Physical Sciences and Mathematics Commons^™

Solar Eclipse Observation On May 21, 2012 From Jvla, Shaheda Begum Shaik

Theses

The annular solar eclipse occurred on May 21, 2012 is studied using the radio data from the Jansky Very Large Array (JVLA), Sorrocco, Mexico. The eclipse is observed in the solar minimum activity period of solar cycle 24. The centimeter wavelength observation of the Sun's surface during the solar eclipse helps in determining the spatially well resolved features not obtained by the man made advanced technology. Even though, the activity on the Sun is observed to be low in the period of eclipse, the study provides a good opportunity to understand the quiet Sun features in the regions occulted by …

Genome Wide Search For Pseudo Knotted Non-Coding Rnas, Meghana S. Vasavada

Theses

Non-coding RNAs (ncRNAs) are the functional RNA molecules that are involved in many biological processes including gene regulation, chromosome replication and RNA modification. Searching genomes using computational methods has become an important asset for prediction and annotation of ncRNAs. To annotate an individual genome for a specific family of ncRNAs, a computational tool is interpreted to scan through the genome and align its sequence segments to some structure model for the ncRNA family. With the recent advances in detecting an ncRNA in the genome, heuristic techniques are designed to perform an accurate search and sequence-structure alignment. This study uses a …

Rna-Sequence Analysis Of Human Melanoma Cells, Jharna Miya

Theses

RNA-sequencing refers to the use of high throughput sequencing technologies that are used to sequence cDNA in order to get the complete information of a sample’s RNA content. The objective of this study is to analyze this data in different aspects and to characterize gene expression. Besides this characterization, the data was also used to investigate the effect of sequencing depth on gene expression measurements.

This research focuses on quantitative measurement of expression levels of genes and their transcripts. In this study, complementary DNA fragments of cultured human melanoma cells are sequenced and a total of 139,501,106 million 200-bp reads …

Performance Comparison Of Five Rna-Seq Alignment Tools, Yuanpeng Lu

Theses

Aligning millions of short reads to a reference genome is a critical task in high throughput sequencing. In recent years, a large number of mapping algorithms have been developed, all of which have in common that they align a vast number of reads to genomic or transcriptomic sequences. RNA-Seq data is discrete in nature, therefore with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. To provide guidance in the choice of alignment algorithms, five different alignment tools for RNA-Seq data are evaluated. In order to compare the …

Polyaseeker: A Computational Framework For Identifying Polyadenylation Cleavage Site From Rna-Seq, Xiao Ling

Theses

Alternative polyadenylation (APA) of mRNA plays a crucial role for post-transcriptional gene regulation. Recently, advances in next generation sequencing technology have made it possible to efficiently characterize the transcriptome and identify the 3’end of polyadenylated RNAs. However, no comprehensive bioi nformatic pipelines have fulfilled this goal. The PolyASeeker, a computational framework for identifying polyadenylation cleavage sites from RNA-Seq data is proposed in this thesis. By using the simulated RNA-seq dataset, a novel method is developed to evaluate the performance of the proposed framework versus the traditional A-stretch approach, and compute accurate Precisions and Recalls that previous estimation could not get. …

Validation Of Solar Flare Forecasting & Evolution Of Magnetic Helicity Of Two Active Regions, Qin Li

Theses

This thesis includes two components: (1) Validation of the NJIT flare-forecasting model that was established in recent years is carried out based on the statistical correlation between solar magnetic parameters and flare productivity of active regions (ARs). 378 ARs are examined, comparing observation with prediction. It is found that the accuracy rate to some extent decreases with the level of flares. (2) The temporal evolution of the relative magnetic helicity of two ARs, AR 11072 and 11158 is investigated. The former is flare-quiet while the latter is flare-productive over the 5-day observation period. It is found that for both regions, …

A Gpu Program To Compute Snp-Snp Interactions In Genome-Wide Association Studies, Srividya Ramakrishnan

Theses

With the recent advances in the next generation sequencing technologies, short read sequences of human genome are made more accessible. Paired end sequencing of short reads is currently the most sensitive method for detecting somatic mutations that arise during tumor development. In this study, a novel approach to optimize the detection of structural variants using a new short read alignment program is presented.

Pairwise interaction effects of the Single Nucleotide Polymorphisms (SNPs) have proven to uncover the underlying complex disease traits. Computing the disease risk based on the interaction effects of SNPs on a case - control study is a …

New Economy : Assessment Of The Institutionalization Of An Emerging Paradigm And Academic Field Through Inquiry Into Prominent Boundary Organizations, Jeanine Cava Rodgers

Theses

It is increasingly acknowledged that in order to reach global and regional sustai nabi l ity goals, economic growth and consumption levels in wealthy developed nations will need to stabilize or reverse. Organizations and projects of a wide variety have emerged and expanded to take on this challenge, and shape the so-called, "new economy". The purpose of this research is to gain a clearer picture of the impacts of efforts to develop a shared new-economy knowledge framework on the broader sustai nabi l ity conversation, and to assess the intellectual institutionalization of same. This thesis focuses in on the influence …