Title of dissertation: TRANSCRIPT ASSEMBLY AND ABUNDANCE ESTIMATION WITH HIGH-THROUGHPUT RNA SEQUENCING Bruce C. Trapnell, Jr., Doctor of Philosophy, 2010 Dissertation directed by: Professor Steven Salzberg Department of Computer Science We present algorithms and statistical methods for the reconstruction and abundance estimation of transcript sequences from high throughput RNA sequencing (“RNA...

The numbers of methane-oxidizing bacteria (methanotrophs) in the sediments of Lake Washington were estimated using three culture-independent methods. Quantitative slot-blot hybridizations were performed with type I and type II methanotroph-specific probes. These data were compared to data from quantitative hybridizations using a pmoA-specific probe and a eubacterial probe. From the combined hyb...

More than two decades of intensive ecological research in the Antarctic have refined the oversimplistic view of "the Antarctic ecosystem" towards identification and investigation of a number of different subsystems. Within the pack-ice zone of the Weddell Sea (Atlantic sector of the Antarctic Ocean), a summer pelagic system breaks up into ice-bound and deep-living systems in winter. Furthermore...

DNA sequencing data is typically a large collection of short strings called reads. We can summarize such data by computing a histogram of the number of occurrences of substrings of a fixed length. Such histograms can be used for example to estimate the size of a genome. In this paper, we study a recent tool, Kmerlight, which computes approximate histograms. We discover an approximation bias, an...

Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but con...

Since the inception of next-generation mRNA sequencing (RNA-Seq) technology, various attempts have been made to utilize RNA-Seq data in assembling full-length mRNA isoforms de novo and estimating abundance of isoforms. However, for genes with more than a few exons, the problem tends to be challenging and often involves identifiability issues in statistical modeling. We have developed a statisti...

Theatrical metaphors abound within the literature on nurse education and perhaps it is no accident that they do so. However much of the nursing literature implies that clinical learning involves the student in developing performance skills, and infers that this type of learning is inferior and superficial. This paper emerges from a discussion between the authors: a nurse educator, and an educat...

A new habitat-based model is developed to improve estimates of relative abundance of Pacific bigeye tuna (Thunnus obesus). The model provides estimates of ‘effective’ longline effort and therefore better estimates of catch-per-unit-of-effort (CPUE) by incorporating information on the variation in longline fishing depth and depth of bigeye tuna preferred habitat. The essential elements in the mo...