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:: Micro, vol. 19, no. 2, 1999, p. 72. 2 Gubbi, Jayavardhana, et al. "Internet of Things (IoT): A

Elemental Markers in Elasmobranchs: Effects of Environmental History and Growth on Vertebral Chemistry

Creator:: Smith, Wade D., Miller, Jessica A., and Heppell, Selina S.
Abstract:: Differences in the chemical composition of calcified skeletal structures (e.g. shells, otoliths) have proven useful for reconstructing the environmental history of many marine species. However, the extent to which ambient environmental conditions can be inferred from the elemental signatures within the vertebrae of elasmobranchs (sharks, skates, rays) has not been...
Resource Type:: Article
Full Text:: , as intended (Kruskal-Wallis, H = 69.96, p < 0.001; Table 1). Salinity varied during the experiment

The Level of Residual Dispersion Variation and the Power of Differential Expression Tests for RNA-Seq Data

Creator:: Mi, Gu and Di, Yanming
Abstract:: RNA-Sequencing (RNA-Seq) has been widely adopted for quantifying gene expression changes in comparative transcriptome analysis. For detecting differentially expressed genes, a variety of statistical methods based on the negative binomial (NB) distribution have been proposed. These methods differ in the ways they handle the NB nuisance parameters (i.e., the dispersion...
Resource Type:: Article
Full Text:: thatVarðYijÞ ¼ mij þ �ijm2ij. 2. A log-linear regression model for the mean μij as a function of p explanatory

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:: and P Users can navigate to the desired pathway via ‘search pathways’ or ‘browse’ options (Figure 1

Status of the European Green Crab in Oregon Estuaries, Fall 2003

Creator:: Yamada, Sylvia Behrens and Becklund, Marsha
Abstract:: Prepared for the Pacific States Marine Fisheries Commission and the Alaska Department of Fish of Game.
Resource Type:: Technical Report
Full Text:: green crab repelled by native red crabs. Radio story and phone interview by Jeff Brady Oregon

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Creator:: Kasschau, Kristin D., Fahlgren, Noah, Chapman, Elisabeth J., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., and Carrington, James C.
Abstract:: Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants...
Resource Type:: Article
Full Text:: no general correlation between cluster prox- imity and expression values (p . 0.30, linear regression

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

Elemental Markers in Elasmobranchs: Effects of Environmental History and Growth on Vertebral Chemistry

The Level of Residual Dispersion Variation and the Power of Differential Expression Tests for RNA-Seq Data

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

Status of the European Green Crab in Oregon Estuaries, Fall 2003

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

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