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: 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: 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: 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: On Compositionally Aware and Naïve Approaches to Normalization of 16S Microbiome Data
Author: Yerke, Aaron
Date Created: 2022
Subjects--Topical: Bioinformatics
Description: Compositional data refers to any data that represents parts of a whole, and DNA sequencing data is compositional in nature. This is due to the constraint on our current sequencing technologies that allow us to record a sample of the sequences rath...

Title: On Whole Genome Classifier Perforamnce in Relation to 16S Classifiers
Author: Johnson, James
Date Created: 2022
Subjects--Topical: Bioinformatics
Description: There is little consensus in the literature as to which approach for classification of Whole Genome Shotgun (WGS) sequences is most accurate unlike 16S classifiers that have had more time to mature. In this dissertation, two of the most popular cl...

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: Sequencing and annotation of diploid oat genomes and the investigation of Avena-specific nutrients
Author: Walstead, Rachel
Date Created: 2019
Subjects--Topical: Bioinformatics, Genetics, Botany
Description: Cultivated hexaploid oat (Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human ...

Title: Structural analysis of protein-DNA binding specificity and its application to protein-DNA docking assessment
Author: Corona de la Fuente, Rosario
Date Created: 2016
Subjects--Topical: Bioinformatics
Description: DNA-binding proteins are involved in essential biological processes including gene expression, DNA packaging and DNA repair. They bind to DNA target sequences with different degrees of binding specificity, ranging from highly specific to non-speci...

Title: The Microbiota Multiverse: From Gut to Brain and Beyond
Author: Brown, Matthew
Date Created: 2019
Subjects--Topical: Microbiology, Bioinformatics
Description: This work explores the microbiomes of diverse biological contexts with various stakeholders and collaborators. It consists of six objectives: the first two relate to interaction between the gut microbiome and host health, the second two investigat...

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: 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: Toward understanding protein-DNA interactions
Author: Lin, Maoxuan
Date Created: 2020
Subjects--Topical: Biology, Bioinformatics, Biochemistry
Description: Knowledge of protein-DNA interactions has important implications in understandingbiological activities and developing therapeutic drugs. Two types of protein-DNAinteractions exist: (1) interactions between double-stranded DNA-binding proteins(DSBs...

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: 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: 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...