Index Catalog // ScholarsArchive@OSU

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

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

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

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

Expression, Splicing, and Evolution of the Myosin Gene Family in Plants

Creator:: Peremyslov, Valera V., Mockler, Todd C., Filichkin, Sergei A., Fox, Samuel E., Jaiswal, Pankaj, Makarova, Kira S., Koonin, Eugene V., and Dolja, Valerian V.
Abstract:: Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
Resource Type:: Article

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

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

Creator:: Filichkin, Sergei A., Breton, Ghislain, Priest, Henry D., Dharmawardhana, Palitha, Jaiswal, Pankaj, Fox, Samuel E., Michael, Todd P., Chory, Joanne, Kay, Steve A., and Mockler, Todd C.
Abstract:: BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day. Synchronized...
Resource Type:: Article

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

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

Nomenclature report on rice WRKY’s - Conflict regarding gene names and its solution

Creator:: Shen, Qingxi J., Yu, Diqiu, Jeon, Jong-Seong, Piffanelli, Pietro, Abbruscato, Pamela, Guo, Ze-Jian, Zhang, Yuanji, Itoh, Takeshi, Lee, Sung S., Buell, C. Robin, Nagato, Yasuo, McCouch, Susan, Yano, Masahiro, Wang, Guo-liang, Jena, Kshirod K., Xiong, Lizhong, Meyers, Blake, Jaiswal, Pankaj, and Yamazaki, Yukiko
Abstract:: Background: Since whole genome sequences of rice were made publically accessible, the number of articles on new rice genes has increased remarkably. The Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative published the gene nomenclature system for rice and encouraged researchers to follow the rules...
Resource Type:: Article

ScholarsArchive@OSU

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

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

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

Emerging semantics to link phenotype and environment

Expression, Splicing, and Evolution of the Myosin Gene Family in Plants

Finding Our Way through Phenotypes

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

Gramene database in 2010: updates and extensions

Maize Metabolic Network Construction and Transcriptome Analysis

Nomenclature report on rice WRKY’s - Conflict regarding gene names and its solution

Limit your search

Academic Affiliation

Creator

Date

Decade

Language

License

Non-Academic Affiliation

Peer Reviewed

Resource Type

Rights Statement

Subject

Search Constraints

Search Results

Limit your search