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DharmawardhanaPalithaBotanyPlantPathologyGramene2013.pdf

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:: resources. Nucleic Acids Research, 42(D1), D1193-D1199. doi:10.1093/nar/gkt1110 10.1093/nar/gkt1110

An Extension of the Plant Ontology Project Supporting Wood Anatomy and Development Research

Creator:: Lens, Frederic, Cooper, Laurel, Gandolfo, Maria Alejandra, Groover, Andrew, Jaiswal, Pankaj, Lachenbruch, Barbara, Spicer, Rachel, Staton, Margaret E., Stevenson, Dennis W., Walls, Ramona L., and Wegrzyn, Jill
Abstract:: A wealth of information on plant anatomy and morphology is available in the current and historical literature, and molecular biologists are producing massive amounts of transcriptome and genome data that can be used to gain better insights into the development, evolution, ecology, and physiological function of plant anatomical attributes. Integrating...
Resource Type:: Article
Full Text:: controlled vocabulary and annotations. Nucleic Acids Res. 36, Database issue D449–D454. Bedon, F., J. Grima

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:: . The Mouse Genome Database (MGD): the model organism database for the laboratory mouse. Nucleic Acids

GenizaMatthewMolecularCellularBiologyDeNovoTranscriptome.pdf

Creator:: Fox, Samuel E., Geniza, Matthew, Hanumappa, Mamatha, Naithani, Sushma, Sullivan, Chris, Preece, Justin, Tiwari, Vijay K., Elser, Justin, Leonard, Jeffrey M., Sage, Abigail, Jaiswal, Pankaj, and et al.
Abstract:: BACKGROUND: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes...
Full Text:: States of America, 2 Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis

DharmawardhanaPalithaBotanyPlantPathologyGramene2013_SupplementaryData.pdf

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:: resource and comparative analysis workbench for rice genomics. Nucleic Acids

PetryszakExpressionAtlasUpdateSupplement.pdf

Creator:: Petryszak, Robert, Keays, Maria, Tang, Y. Amy, Fonseca, Nuno A., Barrera, Elisabet, Burdett, Tony, Füllgrabe, Anja, Muñoz-Pomer Fuentes, Alfonso, Jupp, Simon, Koskinen, Satu, Mannion, Oliver, Huerta, Laura, Megy, Karine, Snow, Catherine, Williams, Eleanor, Barzine, Mitra, Hastings, Emma, Weisser, Hendrik, Wright, James, Jaiswal, Pankaj, Huber, Wolfgang, Choudhary, Jyoti, Parkinson, Helen E., and Brazma, Alvis
Abstract:: Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality...
Full Text:: . Nucleic Acids Research 2013 Jan;41(Database issue):D1063-1069. 3. Sturm M, et al. OpenMS - an open

RajaRajaniBotanyPlantPathologyComparativeAnalysisPredicted.pdf

Creator:: Schaeffer, Scott, Harper, Artemus, Raja, Rajani, Jaiswal, Pankaj, and Dhingra, Amit
Abstract:: Plastids are actively involved in numerous plant processes critical to growth, development and adaptation. They play a primary role in photosynthesis, pigment and monoterpene synthesis, gravity sensing, starch and fatty acid synthesis, as well as oil, and protein storage. We applied two complementary methods to analyze the recently published apple...
Full Text:: 1.60E-10 GO:0006139 P nucleobase, nucleoside, nucleotide and nucleic acid metabolic process 1.60E-12

Maize Metabolic Network Construction and Transcriptome Analysis

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:: integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40:D109–D114. doi

PetryszakExpressionAtlasUpdate.pdf

Creator:: Petryszak, Robert, Keays, Maria, Tang, Y. Amy, Fonseca, Nuno A., Barrera, Elisabet, Burdett, Tony, Füllgrabe, Anja, Muñoz-Pomer Fuentes, Alfonso, Jupp, Simon, Koskinen, Satu, Mannion, Oliver, Huerta, Laura, Megy, Karine, Snow, Catherine, Williams, Eleanor, Barzine, Mitra, Hastings, Emma, Weisser, Hendrik, Wright, James, Jaiswal, Pankaj, Huber, Wolfgang, Choudhary, Jyoti, Parkinson, Helen E., and Brazma, Alvis
Abstract:: Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality...
Full Text:: D746–D752 Nucleic Acids Research, 2016, Vol. 44, Database

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:: the USDA project using re-sequencing technology (40) D1086 Nucleic Acids Research, 2011, Vol. 39

ScholarsArchive@OSU

DharmawardhanaPalithaBotanyPlantPathologyGramene2013.pdf

An Extension of the Plant Ontology Project Supporting Wood Anatomy and Development Research

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

GenizaMatthewMolecularCellularBiologyDeNovoTranscriptome.pdf

DharmawardhanaPalithaBotanyPlantPathologyGramene2013_SupplementaryData.pdf

PetryszakExpressionAtlasUpdateSupplement.pdf

RajaRajaniBotanyPlantPathologyComparativeAnalysisPredicted.pdf

Maize Metabolic Network Construction and Transcriptome Analysis

PetryszakExpressionAtlasUpdate.pdf

Gramene database in 2010: updates and extensions

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