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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:: Enrichment Analysis Using Logistic Regression Gu Mi1*, Yanming Di1,2, Sarah Emerson1, Jason S. Cumbie2,3

Creator:: Fahlgren, Noah, Howell, Miya D., Kasschau, Kristin D., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., Law, Theresa F., Grant, Sarah R., Dangl, Jeffrey L., and Carrington, James C.
Abstract:: In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep...
Resource Type:: Article
Full Text:: q u e n ce d m iR N A m iR N A * V a li d a te d o r p re d ic te d ta rg e t fa m

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:: . Sullivan 1,2 , Jason S. Cumbie 1,2 , Scott A. Givan 1,2 , James C. Carrington 1,2* 1 Center for Genome

Creator:: Traeger, Stefanie, Altegoer, Florian, Freitag, Michael, Gabaldon, Toni, Kempken, Frank, Kumar, Abhishek, Marcet-Houben, Marina, Poggeler, Stefanie, Stajich, Jason E., and Nowrousian, Minou
Abstract:: Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely...
Resource Type:: Article
Full Text:: Pöggeler6, Jason E. Stajich7, Minou Nowrousian1* 1 Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr

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:: *, Rajani Raja1, Pankaj Jaiswal1, Jason S. Cumbie1, Mariko Nonogaki2, Alexander E. Boyd3, C. Alisha

Creator:: Dusek, Daniel
Abstract:: The World Health Organization defines food security as “all people at all times have access to sufficient, safe, nutritious food to maintain a healthy and active life.” The reality is that one in six Americans are not food secure, even though the US produces enough food to feed its national...
Resource Type:: Capstone Project
Full Text:: ..................................................................................................14 V. Physical Challenges

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