Bioinformatics Commons^™

Alcohol Biomarkers As Predictive Factors Of Rearrest In High Risk Repeat Offense Drunk Drivers, Brian Charles Kay

Theses and Dissertations

Alcohol biomarkers, or naturally occurring molecules which occur in response to one's alcohol consumption, are proving to be a value tool in objectively monitoring one's alcohol consumption. Coupling this assessment tool, with advances in computing power, new and powerful predictions are becoming evermore possible. In this retrospective study, data was first collected that consisted of a sample of 249 drivers convicted of driving under the influence charge and who monitored over the course of a year by biomarker blood tests. This data was then analyzed using machine learning methods. TwoStep cluster analysis showed distinct drinking groups within the drivers who …

Rna-Sequencing Applications: Gene Expression Quantification And Methylator Phenotype Identification, Guoshuai Cai

Dissertations & Theses (Open Access)

My dissertation focuses on two aspects of RNA sequencing technology. The first is the methodology for modeling the overdispersion inherent in RNA-seq data for differential expression analysis. This aspect is addressed in three sections. The second aspect is the application of RNA-seq data to identify the CpG island methylator phenotype (CIMP) by integrating datasets of mRNA expression level and DNA methylation status.

Section 1: The cost of DNA sequencing has reduced dramatically in the past decade. Consequently, genomic research increasingly depends on sequencing technology. However it remains elusive how the sequencing capacity influences the accuracy of mRNA expression measurement. We …

Single-Nucleotide Polymorphisms Associated With Performance Traits In Beef Cattle Grazing Endophyte-Infected Tall Fescue, Bryan Christopher Bastin

Masters Theses

Tall fescue (Lolium arundinaceum Schreb.) is the most prevalent forage in the Midsouth United States due in part to the presence of the endophytic fungus Neotyphodium coenophialum. The fungus, while conferring hardiness to tall fescue, contributes to decreased production efficiency in cow-calf operations. A previous genome-wide association study was performed using the Illumina 50k bovine SNP chip. Twenty-four SNP were found to be associated (P < 0.05) with adjusted birth weight and adjusted 205-day weights of calves from 48 beef cows at Ames Plantation. The first objective was to validate each SNP by testing associations with several additional phenotypes. Custom Taqman genotyping assays (Applied Biosystems, Foster City, CA) were subsequently designed to genotype each SNP in beef cattle located at Tennessee Tech University (n = 654), to validate associations in a large, independent herd. The results yielded 15 associations that were significant (P < 0.05) with 6 phenotypes linked to those affected by fescue toxicosis. The second objective investigated the link between fescue toxicosis and the XK, Kell blood group complex subunit-related, member 4 …

Sequence Analysis Of The Genome Of Piscine Orthoreovirus (Prv) Associated With Heart And Skeletal Muscle Inflammation (Hsmi) In Atlantic Salmon (Salmo Salar), Torstein Tengs Dr.

Dr. Torstein Tengs

Piscine orthoreovirus (PRV) is associated with heart- and skeletal muscle inflammation (HSMI) of farmed Atlantic salmon (Salmo salar). We have performed detailed sequence analysis of the PRV genome with focus on putative encoded proteins, compared with prototype strains from mammalian (MRV T3D)- and avian orthoreoviruses (ARV-138), and aquareovirus (GCRV-873). Amino acid identities were low for most gene segments but detailed sequence analysis showed that many protein motifs or key amino acid residues known to be central to protein function are conserved for most PRV proteins. For M-class proteins this included a proline residue in μ2 which, for MRV, has been …

Array-Based Genomic Diversity Measures Portray Mus Musculus Phylogenetic And Genealogical Relationships, And Detect Genetic Variation Among C57bl/6j Mice And Between Tissues Of The Same Mouse, Susan T. Eitutis

Electronic Thesis and Dissertation Repository

Mouse models lack affordable genomic technologies slowing the identification of candidate variants contributing to complex phenotypes. The Mouse Diversity Genotyping Array (MDGA) is a low cost, high-resolution platform permitting genomic diversity assessment. Using a validated list of >500,000 single nucleotide polymorphisms (SNPs), we applied the first comprehensive analysis of SNP differences to detect genetic distance across 362 Mus musculus samples. Genetic distance measured between distantly and closely related mice correlates with known phylogeny and genealogy. Variation detected between C57BL/6J mice is consistent with previous reports of variants within this strain. Putative genetic variation detected between and within tissues indicates somatic …

Bioinformatics Analyses Of Chromium Tolerant Genes In Cyanobacteria And Identification Of Their Operon In Synechococcus Sp. Iu 625, Lee Lee, Richard Garrett, Anna Slusarczyk, Jose Perez, Tin-Chun Chu

Tin-Chun Chu, Ph.D.

No abstract provided.

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

George K. Thiruvathukal

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we …

Identification Of Cyclophilin Gene Family In Soybean And Characterization Of Gmcyp1, Hemanta Raj Mainali

Electronic Thesis and Dissertation Repository

I identified members of the Cyclophilin (CYP) gene family in soybean (Glycine max) and characterized the GmCYP1, one of the members of soybean CYP. CYPs belong to the immunophilin superfamily with peptidyl-prolyl cis-trans isomerase (PPIase) activity. PPIase catalyzes the interconversion of the cis- and trans-rotamers of the peptidyl-prolyl amide bond of peptides. After extensive data mining, I identified 62 different CYP genes in soybean (GmCYP1 to GmCYP62), of which 8 are multi-domain proteins and 54 are single domain proteins. At least 25% of the GmCYP genes are expressed in soybean. GmCYP1 …

A Mathematical Model And Numerical Method For Thermoelectric Dna Sequencing, Liwei Shi

Doctoral Dissertations

DNA sequencing is the process of determining the precise order of nucleotide bases, adenine, guanine, cytosine, and thymine within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases in a strand of DNA. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Thermoelectric DNA sequencing is a novel method to sequence DNA by measuring the heat that is released when DNA polymerase inserts a deoxyribonucleoside triphosphate into a growing DNA strand. The thermoelectric device for this project is composed of four parts: …

From Questions To Effective Answers: On The Utility Of Knowledge-Driven Querying Systems For Life Sciences Data, Amir H. Asiaee, Prashant Doshi, Todd Minning, Satya S. Sahoo, Priti Parikh, Amit P. Sheth, Rick L. Tarleton

Kno.e.sis Publications

We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and provides intuitive form-based interfaces to facilitate querying of the data, commonly used by the life science researchers that we study. The second approach utilizes a large OWL ontology and the same datasets associated as RDF instances of the ontology. Both approaches are being used in parallel by a team of cell biologists in their daily research activities, with the objective of gradually replacing the conventional approach with the knowledge-driven one. We describe several benefits …

Genetic Approaches To Studying Complex Human Disease, Joseph B. Dube

Electronic Thesis and Dissertation Repository

Common, complex diseases such as cardiovascular disease (CVD) represent an intricate interaction between environmental and genetic factors and now account for the leading causes of mortality in western society. By investigating the genetic component of complex disease etiology, we have gained a better understanding of the biological pathways underlying complex disease and the heterogeneity of complex disease risk. However, the development of high throughput genomic technologies and large well-phenotyped multi-ethnic cohorts has opened the door towards more in-depth and trans-disciplinary approaches to studying the genetics of complex disease pathogenesis. Accordingly, we sought to investigate select complex traits and diseases using …

Crisis Response Coordination In Online Communities, Hemant Purohit

Kno.e.sis Publications

During recent crises, citizens (sensors) are increasingly using social media to share variety of information- situation on the ground, emerging needs, donation offers, damage, etc. In such an evolving ad-hoc community, how can we extract actionable nuggets from the social media streams to aid relief efforts? This doctoral consortium presentation summarizes a framework to analyze social data and manage information to assist coordination by focusing on three important questions to answer: Whom to coordinate with, Why to coordinate and How to coordinate, with exemplary insights for needs and availability from the recent disaster events.

Demo: Approximate Semantic Matching In The Collider Event Processing Engine, Souleiman Hasan, Kalpa Gunaratna, Yongrui Qin, Edward Curry

Kno.e.sis Publications

This demo presents a use case from the energy management domain. It builds upon previous work on approximate semantic matching of heterogeneous events and compares two semantic matching scenarios: exact and approximate. It illustrates how a large number of exact matching event subscriptions are needed to match heterogeneous power consumption events. It then demonstrates how a small number of approximate semantic matching subscriptions are needed but possibly with a lower true positives/negatives performance. The demo is delivered via the COLLIDER approximate event processing engine currently under development in DERI.

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. …

Assessing Methods For Assigning Snps To Genes In Gene-Based Tests Of Association Using Common Variants, Ashley Petersen, Carolina Alvarez, Scott Declaire, Nathan L. Tintle

Faculty Work Comprehensive List

Gene-based tests of association are frequently applied to common SNPs (MAF>5%) as an alternative to single-marker tests. In this analysis we conduct a variety of simulation studies applied to five popular gene-based tests investigating general trends related to their performance in realistic situations. In particular, we focus on the impact of non-causal SNPs and a variety of LD structures on the behavior of these tests. Ultimately, we find that non-causal SNPs can significantly impact the power of all gene-based tests. On average, we find that the “noise” from 6–12 non-causal SNPs will cancel out the “signal” of one causal …

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 …

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 …

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 …

Investigating Potential Target Genes Of The Rfx Transcription Factor Daf-19 In Caenorhabditis Elegans, He Zhang

Lawrence University Honors Projects

Neurodegenerative diseases, such as Alzheimer’s disease, are characterized by an age-related decrease in the synaptic activity of the patient’s brain. Previous research suggested that a RFX transcription factor DAF-19 in the nematode Caenorhabditis elegans (C. elegans) may be involved in the maintenance of synaptic protein levels. Particularly, worms that were DAF-19A/B defective showed reduced synaptic activities when compared to their age-matched controls.

This study investigated the role of DAF-19A/B isoforms in the C. elegans nervous system. Three genes, F46G11.3, F57B10.9, and F58E2.3 were selected as potential downstream targets of DAF-19A/B based on their potential neuronal expression. …