Search results | J. Murrey Atkins Library

Title: A virtual pebble game to emsemble average graph rigidity
Author: Gonzalez, Luis
Date Created: 2011
Subjects--Topical: Computer science, Bioinformatics
Description: Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently cal...

Title: APE2 is a Critical Regulator of the DNA Damage Response to Maintain Genome Integrity in Mammalian Cells
Author: HOSSAIN, MD AKRAM
Date Created: 2021
Subjects--Topical: Molecular biology, Biology, Cytology
Description: The maintenance of genome integrity and fidelity is essential for the proper function and survival of all organisms. Recent studies have revealed that APE2 is required for the activation of an ATR-Chk1 DNA damage response (DDR) pathway in response...

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: DO DYNAMIC ALLOSTERIC EFFECTS OCCUR IN IGG4 ANTIBODIES?
Author: Baker, Lonnie
Date Created: 2020
Subjects--Topical: Bioinformatics, Biophysics
Description: Antibodies are large, multi-chain proteins which play a critical roll in the func-tioning of vertebrate immune systems. Immune effector cells which are responsiblefor the destruction of foreign antigens do not randomly target molecules but rely on...

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: 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: ELUCIDATING THE EFFECTS OF MUTATION AND EVOLUTIONARY DIVERGENCE UPON PROTEIN STRUCTURE QUANTITATIVE STABILITY/FLEXIBILITY RELATIONSHIPS
Author: Verma, Deeptak
Date Created: 2012
Subjects--Topical: Bioinformatics
Description: The importance of flexibility and stability on protein function has been recognized for over five decades. A protein must be flexible enough to mediate a reaction pathway, yet rigid enough to achieve high fidelity in molecular recognition. To unde...

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: 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: Functional Dynamics in Beta-Lactamase: Insights into Substrate Recognition and Inhibition
Author: Avery, Christopher
Date Created: 2023
Subjects--Topical: Bioinformatics, Biophysics, Physics
Description: Beta-lactamase proteins are among the most prominent causes of antibiotic resistance. These enzymes confer resistance to beta lactam antibiotics, which are commonly used to treat bacterial infections. In recent years, novel beta-lactamase have eme...

Title: INVESTIGATING THE GENETIC BASIS OF GENE EXPRESSION USING EQTL TECHNIQUES
Author: Quitadamo, Andrew
Date Created: 2018
Subjects--Topical: Bioinformatics
Description: With advances in genome sequencing technology, datasets with large sample sizes can be generated relatively quickly and cheaply, especially compared to the past decade or so. We can utilize this data to analyze the associations between genetic var...

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: Investigating Multidrug Resistance in Escherichia coli with Phylogenetics and Machine Learning
Author: Brown, David
Date Created: 2023
Subjects--Topical: Bioinformatics, Biometry, Computer science
Description: The next pandemic is already underway in the proliferation of antimicrobial resistance(AMR) genes that reduce the effectiveness of therapeutics. The lessened potency of these current drugs results in increased economic costs, higher public health ...

Title: Investigating the Genetic Basis and Selection of Diverse Plant Specialized Metabolites in Wild Soybean, Glycine soja.
Author: Yasmin, Farida
Date Created: 2023
Subjects--Topical: Botany, Genetics, Biochemistry
Description: Plant-specialized metabolites, such as glyceollins and soyasaponins, play vital roles in adapting to dynamic environments and promoting human health. Glyceollins, induced phytoalexins derived from the isoflavonoid branch of the phenylpropanoid pat...

Title: Microbial Mutations - Accumulation in Microfluidics and Collateral Sensitivity
Author: Turner, Nathan
Date Created: 2023
Subjects--Topical: Bioinformatics
Description: Mutations are a primary source of genetic variation and a major driving force in evolution by influencing survivability (fitness), genetic disease, and the development of complex traits such as antibiotic resistance. However, studying the mutation...

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: QUANTITATIVE FALL RISK ASSESSMENT WITH WEARABLE SENSORS
Author: Xu, Zheng
Date Created: 2018
Subjects--Topical: Mechanical engineering, Biomechanics
Description: Falling has become one of the leading causes to both fatal and non-fatal injuries among the elder adults and patients with dysfunctional mobility. The following consequence of a fall will be that the fear of falling can reduce the daily activities...

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...