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Tello-Ruiz, Marcela K.
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Jaiswal, Pankaj
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- 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...
- Full Text:
- genomics and pathway resources Marcela K. Tello-Ruiz1, Joshua Stein1, Sharon Wei1, Justin Preece2, Andrew
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- 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...
- Full Text:
- ., J. Preece, J. A. Kimbrel, G. L. Marchini, A. Sage, K. Youens-Clark, M. B. Cruzan and P. Jaiswal
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- 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
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AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
- Creator:
- Harper, Lisa, Campbell, Jacqueline, Cannon, Steve, Carson, James, Condon, Bradford, Cooper, Laurel, Dunn, Nathan, Elsik, Christine G., Farmer, Andrew, Ficklin, Stephen P., Grant, David, Grau, Emily, Cannon, Ethalinda K. S., Herndon, Nic, Hu, Zhi-Liang, Humann, Jodi, Jaiswal, Pankaj, Jonquet, Clement, Laporte, Marie-Angelique, Larmande, Pierre, Lazo, Gerard, McCarthy, Fiona, Menda, Naama, Jung, Sook, Mungall, Christopher J., Munoz-Torres, Monica C., Naithani, Sushma, Nelson, Rex, Nesdill, Daureen, Park, Carissa, Reecy, James, Reiser, Leonore, Sanderson, Lacey-Anne, Sen, Taner Z., Poelchau, Monica, Staton, Margaret, Subramaniam, Sabarinath, Tello-Ruiz, Marcela Karey, Unda, Victor, Unni, Deepak, Wang, Liya, Ware, Doreen, Wegrzyn, Jill, Williams, Jason, Woodhouse, Margaret, Walls, Ramona, Yu, Jing, Main, Doreen, Andorf, Carson, Arnaud, Elizabeth, Berardini, Tanya Z., and Birkett, Clayton
- Abstract:
- The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require datamanagement plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated...
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- Article
- Full Text:
- , Taner Z. Sen19, Margaret Staton10, Sabarinath Subramaniam7, Marcela Karey Tello-Ruiz25, Victor Unda3
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- Creator:
- Dharmawardhana, Palitha, Ren, Liya, Amarasinghe, Vindhya, Monaco, Marcela, Thomason, Jim, Ravenscroft, Dean, McCouch, Susan, Ware, Doreen, and Jaiswal, Pankaj
- Abstract:
- Background: Functional annotations of large plant genome projects mostly provide information on gene function and gene families based on the presence of protein domains and gene homology, but not necessarily in association with gene expression or metabolic and regulatory networks. These additional annotations are necessary to understand the physiology, development...
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- Article
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- regulation under biotic stress Palitha Dharmawardhana1, Liya Ren2, Vindhya Amarasinghe1, Marcela Monaco2, Jim
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- Creator:
- Monaco, Marcela K., Sen, Taner Z., Dharmawardhana, Palitha D., Ren, Liya, Schaeffer, Mary, Naithani, Sushma, Amarasinghe, Vindhya, Thomason, Jim, Harper, Lisa, Gardiner, Jack, Cannon, Ethalinda K.S., Lawrence, Carolyn J., Ware, Doreen, and Jaiswal, Pankaj
- Abstract:
- A framework for understanding the synthesis and catalysis of metabolites and other biochemicals by proteins is crucial for unraveling the physiology of cells. To create such a framework for Zea mays L. subsp. mays (maize), we developed MaizeCyc, a metabolic network of enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary...
- Resource Type:
- Article
- Full Text:
- Marcela K. Monaco, Taner Z. Sen, Palitha D. Dharmawardhana, Liya Ren, Mary Schaeffer, Sushma Naithani
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- 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...
- Full Text:
- ://cdss.library.oregonstate.edu/sa-termsofuse Gramene 2013: comparative plant genomics resources Marcela K. Monaco1, Joshua
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- 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...
- Full Text:
- Database K-12 MG1655 BioCyc Keseler et al (2013) (Escherichia coli) SUPPLEMENTARY
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- 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
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- Creator:
- Bruskiewich, Richard, Senger, Martin, Davenport, Guy, Ruiz, Manuel, Rouard, Mathieu, Hazekamp, Tom, Takeya, Masaru, Doi, Koji, Satoh, Kouji, Costa, Marcos, Simon, Reinhard, Balaji, Jayashree, Akintunde, Akinnola, Mauleon, Ramil, Wanchana, Samart, Shah, Trushar, Anacleto, Mylah, Portugal, Arllet, Ulat, Victor Jun, Thongjuea, Supat, Braak, Kyle, Ritter, Sebastian, Dereeper, Alexis, Skofic, Milko, Rojas, Edwin, Martins, Natalia, Pappas, Georgios, Alamban, Ryan, Almodiel, Roque, Barboza, Lord Hendrix, Detras, Jeffrey, Manansala, Kevin, Mendoza, Michael Jonathan, Morales, Jeffrey, Peralta, Barry, Valerio, Rowena, Zhang, Yi, Gregorio, Sergio, Hermocilla, Joseph, Echavez, Michael, Yap, Jan Michael, Farmer, Andrew, Schiltz, Gary, Lee, Jennifer, Casstevens, Terry, Jaiswal, Pankaj, Meintjes, Ayton, Wilkinson, Mark, Good, Benjamin, Wagner, James, Morris, Jane, Marshall, David, Collins, Anthony, Kikuchi, Shoshi, Metz, Thomas, McLaren, Graham, and van Hintum, Theo
- Abstract:
- The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the...
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- Article
- Full Text:
- and Workbench for Crop Science Bruskiewich, R., Senger, M., Davenport, G., Ruiz, M., Rouard, M