Index Catalog // ScholarsArchive@OSU

Creator:: Quandt, C. Alisha, Di, Yanming, Elser, Justin, Jaiswal, Pankaj, and Spatafora, Joseph W.
Abstract:: This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Genetics Society of America. The published article can be found at: https://doi.org/10.1534/g3.116.027045
Resource Type:: Article

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

Creator:: Naithani, Sushma, Raja, Rajani, Waddell, Elijah N., Elser, Justin, Gouthu, Satyanarayana, Deluc, Laurent G., and Jaiswal, Pankaj
Abstract:: We have developed VitisCyc, a grapevine-specific metabolic pathway database that allows researchers to (i) search and browse the database for its various components such as metabolic pathways, reactions, compounds, genes and proteins, (ii) compare grapevine metabolic networks with other publicly available plant metabolic networks, and (iii) upload, visualize and analyze...
Resource Type:: Article

Creator:: Myburg, Alexander A., Grattapaglia, Dario, Tuskan, Gerald A., Vining, Kelly, Amarasinghe, Vindhya, Ranik, Martin, Naithani, Sushma, Elser, Justin, Liston, Aaron, Spatafora, Joseph W., Dharmawardhana, Palitha, Raja, Rajani, Strauss, Steven H., Jaiswal, Pankaj, and et al.
Abstract:: Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest...
Resource Type:: Article

Creator:: Fox, Samuel E., Geniza, Matthew, Hanumappa, Mamatha, Naithani, Sushma, Sullivan, Chris, Preece, Justin, Tiwari, Vijay K., Elser, Justin, Leonard, Jeffrey M., Sage, Abigail, Gresham, Cathy, Kerhornou, Arnaud, Bolser, Dan, McCarthy, Fiona, Kersey, Paul, Lazo, Gerard R., and Jaiswal, Pankaj
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...
Resource Type:: Article

Creator:: Bushley, Kathryn E., Raja, Rajani, Jaiswal, Pankaj, Cumbie, Jason S., Nonogaki, Mariko, Boyd, Alexander E., Owensby, C. Alisha, Knaus, Brian J., Elser, Justin, Miller, Daniel, Di, Yanming, McPhail, Kerry L., and Spatafora, Joseph W.
Abstract:: The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of...
Resource Type:: Article

Creator:: Hanumappa, Mamatha, Preece, Justin, Elser, Justin, Nemeth, Denise, Bono, Gina, Wu, Kenny, and Jaiswal, Pankaj
Abstract:: Background: Next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. Despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated...
Resource Type:: Article

Creator:: Cooper, Laurel, Walls, Ramona L., Elser, Justin, Gandolfo, Maria A., Stevenson, Dennis W., Smith, Barry, Preece, Justin, Athreya, Balaji, Mungall, Christopher J., Rensing, Stefan, Hiss, Manuel, Lang, Daniel, Reski, Ralf, Berardini, Tanya Z., Li, Donghui, Huala, Eva, Schaeffer, Mary, Menda, Naama, Arnaud, Elizabeth, Shrestha, Rosemary, Yamazaki, Yukiko, and Jaiswal, Pankaj
Abstract:: The Plant Ontology (PO;http://www.plantontology.org/" is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and...
Resource Type:: Article

Creator:: Walls, Ramona L., Athreya, Balaji, Cooper, Laurel, Elser, Justin, Gandolfo, Maria A., Jaiswal, Pankaj, Mungall, Christopher J., Preece, Justin, Rensing, Stefan, Smith, Barry, and Stevenson, Dennis W.
Abstract:: Premise of the study: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web....
Resource Type:: Article

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