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

3,3'-Diindolylmethane Induces G₁ Arrest and Apoptosis in Human Acute T-Cell Lymphoblastic Leukemia Cells

Creator:: Shorey, Lyndsey E., Hagman, Amanda M., Williams, David E., Ho, Emily, Dashwood, Roderick H., and Benninghoff, Abby D.
Abstract:: Certain bioactive food components, including indole-3-carbinol (I3C) and 3,3'-diindolylmethane (DIM) from cruciferous vegetables, have been shown to target cellular pathways regulating carcinogenesis. Previously, our laboratory showed that dietary I3C is an effective transplacental chemopreventive agent in a dibenzo[def,p]chrysene (DBC)-dependent model of murine T-cell lymphoblastic lymphoma. The primary objective of the...
Resource Type:: Article
Full Text:: Apoptosis in Human Acute T-Cell Lymphoblastic Leukemia Cells Lyndsey E. Shorey1,2, Amanda M. Hagman3, David

Uncertainty analysis: an evaluation metric for synthesis science

Creator:: Harmon, Mark E., Fasth, Becky, Halpern, Charles B., and Lutz, James A.
Abstract:: The methods for conducting reductionist ecological science are well known and widely used. In contrast, those used in the synthesis of ecological science (i.e., synthesis science) are still being developed, vary widely, and often lack the rigor of reductionist approaches. This is unfortunate because the synthesis of ecological parts into...
Resource Type:: Article
Full Text:: science Uncertainty analysis: an evaluation metric for synthesis science Harmon, M. E., Fasth, B

Frequent Alteration of the Tumor Suppressor Gene APC in Sporadic Canine Colorectal Tumors

Creator:: Youmans, Lydia, Taylor, Cynthia, Shin, Edwin, Harrell, Adrienne, Ellis, Angela E., Seguin, Bernard, Ji, Xinglai, and Zhao, Shaying
Abstract:: Sporadic canine colorectal cancers (CRCs) should make excellent models for studying the corresponding human cancers. To molecularly characterize canine CRC, we investigated exonic sequence mutations of adenomatous polyposis coli (APC), the best known tumor suppressor gene of human CRC, in 23 sporadic canine colorectal tumors, including 8 adenomas and 15...
Resource Type:: Article
Full Text:: Harrell1, Angela E. Ellis2, Bernard Séguin3, Xinglai Ji4, Shaying Zhao1* 1 Department of Biochemistry

Does wildfire likelihood increase following insect outbreaks in conifer forests?

Creator:: Meigs, Garrett W., Campbell, John L., Zald, Harold S. J., Bailey, John D., Shaw, David C., and Kennedy, Robert E.
Abstract:: Although there is acute concern that insect-caused tree mortality increases the likelihood or severity of subsequent wildfire, previous studies have been mixed, with findings typically based on stand-scale simulations or individual events. This study investigates landscape- and regional-scale wildfire likelihood following outbreaks of the two most prevalent native insect pests...
Resource Type:: Article
Full Text:: ., & Kennedy, R. E. (2015). Does wildfire likelihood increase following insect outbreaks in conifer forests

Does wildfire likelihood increase following insect outbreaks in conifer forests?

Creator:: Meigs, Garrett W., Campbell, John L., Zald, Harold S. J., Bailey, John D., Shaw, David C., and Kennedy, Robert E.
Abstract:: Although there is acute concern that insect‐caused tree mortality increases the likelihood or severity of subsequent wildfire, previous studies have been mixed, with findings typically based on stand‐scale simulations or individual events. This study investigates landscape‐ and regional‐scale wildfire likelihood following outbreaks of the two most prevalent native insect pests...
Resource Type:: Article
Full Text:: ., & Kennedy, R. E. (2015). Does wildfire likelihood increase following insect outbreaks in conifer forests

Does wildfire likelihood increase following insect outbreaks in conifer forests?

Creator:: Meigs, Garrett W., Campbell, John L., Zald, Harold S. J., Bailey, John D., Shaw, David C., and Kennedy, Robert E.
Abstract:: Although there is acute concern that insect‐caused tree mortality increases the likelihood or severity of subsequent wildfire, previous studies have been mixed, with findings typically based on stand‐scale simulations or individual events. This study investigates landscape‐ and regional‐scale wildfire likelihood following outbreaks of the two most prevalent native insect pests...
Resource Type:: Article
Full Text:: ., & Kennedy, R. E. (2015). Does wildfire likelihood increase following insect outbreaks in conifer forests

Non-Invasive Sampling of Schistosomes from Humans Requires Correcting for Family Structure

Creator:: Steinauer, Michelle L., Christie, Mark R., Blouin, Michael S., Agola, Lelo E., Mwangi, Ibrahim N., Maina, Geoffrey M., Mutuku, Martin W., Kinuthia, Joseph M., Mkoji, Gerald M., and Loker, Eric S.
Abstract:: For ethical and logistical reasons, population-genetic studies of parasites often rely on the non-invasive sampling of offspring shed from their definitive hosts. However, if the sampled offspring are naturally derived from a small number of parents, then the strong family structure can result in biased population-level estimates of genetic parameters,...
Resource Type:: Article
Full Text:: . Blouin2, Lelo E. Agola3, Ibrahim N. Mwangi3, Geoffrey M. Maina3, Martin W. Mutuku3, Joseph M. Kinuthia3

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

3,3'-Diindolylmethane Induces G₁ Arrest and Apoptosis in Human Acute T-Cell Lymphoblastic Leukemia Cells

Uncertainty analysis: an evaluation metric for synthesis science

Frequent Alteration of the Tumor Suppressor Gene APC in Sporadic Canine Colorectal Tumors

Does wildfire likelihood increase following insect outbreaks in conifer forests?

Does wildfire likelihood increase following insect outbreaks in conifer forests?

Does wildfire likelihood increase following insect outbreaks in conifer forests?

Non-Invasive Sampling of Schistosomes from Humans Requires Correcting for Family Structure

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