Search results | J. Murrey Atkins Library

Title: A VISUAL ANALYTICS APPROACH TO FEATURE DISCOVERY AND SUBSPACE EXPLORATION IN PROTEIN FLEXIBILITY MATRICES
Author: Barlowe, Scott
Date Created: 2011
Subjects--Topical: Computer science, Bioinformatics
Description: The vast amount of information generated by domain scientists makes the transitionfrom data to knowledge difficult and often impedes important discoveries. Forexample, the knowledge gained from protein flexibility data sets can speed advancesin ge...

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: 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: 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: Assessment of Methods and Environmental Influence on the Nematostella Vectensis Microbiome
Author: Krueger, Quinton
Date Created: 2022
Subjects--Topical: Microbiology, Bioinformatics
Description: Cnidarians are a diverse clade of marine invertebrates that inhabit a variety of environments. The conditions of these habitats are becoming more extreme with the progression of time. These organisms associate with bacteria, which are composed of ...

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: Bioinformatics and biomolecular tools for biomarker discovery in peripheral blood lymphocytes from patients with Sporadic Amyotrophic Lateral Sclerosis
Author: Baciu, Cristina
Date Created: 2012
Subjects--Topical: Bioinformatics
Description: Sporadic Amyotrophic lateral sclerosis (sALS) is a complex, invariably fatal, disease with a poorly understood cause, despite many studies. Diagnostic biomarkers that precede active symptoms would be an immense help to clinicians, for patient mana...

Title: CHARACTERIZING NEXT-GENERATION SEQUENCING (NGS) PLATFORMS FOR MULTIPLEXED BIOSENSING AND APTAMER DISCOVERY: G-QUADRUPLEX APTAMERS AS A CASE STUDY
Author: Patil, Sushant
Date Created: 2016
Subjects--Topical: Molecular biology, Bioinformatics, Biochemistry
Description: Aptamers are single-stranded DNA or RNA molecules forming unique three dimensional structures that can bind to their targets (generally proteins or metabolites or other nucleic acids) with high specificity and affinity. Screening for aptamers requ...

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: 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: Data Mining the Serous Ovarian Tumor Transcriptome
Author: Tickle, Timothy
Date Created: 2011
Subjects--Topical: Bioinformatics, Genetics
Description: Ovarian cancer is the most lethal gynecologic cancer in the United States. If caught in early stages, patient survival rate is 94%, late stage survival rates drop to 28%. It is because most cases are caught in late stages that high mortality is se...

Title: De Novo Assemblies of Genomes of Four Indigenous Chickens and a White Eared Pheasant Reveal Genetic Basis of Chicken Domestication and Altitude Adaptation
Author: Wu, Siwen
Date Created: 2023
Subjects--Topical: Bioinformatics
Description: High-quality assembly and annotation of the genome of a species are critical in understanding the genetic basis of almost all aspects of the biology of the species. Although many genome assembly pipelines have been developed, they are either diffi...

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: 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: 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: 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: 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...