Search results | J. Murrey Atkins Library

Title: Prediction of Cis-regulatory Modules in Genomes
Author: Ni, Pengyu
Date Created: 2020
Subjects--Topical: Bioinformatics
Description: Annotating all cis-regulatory modules (CRMs) and constituent transcription factor (TF) binding sites (TFBSs) in genomes is essential to understand genome functions, however, the task remains highly challenging. In this dissertation, we first devel...

Title: COMPARATIVE ANALYSIS OF REPEAT LANDSCAPES IN AVENA (OAT)
Author: Burkes, Shelvasha
Date Created: 2020
Subjects--Topical: Biology, Bioinformatics, Botany
Description: Avena sativa, or common oat, is a staple crop and member of the Poaceae or Grass family. Following behind wheat, maize and rice, oats account for 10.5 million hectares of the world’s produced crops as of 2017. Phytocompounds such as β-glucan, aven...

Title: Arboviruses: The hidden path of an imminent threat
Author: de Bernardi Schneider, Adriano
Date Created: 2018
Subjects--Topical: Virology, Bioinformatics, Epidemiology
Description: Arboviruses are a grade of viruses carried by arthropods, which have been in the headlines due to recent epidemics. Members of this grade are the families Flaviviridae which includes Zika (ZIKV), Dengue (DENV), Yellow Fever (YFV), among other viru...

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: Assessments of Indel Annotation Programs and Comparative Somatic Indel Analysis in Cancer Genomes
Author: Chen, Jing
Date Created: 2020
Subjects--Topical: Bioinformatics
Description: Insertions and deletions (indels) represent the second largest variation type in human genomes and have been implicated in the development of cancer. Accurate indel annotation is of paramount importance in variants analysis in both healthy and dis...

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: ELUCIDATING FUNCTIONAL MECHANISMS IN PROTEINS USING THE DISTANCE CONSTRAINT MODEL
Author: Singer, Christopher
Date Created: 2019
Subjects--Topical: Bioinformatics, Biophysics, Physics
Description: Protein thermodynamics has been shown to be insightful and illuminating to the functional mechanisms behind biological function. By characterizing proteins and protein families according to their enthalpy and entropy we can make inferences to the ...

Title: Echinoderm Transcriptomics
Author: Linchangco, Gregorio
Date Created: 2018
Subjects--Topical: Bioinformatics
Description: Tissue regeneration and biomineralization are expressed to a diverse extent across metazoans and their life stages. The potential for repair and regrowth in adult stages varies widely within phyla, class and species. For instance, few adult human ...

Title: Functional Analysis of Structural Variation in the 2D and 3D Human Genome
Author: Nodzak, Conor
Date Created: 2019
Subjects--Topical: Bioinformatics, Genetics
Description: The human genome consists of over 3 billion nucleotides that have an average distance of 3.4 Angstroms between each base, which equates to over two meters of DNA contained within the 125 $\mu m^3$ volume diploid cell nuclei. The dense compaction o...

Title: Hydrogen bond energy-based comparative analysis of protein-ligand interactions and similarity assessment of protein-DNA complex models
Author: Malik, Fareeha
Date Created: 2022
Subjects--Topical: Bioinformatics, Computer science
Description: Hydrogen bonds play a vital role in protein-DNA interactions. In particular, side chain-base hydrogen bonds are crucial to the binding specificity between protein and DNA. Mutations effecting interface hydrogen bonds in protein-DNA complexes have ...

Title: GENETIC MECHANISMS OF OZONE TOLERANCE IN SOYBEAN AND METHODS OF EVOLUTIONARY DISTANCE
Author: Whaley, Adam
Date Created: 2015
Subjects--Topical: Bioinformatics, Genetics
Description: At ground level, ozone is a pollutant that poses serious risk to both human health and crop yields. In addition to being a vital economic crop in the US and abroad, conventional soybean lines are susceptible to damage caused by ozone exposure. In ...

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: Elucidation of miRNAs in Avena sativa
Author: Sheridan, Jaime
Date Created: 2014
Subjects--Topical: Bioinformatics, Agriculture
Description: Micro RNAs (miRNAs) are a class of small non-coding RNAs with post-transcriptional gene regulation responsibilities. In plants, miRNAs regulate development of leaves, roots, shoots, and flowers through targeting families of transcription factors a...

Title: New Algorithms for Protein Structure Analysis: From Nonparametric Density Estimation to Characterization of Molecular Volume Spatial Distributions
Author: Farmer, Jenny
Date Created: 2018
Subjects--Topical: Bioinformatics, Biophysics, Physics
Description: The Flexibility and Stability Test (FAST) is a C++ class library designed in the early 2000’s to execute free energy decomposition and reconstitution operations applied to protein structures. The library has been substantially expanded to include ...

Title: Nutritive Knowledge Based Discovery: Enhancing Precision Nutrition Hypothesis Generation
Author: Trautman, Aaron
Date Created: 2022
Subjects--Topical: Bioinformatics, Nutrition, Information science
Description: Diet-related diseases like obesity and type-2 diabetes are on the rise. Precision nutrition, a way to tailor dietary requirements for each individual, is heralded as a solution to these problems. However, nutritional research is held within sparse...

Title: Next-Generation Sequencing Based Quantification of Microbial Communities and Gene Pathways
Author: Jones, Roshonda
Date Created: 2016
Subjects--Topical: Bioinformatics
Description: Humans act as a host to trillions of microorganisms. The collective of these microorganisms is called a host’s microbiota. There is a growing interest in the bacterial composition of the gut microbiome of humans (structure) and the role of the mic...

Title: The Semantics of Diet and Health: Knowledge Based Discovery Through Data Integration, Text Mining, and Network Analysis
Author: Linchangco, Richard
Date Created: 2018
Subjects--Topical: Bioinformatics
Description: Consumption of fruits and vegetables has been linked to a reduced risk of cancer and other chronic diseases, but the molecular mechanisms supporting these connections remain largely unknown. A wealth of association data linking components of a pla...

Title: Understanding gene transcriptional regulation at single cell resolution
Author: Xu, Chen
Date Created: 2015
Subjects--Topical: Bioinformatics
Description: The recent advance of single-cell technologies has provided an unprecedented opportunity to bring new insights into many complex biological phenomena, such as the regulation of cell differentiation in a multi-cellular organism and cell-to-cell var...

Title: The evolution of flavonoid pathway in legumes
Author: Safari, Sajedeh
Date Created: 2016
Subjects--Topical: Bioinformatics
Description: Considering the ever growing world population as well as climate change, it has become essential to improve crops in order to reach higher yields, more tolerance to pests and droughts, and better adaptation to different environments. The advanceme...

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...