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Assessments of Indel Annotation Programs and Comparative Somatic Indel Analysis in Cancer Genomes
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...
THE ROLE OF XRCC1 AND POLYMERASE BETA IN GENOME INTEGRITY IN XENOPUS EGG EXTRACTS
Title
THE ROLE OF XRCC1 AND POLYMERASE BETA IN GENOME INTEGRITY IN XENOPUS EGG EXTRACTS
Author
Cupello, Steven
Date Created
2019
Subjects--Topical
Molecular biology, Biology, Cytology
Description
Cells of organisms are constantly exposed to genomic insults such as oxidative stress from endogenous sources or environmental agents. Oxidative stress induces oxidative DNA damage such as apurinic/apyrimidinic (AP) sites, single-strand breaks (SS...
Next-Generation Sequencing Based Quantification of Microbial Communities and Gene Pathways
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...
Evolution and dynamics of transcriptional regulation in bacteria
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...
Prediction of Cis-regulatory Modules in Genomes
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...
USING BIOINFORMATICS TO ANALYZE THE ROLE OF MICROBIAL TAXA IN COMPLEX ECOSYSTEMS
Title
USING BIOINFORMATICS TO ANALYZE THE ROLE OF MICROBIAL TAXA IN COMPLEX ECOSYSTEMS
Author
Sanapareddy, Nina
Date Created
2011
Subjects--Topical
Medicine, Bioinformatics, Information technology
Description
Microbes are abundant on earth and play a crucial role in the environment they inhabit. Before the dawn of metagenomics, the study of the effect of microorganisms on their environment was limited due to use of low throughput techniques that could ...
High Order H(div) Discontinuous Galerkin Methods for MHD Equations
Title
High Order H(div) Discontinuous Galerkin Methods for MHD Equations
Author
Wu, Jian
Date Created
2016
Subjects--Topical
Mathematics
Description
In this dissertation, we investigate the divergence-free discontinuous Galerkin method using the $\mathcal{H}$(\textbf{div}) basis, to solve the nonlinear ideal magnetohydrodynamics (MHD) equations. This is a novel approach to ensure the divergenc...
On Compositionally Aware and Naïve Approaches to Normalization of 16S Microbiome Data
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...