Index Catalog // ScholarsArchive@OSU

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:: ophioglossoides C. Alisha Quandt,*,1 Yanming Di,† Justin Elser,* Pankaj Jaiswal,* and Joseph W. Spatafora

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
Full Text:: , P. L., Cooper, L. D., Dahdul, W. M., Domisch, S., ... & Mungall, C. J. (2015). Emerging semantics

Ontologies as Integrative Tools for Plant Science

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
Full Text:: , JUSTIN PREECE 3 , STEFAN RENSING 6 , BARRY SMITH 7 , AND DENNIS W

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:: spicer6, margaret e. staton7, dennis w. stevenson8, ramona l. walls8 and jill wegrzyn9 A wealth of

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
Full Text:: iehs .n ih .gov/ homePage/slideshow/september_15_2014_ w o r k s h o p _ o f _ t h e _ d e v e l o p

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:: Owensby1, Brian J. Knaus1, Justin Elser1, Daniel Miller1, Yanming Di4, Kerry L. McPhail2, Joseph W

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

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
Full Text:: A. Gandolfo3,17, Dennis W. Stevenson2,17, Barry Smith4,17, Justin Preece1, Balaji Athreya1

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

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...
Resource Type:: Article
Full Text:: , Wallingford, UK, 1996. [3] R. Bruskiewich, A. B. Cosico, W. Eusebio, et al., “Linking geno- type to phenotype

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:: sequence (e.g. ‘non-synonymous’). Nucleic Acids Research, 2011, Vol. 39, Database issue D1087 at O xford

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:: . 36, Database issue D949 F ig u re 2 . A sy n te n ic re g io n sh o w in g re la te d Q T L s a

ScholarsArchive@OSU

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

Emerging semantics to link phenotype and environment

Ontologies as Integrative Tools for Plant Science

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

Finding Our Way through Phenotypes

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

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

Gramene database in 2010: updates and extensions

Gramene: a growing plant comparative genomics resource

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