Index Catalog // ScholarsArchive@OSU

Gramene database in 2010: updates and extensions

Creator:: Youens-Clark, Ken, Buckler, Ed, Casstevens, Terry, Chen, Charles, DeClerck, Genevieve, Derwent, Paul, Dharmawardhana, Palitha, Jaiswal, Pankaj, Kersey, Paul, Karthikeyan, A. S., Lu, Jerry, McCouch, Susan R., Ren, Liya, Spooner, William, Stein, Joshua C., Thomason, Jim, Wei, Sharon, and Ware, Doreen
Abstract:: Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with...
Resource Type:: Article
Full Text:: . Bioinformatics, 23, 2633–2635. 27. Youens-Clark,K., Faga,B., Yap,I.V., Stein,L. and Ware,D. (2009) CMap 1.01: a

Gramene 2013: comparative plant genomics resources

Creator:: Monaco, Marcela K., Stein, Joshua, Naithani, Sushma, Wei, Sharon, Dharmawardhana, Palitha, Kumari, Sunita, Amarasinghe, Vindhya, Youens-Clark, Ken, Thomason, James, Preece, Justin, Pasternak, Shiran, Olson, Andrew, Jiao, Yinping, Lu, Zhenyuan, Bolser, Dan, Kerhornou, Arnaud, Staines, Dan, Walts, Brandon, Wu, Guanming, D'Eustachio, Peter, Haw, Robin, Croft, David, Kersey, Paul J., Stein, Lincoln, Jaiswal, Pankaj, and Ware, Doreen
Abstract:: Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies...
Resource Type:: Article

Gramene: a resource for comparative grass genomics

Creator:: Ware, Doreen, Jaiswal, Pankaj, Ni, Junjian, Pan, Xiaokang, Chang, Kuan, Clark, Kenneth, Teytelman, Leonid, Schmidt, Steve, Zhao, Wei, Cartinhour, Samuel, McCouch, Susan, and Stein, Lincoln
Abstract:: Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. Rice, in addition to being an economically important crop, is also a model monocot for understanding other agronomically important grass genomes. Gramene replaces the existing AceDB database ‘RiceGenes’ with a relational database based on...
Resource Type:: Article
Full Text:: Acids Research, 2002, Vol. 30, No. 1 103–105 Gramene: a resource for comparative grass genomics Doreen

Gramene: a bird's eye view of cereal genomes

Creator:: Jaiswal, Pankaj, Ni, Junjian, Yap, Immanuel, Ware, Doreen, Spooner, William, Youens-Clark, Ken, Canaran, Payan, Fogleman, Molly, Hebbard, Claire, Ren, Liya, Liang, Chengzhi, Zhao, Wei, Ratnapu, Kiran, Faga, Benjamin, Avraham, Shuly, Schmidt, Steven, Casstevens, Terry M., Buckler, Edward S., Stein, Lincoln, and McCouch, Susan
Abstract:: Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind’s most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order...
Resource Type:: Article
Full Text:: scientists. Plant Physiol., 138, 1268–1279. 15. Harris,M.A., Clark,J., Ireland,A., Lomax,J., Ashburner,M

Gramene: a growing plant comparative genomics resource

Creator:: Liang, Chengzhi, Jaiswal, Pankaj, Hebbard, Claire, Avraham, Shuly, Buckler, Edward S., Casstevens, Terry, Hurwitz, Bonnie, McCouch, Susan, Ni, Junjian, Pujar, Anuradha, Ravenscroft, Dean, Ren, Liya, Spooner, William, Tecle, Isaak, Thomason, Jim, Tung, Chih-wei, Wei, Xuehong, Yap, Immanuel, Youens-Clark, Ken, Ware, Doreen, and Stein, Lincoln
Abstract:: Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use...
Resource Type:: Article
Full Text:: ., Ware,D., Spooner,W., Youens-Clark,K., Ren,L., Liang,C., Zhao,W. et al. (2006) Gramene: a bird’s eye

Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)

Creator:: Fox, Samuel E., Preece, Justin, Kimbrel, Jeffrey A., Marchini, Gina L., Sage, Abigail, Youens-Clark, Ken, Cruzan, Mitchell B., and Jaiswal, Pankaj
Abstract:: PREMISE OF THE STUDY: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. METHODS AND RESULTS: More than 350 million sequence reads from the mRNA libraries...
Resource Type:: Article
Full Text:: sylvaticum (Poaceae) Fox, S. E., Preece, J., Kimbrel, J. A., Marchini, G. L., Sage, A., Youens-Clark, K

Gramene: Development and Integration of Trait and Gene Ontologies for Rice

Creator:: Jaiswal, Pankaj, Ware, Doreen, Ni, Junjian, Chang, Kuan, Zhao, Wei, Schmidt, Steven, Pan, Xiaokang, Clark, Kenneth, Teytelman, Leonid, Cartinhour, Samuel, Stein, Lincoln, and McCouch, Susan
Abstract:: Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait Loci (QTL). In order to support queries...
Resource Type:: Article
Full Text:: February 2002 Accepted: 14 February 2002 Abstract Gramene (http://www.gramene.org/) is a comparative

Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

Creator:: Graebner, Ryan C., Wise, Mitchell, Cuesta-Marcos, Alfonso, Geniza, Matthew, Blake, Tom, Blake, Victoria C., Butler, Joshua, Chao, Shiaoman, Hole, David J., Horsley, Rich, Jaiswal, Pankaj, Obert, Don, Smith, Kevin P., Ullrich, Steven, and Hayes, Patrick M.
Abstract:: The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of...
Resource Type:: Article
Full Text:: E) Pathway in Barley Graebner, R. C., Wise, M., Cuesta-Marcos, A., Geniza, M., Blake, T., Blake, V

Gramene 2016: comparative plant genomics and pathway resources

Creator:: Tello-Ruiz, Marcela K., Stein, Joshua, Wei, Sharon, Preece, Justin, Olson, Andrew, Naithani, Sushma, Amarasinghe, Vindhya, Dharmawardhana, Palitha, Jiao, Yinping, Mulvaney, Joseph, Kumari, Sunita, Chougule, Kapeel, Elser, Justin, Wang, Bo, Thomason, James, Bolser, Daniel M., Kerhornou, Arnaud, Walts, Brandon, Fonseca, Nuno A., Huerta, Laura, Keays, Maria, Tanga, Y. Amy, Parkinson, Helen, Fabregat, Antonio, McKay, Sheldon, Weiser, Joel, D'Eustachio, Peter, Stein, Lincoln, Petryszak, Robert, Kersey, Paul J., Jaiswal, Pankaj, and Ware, Doreen
Abstract:: Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
Resource Type:: Article

Gramene QTL database: development, content and applications

Creator:: Ni, Junjian, Pujar, Anuradha, Youens-Clark, Ken, Yap, Immanuel, Jaiswal, Pankaj, Tecle, Isaak, Tung, Chih-Wei, Ren, Liya, Spooner, William, Wei, Xuehong, Avraham, Shuly, Ware, Doreen, Stein, Lincoln, and McCouch, Susan
Abstract:: Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the...
Resource Type:: Article

ScholarsArchive@OSU

Gramene database in 2010: updates and extensions

Gramene 2013: comparative plant genomics resources

Gramene: a resource for comparative grass genomics

Gramene: a bird's eye view of cereal genomes

Gramene: a growing plant comparative genomics resource

Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)

Gramene: Development and Integration of Trait and Gene Ontologies for Rice

Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

Gramene 2016: comparative plant genomics and pathway resources

Gramene QTL database: development, content and applications

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