Index Catalog // ScholarsArchive@OSU

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:: ) Comparative genetics in the grasses. Proc. Natl Acad. Sci. USA, 95, 1971–1974. 2. Tarchini,R., Biddle,P

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides

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
Full Text:: immediately transferred to –80�, where samples were held until RNA extraction. Nucleic acid preparation and

Finding Our Way through Phenotypes

Creator:: Deans, Andrew R., Lewis, Suzanna E., Huala, Eva, Anzaldo, Salvatore S., Ashburner, Michael, Balhoff, James P., Blackburn, David C., Blake, Judith A., Burleigh, J. Gordon, Chanet, Bruno, Cooper, Lauren D., Courtot, Mélanie, Csösz, Sándor, Cul, Hong, Dahdul, Wasila, Das, Sandip, Dececchi, T. Alexander, Dettal, Agnes, Diogo, Rui, Druzinsky, Robert E., Dumontier, Michel, Franz, Nico M., Friedrich, Frank, Gkoutos, George V., Haendel, Melissa, Harmon, Luke J., Hayamizu, Terry F., He, Yongqun, Hines, Heather M., Ibrahim, Nizar, Jackson, Laura M., Jaiswal, Pankaj, James-Zorn, Christina, Köhler, Sebastian, Lecointre, Guillaume, Lapp, Hilmar, Lawrence, Carolyn J., Le Novère, Nicolas, Lundberg, John G., Macklin, James, Mast, Austin R., Midford, Peter E., Mikó, István, Mungall, Christopher J., Oellrich, Anika, Osumi-Sutherland, David, Parkinson, Helen, Ramírez, Martín J., Richter, Stefan, Robinson, Peter N., Ruttenberg, Alan, Schulz, Katja S., Segerdell, Erik, Seltmann, Katja C., Sharkey, Michael J., Smith, Aaron D., Smith, Barry, Specht, Chelsea D., Squires, R. Burke, Thacker, Robert W., Thessen, Anne, Fernandez-Triana, Jose, Vihinen, Mauno, Vize, Peter D., Vogt, Lars, Wall, Christine E., Walls, Ramona L., Westerfeld, Monte, Wharton, Robert A., Wirkner, Christian S., Woolley, James B., Yoder, Matthew J., Zorn, Aaron M., and Mabee, Paula
Abstract:: Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across...
Resource Type:: Article

Emerging semantics to link phenotype and environment

Creator:: Thessen, Anne E., Bunkers, Daniel E., Buttigieg, Pier Luigi, Cooper, Laurel D., Dahdul, Wasila M., Domisch, Sami, Franz, Nico M., Jaiswal, Pankaj, Lawrence-Dill, Carolyn J., Midford, Peter E., Mungall, Christopher J., Ramírez, Martín J., Specht, Chelsea D., Vogt, Lars, Aldo Vos, Rutger, Walls, Ramona L., White, Jeffrey W., Zhang, Guanyang, Deans, Andrew R., Huala, Eva, Lewis, Suzanna E., and Mabee, Paula M.
Abstract:: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize...
Resource Type:: Article

The Gene Ontology in 2010: extensions and refinements

Creator:: Gene Ontology Consortium, Berardini, Tanya Z., Li, Donghui, Huala, Eva, Bridges, Susan, Burgess, Shane, McCarthy, Fiona, Carbon, Seth, Lewis, Suzanna E., Mungall, Christopher J., Abdulla, Amina, Wood, Valerie, Feltrin, Erika, Valle, Giorgio, Chisholm, Rex L., Fey, Petra, Gaudet, Pascale, Kibbe, Warren, Basu, Siddhartha, Bushmanova, Yulia, Eilbeck, Karen, Siegele, Deborah A., McIntosh, Brenley, Renfro, Daniel, Zweifel, Adrienne, Hu, James C., Harris, Midori A., Deegan, Jennifer I., Ireland, Amelia, Lomax, Jane, Jaiswal, Pankaj, Chibucos, Marcus, Gwinn-Giglio, Michelle, Wortman, Jennifer, Hannick, Linda, Madupu, Ramana, Botstein, David, Dolinski, Kara, Livstone, Michael S., Oughtred, Rose, Blake, Judith A., Bult, Carol, Diehl, Alexander D., Dolan, Mary, Drabkin, Harold, Eppig, Janan T., Hill, David P., Ni, Li, Ringwald, Martin, Sitnikov, Dmitry, Collmer, Candace, Torto-Alalibo, Trudy, Laulederkind, Stan, Shimoyama, Mary, Twigger, Simon, D'Eustachio, Peter, Matthews, Lisa, Balakrishnan, Rama, Binkley, Gail, Cherry, J. Michael, Christie, Karen R., Costanzo, Maria C., Engel, Stacia R., Fisk, Dianna G., Hirschman, Jodi E., Hitz, Benjamin C., Hong, Eurie L., Krieger, Cynthia J., Miyasato, Stuart R., Nash, Robert S., Park, Julie, Skrzypek, Marek S., Weng, Shuai, Wong, Edith D., Aslett, Martin, Chan, Juancarlos, Kishore, Ranjana, Sternberg, Paul, Van Auken, Kimberly, Khodiyar, Varsha K., Lovering, Ruth C., and Talmud, Philippa J.
Abstract:: The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with...
Resource Type:: Article

Constructing a gene expression atlas of Chia (Salvia hispanica)

Creator:: Phillips, Jeremy Levi, Geniza, Matthew, Haq, Ebaad, and Jaiswal, Pankaj
Abstract:: • Salvia hispanica, also known as Chia, is an annual plant of the mint family, Lamiaceae. Chia is a vascular plant with perennating buds initially formed at or within the soil surface. Chia grows to roughly one meter tall at maturity, with leaves growing in opposite arrangement, small purple flowers,...
Resource Type:: Poster

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

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
Full Text:: a single monophyletic group with 100% bootstrap support and many share over 95% sequence

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

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...
Resource Type:: Article
Full Text:: LO C _O S 07 G 19 13 0 R 2 LO C _O s0 5g 43 51 0 R 1 LO C _O S 01 G 56 38 0 R 1 es

Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology

Creator:: Pujar, Anuradha, Jaiswal, Pankaj, Kellogg, Elizabeth A., Ilic, Katica, Vincent, Leszek, Avraham, Shulamit, Stevens, Peter, Zapata, Felipe, Reiser, Leonore, Rhee, Seung Y., Sachs, Martin M., Schaeffer, Mary, Stein, Lincoln, Ware, Doreen, and McCouch, Susan
Abstract:: Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth...
Resource Type:: Article
Full Text:: . The numerical portion uses double digits starting with 01, 02, and so on. Each of the substages may

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:: extracted by addition of 0.5 ml 10M KOH, 0.5 ml 95% ethanol, 0.5 ml 0.15M NaCl and 1.25 ml of a 0.5M

ScholarsArchive@OSU

Gramene: a resource for comparative grass genomics

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides

Finding Our Way through Phenotypes

Emerging semantics to link phenotype and environment

The Gene Ontology in 2010: extensions and refinements

Constructing a gene expression atlas of Chia (Salvia hispanica)

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology

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

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