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The Plant Structure Ontology, A Unified Vocabulary Of Anatomy And Morphology Of A Flowering Plant, Katica Ilic, Elizabeth A. Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter F. Stevens, Leszek P. Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin M. Sachs, Noah T. Whitman, Susan R. Mccouch, Mary L. Schaeffer, Doreen H. Ware, Lincoln D. Stein, Seung Y. Rhee

Peter Stevens

Nonparametric Pathway-Based Regression Models For Analysis Of Genomic Data, Zhi Wei, Hongzhe Li

Hongzhe Li

High-throughout genomic data provide an opportunity for identifying pathways and genes that are related to various clinical phenotypes. Besides these genomic data, another valuable source of data is the biological knowledge about genes and pathways that might be related to the phenotypes of many complex diseases. Databases of such knowledge are often called the metadata. In microarray data analysis, such metadata are currently explored in post hoc ways by gene set enrichment analysis but have hardly been utilized in the modeling step. We propose to develop and evaluate a pathway-based gradient descent boosting procedure for nonparametric pathways-based regression(NPR) analysis to …

Group Additive Regression Models For Genomic Data Analysis, Yihui Luan, Hongzhe Li

Hongzhe Li

One important problem in genomic research is to identify genomic features such as gene expression data or DNA single nucleotide polymorphisms (SNPs) that are related to clinical phenotypes. Often these genomic data can be naturally divided into biologically meaningful groups such as genes belonging to the same pathways or SNPs within genes. In this paper, we propose group additive regression models and a group gradient descent boosting procedure for identifying groups of genomic features that are related to clinical phenotypes. Our simulation results show that by dividing the variables into appropriate groups, we can obtain better identification of the group …

Interacting Endogenous And Exogenous Rnai Pathways In Caenorhabditis Elegans., Rosalind C. Lee, Christopher M. Hammell, Victor R. Ambros

Victor R. Ambros

C. elegans contains numerous small RNAs of ~21-24 nt in length. The microRNAs (miRNAs) are small noncoding RNAs produced by DCR-1- and ALG-dependent processing of self-complementary hairpin transcripts. Endogenous small interfering RNAs (endo-siRNAs), associated with ongoing silencing of protein-coding genes in normal worms, are produced by mechanisms that involve DCR-1 but, unlike miRNAs, also involve RDE-2, RDE-3, RDE-4, RRF-1, and RRF-3. The tiny noncoding (tncRNAs) are similar to endo-siRNAs in their biogenesis except that they are derived from noncoding sequences. These endo-siRNA- and tncRNA-based endogenous RNAi pathways involve some components, including DCR-1 and RDE-4, that are shared with exogenous RNAi, …

Comparative Efficiency Of Six Stable Fly Traps., David B. Taylor, Dennis R. Berkebile

David B. Taylor

Five adhesive traps and the Nzi cloth-target trap were compared to determine their trapping efficiency and biases for stable flies, Stomoxys calcitrans (L.) (Diptera: Muscidae). Two configurations of the BiteFree prototype trap, constructed of polyethylene terephthalate, were most efficient for trapping stable flies, whereas the EZ trap was least efficient. The two Alsynite traps, Broce and Olson, were intermediate to the BiteFree prototype and EZ traps. All adhesive traps collected a ratio of approximately two males for each female. Approximately 50% of the flies collected on the adhesive traps, both male and female, were blood fed, and 20% were vitellogenic. …

Multiple Sequence Alignment Accuracy And Phylogenetic Inference, T. Heath Ogden

T. Heath Ogden

Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our …