Index Catalog // ScholarsArchive@OSU

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Creator:: Mi, Gu, Di, Yanming, Emerson, Sarah, Cumbie, Jason S., and Chang, Jeff H.
Abstract:: When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology...
Resource Type:: Article
Full Text:: , Jeff H. Chang2,3,4 1 Department of Statistics, Oregon State University, Corvallis, Oregon, United

Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

Creator:: Kimbrel, Jeffrey A., Thomas, William J., Jiang, Yuan, Creason, Allison L., Thireault, Caitlin A., Sachs, Joel L., and Chang, Jeff H.
Abstract:: Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing...
Resource Type:: Article
Full Text:: ., Yuan Jiang3,4, Allison L. Creason1,2, Caitlin A. Thireault1, Joel L. Sachs5, Jeff H. Chang1,2,4* 1

The Plant Actin Cytoskeleton Responds to Signals from Microbe-Associated Molecular Patterns

Creator:: Henty-Ridilla, Jessica L., Shimono, Masaki, Li, Jiejie, Chang, Jeff H., Day, Brad, and Staiger, Christopher J.
Abstract:: Plants are constantly exposed to a large and diverse array of microbes; however, most plants are immune to the majority of potential invaders and susceptible to only a small subset of pathogens. The cytoskeleton comprises a dynamic intracellular framework that responds rapidly to biotic stresses and supports numerous fundamental cellular...
Resource Type:: Article
Full Text:: , Jeff H. Chang3, Brad Day2*, Christopher J. Staiger1,4* 1 Department of Biological Sciences, Purdue

AI, Robot: A Rhetorical Analysis of Jeopardy! Matches Featuring IBM’s Artificial Intelligence

Creator:: Steele, Evan T.
Abstract:: The relationship between the public and new technologies has historically been a tumultuous one, with public perceptions ranging from excited rapid adoption to standoffish pessimism. In 2011, IBM tried to use competition as a means of showcasing a new technology to the public. This thesis is a work of rhetorical...
Resource Type:: Masters Thesis
Full Text:: . 1, 1968, p. 1. 4 Rahwan, Iyad, and Guillermo R. Simari. Argumentation in Artificial Intelligence

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:: and Workbench for Crop Science Bruskiewich, R., Senger, M., Davenport, G., Ruiz, M., Rouard, M

Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests

Creator:: Wagner, Fabien H., Hérault, Bruno, Bonal, Damien, Stahl, Clément, Anderson, Liana O., Baker, Timothy R., Becker, Gabriel Sebastian, Beeckman, Hans, Boanerges Souza, Danilo, Botosso, Paulo Cesar, Bowman, David M. J. S., Bräuning, Achim, Brede, Benjamin, Brown, Foster Irving, Camarero, Jesus Julio, Camargo, Plínio Barbosa, Cardoso, Fernanda C. G., Carvalho, Fabrício Alvim, Castro, Wendeson, Chagas, Rubens Koloski, Chave, Jérome, Chidumayo, Emmanuel N., Clark, Deborah A., Costa, Flavia Regina Capellotto, Couralet, Camille, da Silva Mauricio, Paulo Henrique, Dalitz, Helmut, de Castro, Vinicius Resende, de Freitas Milani, Jaçanan Eloisa, de Oliveira, Edilson Consuelo, de Souza Arruda, Luciano, Devineau, Jean-Louis, Drew, David M., Dünisch, Oliver, Durigan, Giselda, Elifuraha, Elisha, Fedele, Marcio, Ferreira Fedele, Ligia, Figueiredo Filho, Afonso, Finger, César Augusto Guimarães, Franco, Augusto César, Freitas Júnior, João Lima, Galvão, Franklin, Gebrekirstos, Aster, Gliniars, Robert, Graça, Paulo Maurício Lima de Alencastro, Griffiths, Anthony D., Grogan, James, Guan, Kaiyu, Homeier, Jürgen, Kanieski, Maria Raquel, Kho, Lip Khoon, Koenig, Jennifer, Kohler, Sintia Valerio, Krepkowski, Julia, Lemos-Filho, José Pires, Lieberman, Diana, Lieberman, Milton Eugene, Lisi, Claudio Sergio, Longhi Santos, Tomaz, López Ayala, José Luis, Maeda, Eduardo Eijji, Malhi, Yadvinder, Maria, Vivian R. B., Marques, Marcia C. M., Marques, Renato, Maza Chamba, Hector, Mbwambo, Lawrence, Melgaço, Karina Liana Lisboa, Mendivelso, Hooz Angela, Murphy, Brett P., O'Brien, Joseph J., Oberbauer, Steven F., Okada, Naoki, Pélissier, Raphaël, Prior, Lynda D., Roig, Fidel Alejandro, Ross, Michael, Rossatto, Davi Rodrigo, Rossi, Vivien, Rowland, Lucy, Rutishauser, Ervan, Santana, Hellen, Schulze, Mark, Selhorst, Diogo, Silva, Williamar Rodrigues, Silveira, Marcos, Spannl, Susanne, Swaine, Michael D., Toledo, José Julio, Toledo, Marcos Miranda, Toledo, Marisol, Toma, Takeshi, Tomazello Filho, Mario, Valdez Hernández, Juan Ignacio, Verbesselt, Jan, Vieira, Simone Aparecida, Vincent, Grégoire, Volkmer de Castilho, Carolina, Volland, Franziska, Worbes, Martin, Zanon, Magda Lea Bolzan, and Aragão, Luiz E. O. C.
Abstract:: The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and...
Resource Type:: Article

Evolution of a Higher Intracellular Oxidizing Environment in Caenorhabditis elegans under Relaxed Selection

Creator:: Joyner-Matos, Joanna, Hicks, Kiley A., Cousins, Dustin, Keller, Michelle, Denver, Dee R., Baer, Charles F., and Estes, Suzanne
Abstract:: We explored the relationship between relaxed selection, oxidative stress, and spontaneous mutation in a set of mutation-accumulation (MA) lines of the nematode Caenorhabditis elegans and in their common ancestor. We measured steady-state levels of free radicals and oxidatively damaged guanosine nucleosides in the somatic tissues of five MA lines for...
Resource Type:: Article
Full Text:: . Hicks2., Dustin Cousins1, Michelle Keller1, Dee R. Denver3, Charles F. Baer4, Suzanne Estes2

The status and challenge of global fire modelling

Creator:: Hantson, Stijn, Arneth, Almut, Harrison, Sandy P., Kelley, Douglas I., Prentice, I. Colin, Rabin, Sam S., Archibald, Sally, Mouillot, Florent, Arnold, Steve R., Artaxo, Paulo, Bachelet, Dominique, Ciais, Philippe, Forrest, Matthew, Friedlingstein, Pierre, Hickler, Thomas, Kaplan, Jed O., Kloster, Silvia, Knorr, Wolfgang, Lasslop, Gitta, Li, Fang, Mangeon, Stephane, Melton, Joe R., Meyn, Andrea, Sitch, Stephen, Spessa, Allan, van der Werf, Guido R., Voulgarakis, Apostolos, and Yue, Chao
Abstract:: Biomass burning impacts vegetation dynamics, biogeochemical cycling, atmospheric chemistry, and climate, with sometimes deleterious socio-economic impacts. Under future climate projections it is often expected that the risk of wildfires will increase. Our ability to predict the magnitude and geographic pattern of future fire impacts rests on our ability to model...
Resource Type:: Article
Full Text:: . Kelley2,3, I. Colin Prentice3,4, Sam S. Rabin5, Sally Archibald6,7, Florent Mouillot8, Steve R. Arnold9

Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology

Creator:: Peterson, G. Jack, Pressé, Steve, Peterson, Kristin S., and Dill, Ken A.
Abstract:: We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate interactions. (2) Neofunctionalization, in which a mutation leads to a new interaction with some other protein. Since many...
Resource Type:: Article
Full Text:: –441. 2. Cirz R, Chin J, Andes D, de Crécy-Lagard V, Craig W, et al. (2005) Inhibition of mutation

Differential surface activation of the A1 domain of von Willebrand factor

Creator:: Tronic, Elaine H., Yakovenko, Olga, Weidner, Tobias, Baio, Joe E., Penkala, Rebecca, Castner, David G., and Thomas, Wendy E.
Abstract:: The clotting protein von Willebrand factor (VWF) binds to platelet receptor glycoprotein Ibα (GPIbα) when VWF is activated by chemicals, high shear stress, or immobilization onto surfaces. Activation of VWF by surface immobilization is an important problem in the failure of cardiovascular implants, but is poorly understood. Here, the authors...
Resource Type:: Article
Full Text:: . Schade, L. V. McIntire, R. K. Andrews, and J. A. Lopez, Blood 97, 162 (2001). 41M. S. Wagner and D. G

ScholarsArchive@OSU

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

The Plant Actin Cytoskeleton Responds to Signals from Microbe-Associated Molecular Patterns

AI, Robot: A Rhetorical Analysis of Jeopardy! Matches Featuring IBM’s Artificial Intelligence

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

Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests

Evolution of a Higher Intracellular Oxidizing Environment in Caenorhabditis elegans under Relaxed Selection

The status and challenge of global fire modelling

Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology

Differential surface activation of the A1 domain of von Willebrand factor

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