome Resources Using Long-Read Sequencing Technology
Bo Wang, Cold Spring Harbor Laboratory; Elizabeth Tseng, Pacific Biosciences; Michael Regulski, Cold Spring Harbor Laboratory; Tyson A. Clark, Pacific Biosciences; Ting Hon, Pacific Biosciences; Yinping Jiao, USDA-ARS/Cold Spring Harbor Laboratory; Jerry Lu, Cold Spring Harbor Laboratory; Andrew Olson, Cold Spring Harbor Laboratory; Joshua Stein, Cold Spring Harbor Laboratory; Doreen Ware, Cold Spring Harbor Laboratory/USDA-ARS

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