Search results
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Title
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A virtual pebble game to emsemble average graph rigidity
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Author
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Gonzalez, Luis
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Date Created
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2011
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Subjects--Topical
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Computer science, Bioinformatics
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Description
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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...
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Title
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DE NOVO PREDICTION OF CIS-REGULATORY MODULES IN EUKARYOTIC ORGANISMS
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Author
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Niu, Meng
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Date Created
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2014
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Subjects--Topical
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Bioinformatics
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Description
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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...
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Title
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DO DYNAMIC ALLOSTERIC EFFECTS OCCUR IN IGG4 ANTIBODIES?
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Author
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Baker, Lonnie
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Date Created
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2020
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Subjects--Topical
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Bioinformatics, Biophysics
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Description
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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...
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Title
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Development of Structural Informatics Method For Binding Peptides
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Author
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Patterson, John
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Date Created
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2023
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Subjects--Topical
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Bioinformatics
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Description
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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...
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Title
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ELUCIDATING FUNCTIONAL MECHANISMS IN PROTEINS USING THE DISTANCE CONSTRAINT MODEL
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Author
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Singer, Christopher
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Date Created
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2019
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Subjects--Topical
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Bioinformatics, Biophysics, Physics
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Description
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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 ...
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Title
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Evolution and dynamics of transcriptional regulation in bacteria
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Author
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Li, Shan
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Date Created
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2013
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Subjects--Topical
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Computer science, Statistics, Bioinformatics
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Description
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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...
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Title
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Functional Analysis of Structural Variation in the 2D and 3D Human Genome
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Author
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Nodzak, Conor
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Date Created
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2019
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Subjects--Topical
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Bioinformatics, Genetics
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Description
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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...
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Title
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Functional Dynamics in Beta-Lactamase: Insights into Substrate Recognition and Inhibition
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Author
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Avery, Christopher
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Date Created
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2023
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Subjects--Topical
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Bioinformatics, Biophysics, Physics
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Description
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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...
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Title
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INVESTIGATING THE GENETIC BASIS OF GENE EXPRESSION USING EQTL TECHNIQUES
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Author
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Quitadamo, Andrew
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Date Created
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2018
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Subjects--Topical
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Bioinformatics
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Description
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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...
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Title
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Integrative Network Approaches to Understanding MicroRNA and Gene Expressions in Cancer
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Author
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Hall, Benika
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Date Created
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2017
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Subjects--Topical
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Computer science, Bioinformatics, Medical sciences
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Description
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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...
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Title
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Microbial Mutations - Accumulation in Microfluidics and Collateral Sensitivity
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Author
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Turner, Nathan
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Date Created
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2023
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Subjects--Topical
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Bioinformatics
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Description
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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...
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Title
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Neural Network and Random Forest Based Eukaryotic Gene Prediction Methods
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Author
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Baker, Lonnie
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Date Created
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2023
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Subjects--Topical
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Bioinformatics
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Description
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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...
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Title
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QUANTITATIVE FALL RISK ASSESSMENT WITH WEARABLE SENSORS
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Author
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Xu, Zheng
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Date Created
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2018
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Subjects--Topical
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Mechanical engineering, Biomechanics
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Description
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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...
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Title
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UNDERSTANDING GENOME-WIDE GENE REGULATION IN PROKARYOTES USING OMICS DATA
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Author
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Seyedi Tabari, Seyed Ehsan
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Date Created
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2016
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Subjects--Topical
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Bioinformatics, Information science, Biometry
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Description
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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...
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Title
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Understanding gene transcriptional regulation at single cell resolution
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Author
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Xu, Chen
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Date Created
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2015
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Subjects--Topical
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Bioinformatics
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Description
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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...