Computer Engineering Commons^™

Novel Bioinformatic Approaches For Analyzing Next-Generation Sequencing Data, Yan Peng

Dissertations

In general, DNA reconstruction is deemed as the key of molecular biology since it makes people realize how genotype affects phenotypes. The DNA sequencing technology emerged exactly towards this and has greatly promoted molecular biology’s development. The traditional method, "Sanger," is effective but extremely expensive on a cost-per-base basis. This shortcoming of Sanger method leads to the rapid development of next-generation sequencing technologies. The NGS technologies are widely used by virtue of their low-cost, high-throughput, and fast nature. However, they still face major drawbacks such as huge amounts of data as well as relatively short read length compared with traditional …

Inferring Gene Regulatory Networks From Time Series Microarray Data, Peng Li

Dissertations

The innovations and improvements in high-throughput genomic technologies, such as DNA microarray, make it possible for biologists to simultaneously measure dependencies and regulations among genes on a genome-wide scale and provide us genetic information. An important objective of the functional genomics is to understand the controlling mechanism of the expression of these genes and encode the knowledge into gene regulatory network (GRN). To achieve this, computational and statistical algorithms are especially needed.

Inference of GRN is a very challenging task for computational biologists because the degree of freedom of the parameters is redundant. Various computational approaches have been proposed for …