Search results | J. Murrey Atkins Library

Title: Neural Network and Random Forest Based Eukaryotic Gene Prediction Methods
Author: Baker, Lonnie
Date Created: 2023
Subjects--Topical: Bioinformatics
Description: Gene prediction, a fundamental task in genomics, plays a pivotal role in decipheringthe functional elements of genomes. However, accurate gene prediction remains a challenging endeavor, especially when dealing with non-model organisms that often l...

Title: Topoisomerase II Inhibitors Induce an Illegitimate Genome Rearrangement Common in Infant Leukemia
Author: Bariar, Bhawana
Date Created: 2013
Subjects--Topical: Molecular biology
Description: Infant acute leukemias account for ~30% of all malignancy seen in childhood across the Western world. They are aggressive and characterized by rapid onset shortly after birth. The majority of these have rearrangements involving the MLL (mixed line...

Title: IDENTIFICATION OF EPITHELIAL OVARIAN TUMOR SPECIFIC APTAMERS THAT BIND AND INTERNALIZE INTO TARGET CELLS
Author: Benedetto, Gregory
Date Created: 2015
Subjects--Topical: Chemistry, Biology
Description: New clinical tools that aid in the early diagnosis of ovarian malignancies will significantly help reduce mortality and improve current long-term survival rates. The objective of the work presented here was to identify ovarian tumor specific singl...

Title: RECIPROCAL REGULATION OF MYC AND MICRORNA MIR-308 DURING DROSOPHILA EMBRYOGENESIS
Author: Daneshvar, Kaveh
Date Created: 2012
Subjects--Topical: Molecular biology, Biology, Genetics
Description: Myc is a conserved transcription factor with a role in the regulation of genes that are involved in growth and development. The abundance of Myc protein in the cells must be exquisitely controlled to avoid growth abnormalities caused by too much o...

Title: ESSENTIAL DYNAMICS OF PROTEINS USING GEOMETRICAL SIMULATIONS AND SUBSPACE ANALYSIS
Author: David, Charles
Date Created: 2012
Subjects--Topical: Physics, Bioinformatics, Biophysics
Description: Essential dynamics is the application of principal component analysis to a dynamic trajectory derived from a simulation protocol in order to extract biologically relevant information contained in the high dimensional data. In this work, we apply t...

Title: ALGORITHMS FOR STRUCTURE BASED-PREDICTION OF TRANSCRIPTION FACTOR BINDING SITES
Author: Farrel, Alvin
Date Created: 2016
Subjects--Topical: Computer science, Biology, Bioinformatics
Description: Transcription factors (TFs) regulate gene expression through binding to specific target DNA sites. Accurate annotation of transcription factor binding sites (TFBSs) at genome scale represents an essential step toward our understanding of gene regu...

Title: An Integrated Phylogeographic Analysis of the Bantu Migration
Author: Ford, Colby
Date Created: 2018
Subjects--Topical: Computer science, Mathematics, Genetics
Description: "Bantu" is a term used to describe lineages of people in around 600 different ethnic groups on the African continent ranging from modern-day Cameroon to South Africa. The migration of the Bantu people, which occurred around 3,000 years ago, was in...

Title: Studies on the relationships between oligonucleotide probe properties and hybridization signal intensities
Author: Gharaibeh, Raad
Date Created: 2009
Subjects--Topical: Computer science, Statistics, Bioinformatics
Description: Microarray technology is a commonly used tool in biomedical research for assessing global gene expression, surveying DNA sequence variations, and studying alternative gene splicing. Given the wide range of applications of this technology, comprehe...

Title: Integrative Network Approaches to Understanding MicroRNA and Gene Expressions in Cancer
Author: Hall, Benika
Date Created: 2017
Subjects--Topical: Computer science, Bioinformatics, Medical sciences
Description: Cancer is among the leading cause of deaths in men and women today. Regulation of gene expression by microRNAs (miRNA) has been linked to cancer progression in recent years. Therefore there has been a growing interest understanding how miRNAs medi...

Title: IMPROVEMENTS IN MICROBE RECOVERY AND DETECTION IN WATER SAMPLES: MULTIPLE APPROACHES TO METHOD OPTIMIZATION
Author: Kimble, Gina
Date Created: 2015
Subjects--Topical: Environmental engineering, Environmental sciences
Description: The accurate recovery and detection of microbes from water samples is important for the protection of public health. However, not all microbes behave similarly, not all water samples have comparable physical properties, and the constituents presen...

Title: Evolution and dynamics of transcriptional regulation in bacteria
Author: Li, Shan
Date Created: 2013
Subjects--Topical: Computer science, Statistics, Bioinformatics
Description: Although transcription is one of the most important biological functions of cells, our understanding of its regulation is still limited. In this dissertation, we have studied the transcriptional regulation in prokaryotes in three aspects. First, w...

Title: DATA ANALYSIS WORKFLOW FOR GAS CHROMATOGRAPHY MASS SPECTROMETRY-BASED METABOLOMICS STUDIES
Author: Ni, Yan
Date Created: 2014
Subjects--Topical: Bioinformatics
Description: Metabolomics has emerged as an integral part of systems biology research that attempts to comprehensively study low molecular weight organic and inorganic metabolites under certain conditions within a biological system. Technological advances in t...

Title: DE NOVO PREDICTION OF CIS-REGULATORY MODULES IN EUKARYOTIC ORGANISMS
Author: Niu, Meng
Date Created: 2014
Subjects--Topical: Bioinformatics
Description: Gene regulation networks (GRNs) are the bases for virtually all biological processes. To gain a global understanding of GRNs encoded in a genome, we first need to identify in all the cis-regulatory elements (CREs) recognized by transcription facto...

Title: Microarray tools and analysis methods to better characterize biological networks
Author: Overall, Christopher
Date Created: 2012
Subjects--Topical: Bioinformatics
Description: To accurately model a biological system (e.g. cell), we first need to characterize each of its distinct networks. While omics data has given us unprecedented insight into the structure and dynamics of these networks, the associated analysis routin...

Title: Development of Structural Informatics Method For Binding Peptides
Author: Patterson, John
Date Created: 2023
Subjects--Topical: Bioinformatics
Description: In the continuous pursuit of advanced therapeutics, the field of bioinformatics hasinnovated tools that allow unprecedented control over the proteome, profoundly shaping our understanding and manipulation of biological domains. Computational appro...

Title: Investigation and Analysis of Context Dependent Mutation Rates Contribution to Synonymous Mutation Codon Usage via Development of CDMAP.
Author: Patton, David
Date Created: 2022
Subjects--Topical: Bioinformatics, Molecular biology, Biometry
Description: Mutations play a pivotal role as a driver of genome evolution in organisms across the tree of life. However, site-specific mutation rates appear to have a non-uniform mutation rate and vary across the genome. Currently, site-specific variation has...

Title: UNDERSTANDING BIAS IN NEXT-GENERATION SEQUENCING TECHNOLOGIES AND ANALYSES
Author: Price, Adam
Date Created: 2017
Subjects--Topical: Biology, Bioinformatics, Biophysics
Description: The problem of bias resulting from biological and technological sources is one that must be consistently reexamined alongside the development of new technologies and methods of analysis. This dissertation addresses the complexities of bias identif...

Title: THE EFFECT OF TARGET SECONDARY STRUCTURE ON MICROARRAY DATA QUALITY
Author: Ratushna, Vladyslava
Date Created: 2010
Subjects--Topical: Bioinformatics, Biophysics
Description: DNA microarrays have become an invaluable high throughput biotechnology method, which allows a parallel investigation of thousands of cellular events in a single experiment. The principle behind the technology is very simple: fluorescently labeled...

Title: UNDERSTANDING GENOME-WIDE GENE REGULATION IN PROKARYOTES USING OMICS DATA
Author: Seyedi Tabari, Seyed Ehsan
Date Created: 2016
Subjects--Topical: Bioinformatics, Information science, Biometry
Description: Gene annotation is a critical step for understanding functions of genomes and host organisms. However, accurately annotating thousands of sequenced genomes can be a challenging task. Further, although gene transcriptional regulation is crucial for...

Title: The influence of wastewater treatment on community dynamics among antibiotic-resistant bacteria during treatment, stream release, and biosolids land application.
Author: Sorgen, Alicia
Date Created: 2020
Subjects--Topical: Microbiology, Bioinformatics, Ecology
Description: Wastewater treatment plants (WWTP) are a key link between anthropogenic activity and the environment, facilitating the development and horizontal transfer of antibiotic resistance among populations of commensal environmental microorganisms and cli...