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Relevant bibliographies by topics / Genomics; DNA sequencing; Bioinformatics / Dissertations / Theses

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Dissertations / Theses on the topic 'Genomics; DNA sequencing; Bioinformatics'

Author: Grafiati

Published: 4 June 2021

Last updated: 12 February 2022

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1

Jones, Steven John Mathias. "Computational analysis of the Caenorhabditis elegans genome sequence." Thesis, Open University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301886.

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Klevebring, Daniel. "On Transcriptome Sequencing." Doctoral thesis, KTH, Genteknologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-11446.

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This thesis is about the use of massive DNA sequencing to investigate the transcriptome. During recent decades, several studies have made it clear that the transcriptome comprises a more complex set of biochemical machinery than was previously believed. The majority of the genome can be expressed as transcripts; and overlapping and antisense transcription is widespread. New technologies for the interroga- tion of nucleic acids have made it possible to investigate such cellular phenomena in much greater detail than ever before. For each application, special requirements need to be met. The work

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3

Bhasin, Jeffrey M. "Methylome Sequencing Reveals the Context-Specific Functions of DNA Methylation in Indolent Versus Aggressive Prostate Cancer." Case Western Reserve University School of Graduate Studies / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=case148120498969955.

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Zhuang, Jiali. "Structural Variation Discovery and Genotyping from Whole Genome Sequencing: Methodology and Applications: A Dissertation." eScholarship@UMMS, 2009. http://escholarship.umassmed.edu/gsbs_diss/875.

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A comprehensive understanding about how genetic variants and mutations contribute to phenotypic variations and alterations entails experimental technologies and analytical methodologies that are able to detect genetic variants/mutations from various biological samples in a timely and accurate manner. High-throughput sequencing technology represents the latest achievement in a series of efforts to facilitate genetic variants discovery and genotyping and promises to transform the way we tackle healthcare and biomedical problems. The tremendous amount of data generated by this new technology, how

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5

Zhuang, Jiali. "Structural Variation Discovery and Genotyping from Whole Genome Sequencing: Methodology and Applications: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/875.

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A comprehensive understanding about how genetic variants and mutations contribute to phenotypic variations and alterations entails experimental technologies and analytical methodologies that are able to detect genetic variants/mutations from various biological samples in a timely and accurate manner. High-throughput sequencing technology represents the latest achievement in a series of efforts to facilitate genetic variants discovery and genotyping and promises to transform the way we tackle healthcare and biomedical problems. The tremendous amount of data generated by this new technology, how

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Clarke, Andrew, Stefan Prost, Jo-Ann Stanton, et al. "From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes." BioMed Central, 2014. http://hdl.handle.net/10150/610024.

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BACKGROUND:Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users.RESULTS:Here we present an 'A to Z' protocol for obtaining comp

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Martinez, Juan Carlos. "Towards the Prediction of Mutations in Genomic Sequences." FIU Digital Commons, 2013. http://digitalcommons.fiu.edu/etd/987.

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Bio-systems are inherently complex information processing systems. Furthermore, physiological complexities of biological systems limit the formation of a hypothesis in terms of behavior and the ability to test hypothesis. More importantly the identification and classification of mutation in patients are centric topics in today’s cancer research. Next generation sequencing (NGS) technologies can provide genome-wide coverage at a single nucleotide resolution and at reasonable speed and cost. The unprecedented molecular characterization provided by NGS offers the potential for an individualized a

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Oikonomopoulos, Spyridon. "Inferring structural properties of protein-DNA binding using high-throughput sequencing : the paradigm of GATA1, KLF1 and their complexes GATA1/FOG1 and GATA1/KLF1 : insights into the transcriptional regulation of the erythroid cell lineage." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:72b92906-4ef6-4c1d-9155-484521027e2e.

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GATA1 and KLF1 are transcription factors that regulate genes which are important for the development of erythroid cells. The GATA1 transcriptional co-factor FOG1 has been shown to be essential in a wide range of GATA1 dependent cellular functions. Here we tried to understand the diverse mechanisms by which GATA1 and KLF1 recognize their binding sites, how the GATA1 recognition mechanisms are affected by complexation with either FOG1 or KLF1 and how the GATA1 recognition mechanisms affect the transcriptional regulation of the erythroid differentiation. We profiled the DNA binding specificities/

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Delhomme, Tiffany. "Using the systematic nature of errors in NGS data to efficiently detect mutations : computational methods and application to early cancer detection." Thesis, Lyon, 2019. http://www.theses.fr/2019LYSE1098/document.

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La caractérisation exaustive des variations de l'ADN peut aider à progresser dans de nombreux champs liés à la génomique du cancer. Le séquençage nouvelle génération (NGS en anglais pour Next Generation Sequencing) est actuellement la technique la plus efficace pour déterminer une séquence ADN, du aux faibles coûts et durées des expériences comparé à la méthode de séquençage traditionnelle de Sanger. Cependant, la détection de mutations à partir de données NGS reste encore un problème difficile, en particulier pour les mutations somatiques présentes en très faible abondance comme lorsque l'on

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10

Roy, Christian K. "Putting the Pieces Together: Exons and piRNAs: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/726.

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Analysis of gene expression has undergone a technological revolution. What was impossible 6 years ago is now routine. High-throughput DNA sequencing machines capable of generating hundreds of millions of reads allow, indeed force, a major revision toward the study of the genome’s functional output—the transcriptome. This thesis examines the history of DNA sequencing, measurement of gene expression by sequencing, isoform complexity driven by alternative splicing and mammalian piRNA precursor biogenesis. Examination of these topics is framed around development of a novel RNA-templated DNA-DNA li

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Roy, Christian K. "Putting the Pieces Together: Exons and piRNAs: A Dissertation." eScholarship@UMMS, 2005. http://escholarship.umassmed.edu/gsbs_diss/726.

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Analysis of gene expression has undergone a technological revolution. What was impossible 6 years ago is now routine. High-throughput DNA sequencing machines capable of generating hundreds of millions of reads allow, indeed force, a major revision toward the study of the genome’s functional output—the transcriptome. This thesis examines the history of DNA sequencing, measurement of gene expression by sequencing, isoform complexity driven by alternative splicing and mammalian piRNA precursor biogenesis. Examination of these topics is framed around development of a novel RNA-templated DNA-DNA li

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12

Quinlan, Aaron Ryan. "Discovery and interpretation of genetic variation with next‐generation sequencing technologies." Thesis, Boston College, 2008. http://hdl.handle.net/2345/32.

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Thesis advisor: Gabor T. Marth<br>Improvements in molecular and computational technologies have driven and will continue to drive advances in our understanding of genetic variation and its relationship to phenotypic diversity. Over the last three years, several new DNA sequencing technologies have been developed that greatly improve upon the cost and throughput of the capillary DNA sequencing technologies that were used to sequence the first human genome. The economy of these so‐called “next‐generation” technologies has enabled researchers to conduct genome‐wide studies in genetic variation th

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Fritz, Markus Hsi-Yang. "Exploiting high throughput DNA sequencing data for genomic analysis." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610819.

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Highnam, Gareth Wei An. "Optimizing analysis pipelines for improved variant discovery." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/47451.

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Sigurgeirsson, Benjamín. "Analysis of RNA and DNA sequencing data : Improved bioinformatics applications." Doctoral thesis, KTH, Genteknologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-184158.

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Massively parallel sequencing has rapidly revolutionized DNA and RNA research. Sample preparations are steadfastly advancing, sequencing costs have plummeted and throughput is ever growing. This progress has resulted in exponential growth in data generation with a corresponding demand for bioinformatic solutions. This thesis addresses methodological aspects of this sequencing revolution and applies it to selected biological topics. Papers I and II are technical in nature and concern sample preparation and data anal- ysis of RNA sequencing data. Paper I is focused on RNA degradation and paper I

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Rose, B. A. (Beverley Ann). "The characterisation and partial sequencing of the grapevine chloroplast genome." Thesis, Stellenbosch : Stellenbosch University, 2004. http://hdl.handle.net/10019.1/53763.

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Thesis (MSc)--University of Stellenbosch, 2004.<br>ENGLISH ABSTRACT: A number of proteins essential for the survival of a plant are encoded by the chloroplast genome. The characterization and sequencing of a number of algal and plant chloroplast genomes has facilitated researchers understanding of cellular functions and metabolism. Chloroplast DNA (cpDNA) has also been used to determine inter- and intraspecies evolutionary relationships and this organelle offers an alternative means of expressing foreign genes. Although a number of species' chloroplast genomes have been characterized and

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Ye, Lin, and 叶林. "Exploring microbial community structures and functions of activated sludge by high-throughput sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B48079649.

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To investigate the diversities and abundances of nitrifiers and to apply the highthroughput sequencing technologies to analyze the overall microbial community structures and functions in the wastewater treatment bioreactors were the major objectives of this study. Specifically, this study was conducted: (1) to investigate the diversities and abundances of AOA, AOB and NOB in bioreactors, (2) to explore the bacterial communities in bioreactors using 454 pyrosequencing, and (3) to analyze the metagenomes of activated sludge using Illumina sequencing. A lab-scale nitrification bioreactor

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Hershman, Steven Gregory. "Personal Genomics and Mitochondrial Disease." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10863.

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Mitochondrial diseases involving dysfunction of the respiratory chain are the most common inborn errors of metabolism. Mitochondria are found in all cell types besides red blood cells; consequently, patients can present with any symptom in any organ at any age. These diseases are genetically heterogeneous, and exhibit maternal, autosomal dominant, autosomal recessive and X-linked modes of inheritance. Historically, clinical genetic evaluation of mitochondrial disease has been limited to sequencing of the mitochondrial DNA (mtDNA) or several candidate genes. As human genome sequencing trans

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Smiley, Shawn Johnston. "Sequence Extension of the Tryptophan and Shikimate Operons in Clostridium Scatologenes ATCC 25775." TopSCHOLAR®, 2017. https://digitalcommons.wku.edu/theses/2058.

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3-Methylindole and 4-methylphenol are cytotoxic and malodorant compounds derived from tryptophan and tyrosine, respectively. Each is present in swine waste lagoons and contributes to malodorous emissions from agricultural facilities. Clostridium scatologenes ATCC 25775 produces both compounds and serves as a model organism to study their metabolism and function. Through the repeated assembly and annotation of the Clostridium scatologenes genome, we propose a novel pathway for tryptophan degradation and 3-methylindole production by this organism. The genome of Clostridium scatologenes was seque

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Hu, Yue. "Microbial DNA Sequencing in Environmental Studies." Doctoral thesis, KTH, Skolan för bioteknologi (BIO), 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-204897.

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The field of microbial ecology has just entered a new era of rapid technological development and generation of big data. The high-throughput sequencing techniques presently available provide an opportunity to extensively inventorize the blueprints of life. Now, millions of microbes of natural microbial communities can be studied simultaneously without prior cultivation. New species and new functions (genes) can be discovered just by mining sequencing data. However, there is still a tremendous number of microorganisms not yet examined, nor are the ecosystem functions these carry out. The modern

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Camerlengo, Terry Luke. "Techniques for Storing and Processing Next-Generation DNA Sequencing Data." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1388502159.

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Page, Justin Thomas. "Bioinformatics for the Comparative Genomic Analysis of the Cotton (Gossypium) Polyploid Complex." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/5557.

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Understanding the composition, evolution, and function of the cotton (Gossypium) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). Specifically, read-mapping (a fundamental part of next-generation sequence analysis) cannot adequately differentiate reads as belonging to one genome or the other. These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we developed PolyCat to categorize reads according to their genome of origin based on homoe

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Thölken, Clemens [Verfasser], and Marcus [Akademischer Betreuer] Lechner. "Applied Bioinformatics for ncRNA Characterization - Case Studies Combining Next Generation Sequencing & Genomics / Clemens Thölken ; Betreuer: Marcus Lechner." Marburg : Philipps-Universität Marburg, 2020. http://d-nb.info/1204199736/34.

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Migeon, Pierre. "Comparative genomics of repetitive elements between maize inbred lines B73 and Mo17." Thesis, Kansas State University, 2017. http://hdl.handle.net/2097/35377.

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Master of Science<br>Genetics Interdepartmental Program<br>Sanzhen Liu<br>The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17

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Liu, Xinan. "NOVEL COMPUTATIONAL METHODS FOR SEQUENCING DATA ANALYSIS: MAPPING, QUERY, AND CLASSIFICATION." UKnowledge, 2018. https://uknowledge.uky.edu/cs_etds/63.

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Over the past decade, the evolution of next-generation sequencing technology has considerably advanced the genomics research. As a consequence, fast and accurate computational methods are needed for analyzing the large data in different applications. The research presented in this dissertation focuses on three areas: RNA-seq read mapping, large-scale data query, and metagenomics sequence classification. A critical step of RNA-seq data analysis is to map the RNA-seq reads onto a reference genome. This dissertation presents a novel splice alignment tool, MapSplice3. It achieves high read alignme

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Leader, Debbie. "Methods for incorporating biological information into the statistical analysis of gene expression microarray data." Thesis, University of Auckland, 2009. http://hdl.handle.net/2292/5609.

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Microarray technology has made it possible for researchers to simultaneously measure the expression levels of tens of thousands of genes. It is believed that most human diseases and biological phenomena occur through the interaction of groups of genes that are functionally related. To investigate the feasibility of incorporating functional information and/or constraints (based on biological and technical needs) into the classification process two approaches were examined in this thesis. The first of these approaches investigated the effect of incorporating a pre-filter into the gene sel

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Katz, Lee Scott. "Computational tools for molecular epidemiology and computational genomics of Neisseria meningitidis." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/42934.

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Neisseria meningitidis is a gram negative, and sometimes encapsulated, diplococcus that causes devastating disease worldwide. For the worldwide genetic surveillance of N. meningitidis, the gold standard for profiling the bacterium uses genetic loci found around the genome. Unfortunately, the software for analyzing the data for these profiles is difficult to use for a variety of reasons. This thesis shows my suite of tools called the Meningococcus Genome Informatics Platform for the analysis of these profiling data. To better understand N. meningitidis, the CDC Meningitis Laboratory and oth

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Sathirapongsasuti, Jarupon Fah. "Post-Genomic Approaches to Personalized Medicine: Applications in Exome Sequencing, Microbiome, and COPD." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11574.

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Since the completion of the sequencing of the human genome at the turn of the century, genomics has revolutionized the study of biology and medicine by providing high-throughput and quantitative methods for measuring molecular activities. Microarray and next generation sequencing emerged as important inflection points where the rate of data generation skyrocketed. The high dimensionality nature and the rapid growth in the volume of data precipitated a unique computational challenge in massive data analysis and interpretation. Noise and signal structure in the data varies significantly across t

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Oelofse, Andries Johannes. "Development of a MAIME-compliant microarray data management system for functional genomics data integration." Pretoria : [s.n.], 2006. http://upetd.up.ac.za/thesis/available/etd-08222007-135249.

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Kislyuk, Andrey O. "Algorithm development for next generation sequencing-based metagenome analysis." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/42779.

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We present research on the design, development and application of algorithms for DNA sequence analysis, with a focus on environmental DNA (metagenomes). We present an overview and primer on algorithm development for bioinformatics of metagenomes; work on frameshift detection in DNA sequencing data; work on a computational pipeline for the assembly, feature prediction, annotation and analysis of bacterial genomes; work on unsupervised phylogenetic clustering of metagenomic fragments using Markov Chain Monte Carlo methods; and work on estimation of bacterial genome plasticity and diversity, pote

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Smith, Brandon Chase. "Low-level variant detection in human mitochondrial DNA using the Illumina(RTM) MiSeqtm next-generation sequencing (NGS) platform." Thesis, Western Carolina University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=1537163.

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<p> When challenged by difficult biological samples, the forensic analyst is far more likely to obtain useful data by sequencing the human mitochondrial DNA (mtDNA). Nextgeneration sequencing (NGS) technologies are currently being evaluated by the Forensic Science Program at Western Carolina University for their ability to reliably detect lowlevel variants in mixtures of mtDNA. The sequence profiles for twenty individuals were obtained by sequencing amplified DNA derived from the mitochondrial hypervariable (HV) regions using Sanger methods. Two-person mixtures were then constructed by mixin

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Jjingo, Daudi. "Effects of repetitive DNA and epigenetics on human genome regulation." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/49120.

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The highly developed and specialized anatomical and physiological characteristics observed for eukaryotes in general and mammals in particular are underwritten by an elaborate and intricate process of genome regulation. This precise control of the location, timing and amplitude of gene expression is achieved by a variety of genetic and epigenetic tools and mechanisms. While several of these regulatory mechanisms have been extensively studied, our understanding of the complex and diverse associations between various epigenetic marks and genetic elements with genome regulatory systems has remain

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Hu, Ke. "METHODS AND ANALYSES IN THE STUDY OF HUMAN DNA METHYLATION." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1522760441838452.

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Zheng, Hao. "Prediction and analysis of the methylation status of CpG islands in human genome." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/43631.

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DNA methylation serves as a major epigenetic modification crucial to the normal organismal development and the onset and progression of complex diseases such as cancer. Computational predictions for DNA methylation profiling serve multiple purposes. First, accurate predictions can contribute valuable information for speeding up genome-wide DNA methylation profiling so that experimental resources can be focused on a few selected while computational procedures are applied to the bulk of the genome. Second, computational predictions can extract functional features and construct useful models of D

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Hedberg, Lilia. "Identification of obesity-associated SNPs in the human genome : Method development and implementation for SOLiD sequencing data analysis." Thesis, Linköpings universitet, Institutionen för klinisk och experimentell medicin, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-57932.

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Over the last few years, genome-wide association studies (GWAS) have been used to identify numerous obesity associated SNPs in the human genome. By using linkage studies, candidate obesity genes have been identified. When SNPs in the first intron of FTO were found to be associated to BMI, it became the first gene to be linked to common obesity. In order to look for causative explanations behind the associated SNPs, a re-sequencing of FTO had been performed on the SOLiD sequencing platform. In-house candidate gene, SLCX, was also sequenced in order to evaluate a potential obesity association. T

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Mittal, Vinay K. "Detection and characterization of gene-fusions in breast and ovarian cancer using high-throughput sequencing." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/54014.

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Gene-fusions are a prevalent class of genetic variants that are often employed as cancer biomarkers and therapeutic targets. In recent years, high-throughput sequencing of the cellular genome and transcriptome have emerged as a promising approach for the investigation of gene-fusions at the DNA and RNA level. Although, large volumes of sequencing data and complexity of gene-fusion structures presents unique computational challenges. This dissertation describes research that first addresses the bioinformatics challenges associated with the analysis of the massive volumes of sequencing data by d

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Mooney, Alex M. "The Influence of DNA Sequence and Post Translational Modifications on Nucleosome Positioning and Stability." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1354733493.

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Cortese, Diego. "Genomic and transcriptomic sequencing in chronic lymphocytic leukemia." Doctoral thesis, Uppsala universitet, Institutionen för immunologi, genetik och patologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-303703.

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Identification of recurrent mutations through next-generation sequencing (NGS) has given us a deeper understanding of the molecular mechanisms involved in chronic lymphocytic leukemia (CLL) development and progression and provided novel means for risk assessment in this clinically heterogeneous disease. In paper I, we screened a population-based cohort of CLL patients (n=364) for TP53, NOTCH1, SF3B1, BIRC3 and MYD88 mutations using Sanger sequencing, and confirmed the negative prognostic impact of TP53, SF3B1 or NOTCH1 aberrations, though at lower frequencies compared to previous studies. In p

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Lieber, Daniel Solomon. "Computational and Experimental Approaches For Evaluating the Genetic Basis of Mitochondrial Disorders." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10830.

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Mitochondria are responsible for many fundamental biological pathways and metabolic processes, including aerobic ATP production by the mitochondrial respiratory chain. In humans, mitochondrial dysfunction can lead to severe disorders of energy metabolism, which are collectively referred to as mitochondrial disorders and affect approximately 1:5,000 individuals. These disorders are clinically heterogeneous and can affect multiple organ systems, often within a single individual. Symptoms can include myopathy, exercise intolerance, hearing loss, blindness, stroke, seizures, diabetes, and GI dysmo

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Venn, Oliver Claude. "Inferring the fine-scale structure and evolution of recombination from high-throughput genome sequencing." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:b74f6706-a37d-4d71-975d-02e0f79ccdf1.

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In eukaryotes, recombination plays a critical role in both the production of viable gametes and as a population genetic process. Here, we are interested in studying recombination as it provides insight into a process that has shaped variation. To this end, we study the evolution of cross-over rates in chimpanzees and humans through two experiments. Components of the recombination machinery are well described in yeast and C. elegans, but less so in other species. In humans, cross-over rates vary across physical scales and occur predominantly in narrow ∼2 kb regions called hotspots, where hotspo

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Takahashi, Koichi. "Integrative genomic analysis of adult mixed phenotype acute leukemia (MPAL) delineates lineage associated molecular subtypes." Kyoto University, 2020. http://hdl.handle.net/2433/252977.

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Manser, Paul. "Methods for Integrative Analysis of Genomic Data." VCU Scholars Compass, 2014. http://scholarscompass.vcu.edu/etd/3638.

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In recent years, the development of new genomic technologies has allowed for the investigation of many regulatory epigenetic marks besides expression levels, on a genome-wide scale. As the price for these technologies continues to decrease, study sizes will not only increase, but several different assays are beginning to be used for the same samples. It is therefore desirable to develop statistical methods to integrate multiple data types that can handle the increased computational burden of incorporating large data sets. Furthermore, it is important to develop sound quality control and normal

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LAMONTANARA, ANTONELLA. "Sviluppo ed applicazione di pipilines bioinformatiche per l'analisi di dati NGS." Doctoral thesis, Università Cattolica del Sacro Cuore, 2015. http://hdl.handle.net/10280/6068.

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Lo sviluppo delle tecnologie di sequenziamento ha portato alla nascita di strumenti in grado di produrre gigabasi di dati di sequenziamento in una singola corsa. Queste tecnologie, comunemente indicate come Next Generation Sequencing o NGS, producono grandi e complessi dataset la cui analisi comporta diversi problemi a livello bioinformatico. L'analisi di questo tipo di dati richiede la messa a punto di pipelines computazionali il cui sviluppo richiede un lavoro di scripting necessario per concatenare i softwares già esistenti. Questa tesi tratta l'aspetto metodologico dell'analisi di dati NGS

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Merrill, Bryan Douglas. "Advancing Phage Genomics and Honeybee Health Through Discovery and Characterization of Paenibacillaceae Bacteriophages." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/5641.

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The Paenibacillaceae family of bacteria includes two species known to infect the hives of honeybees, Paenibacillus larvae and Brevibacillus laterosporus. P. larvae, the causative agent of American Foulbrood (AFB) causes a lethal infection of honeybee larvae, while B. laterosporus is a secondary invader following European Foulbrood (EFB) infection. Increasing antibiotic resistance of P. larvae bacteria has prompted a search for alternative treatment methods for this disease. Bacteriophages are the most diverse life forms on earth and can provide important insights about the bacterial hosts they

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Reinsborough, Calder. "Search for Novel DNA Modifications in Saccharomyces cerevisiae mtDNA using Single Molecule Real Time Sequencing and Effects of Mitochondrial Metabolic Dynamics on Gene Expression." Thesis, Icahn School of Medicine at Mount Sinai, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=1569125.

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<p> In the past five years, Single Molecule Real Time (SMRT) sequencing technology has been found to be a reliable indicator of certain epigenetic modifications in bacterial genomes. The genome of the model organism <i>Saccharomyces cerevisiae</i> has long been thought to be free of DNA level modification, but literature surrounding this subject is conflicting. Additionally, the mitochondria of <i>S. cerevisiae</i> control the transition between three distinct chronological life phases – exponential, postdiauxic, and stationary - as defined by their main metabolic processes. This study a

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Drong, Alexander Werner. "Comprehensive assessment of the role of DNA methylation in obesity and type 2 diabetes." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:c2df87d9-9929-4eb1-8c44-61452b88ea3c.

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Obesity and type 2 diabetes (T2D) are major risk factors for cardiovascular and other diseases and are currently undergoing an increase in global prevalence. The work presented in my thesis addresses the role epigenetics, specifically DNA methylation, plays in the susceptibility to obesity and T2D and deals with methodological issues in the analysis of DNA methylation data. I first combined epigenome-wide DNA methylation data across 38 adipose tissue samples with corresponding SNP and mRNA data for the same subjects. At 5&percnt; false discovery rate (FDR), methylation of 149 regions associate

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Eslabão, Marcus Redü. "Square: uma plataforma gráfica e intuitiva para anotação de genomas bacterianos." Universidade Federal de Pelotas, 2016. http://repositorio.ufpel.edu.br:8080/handle/prefix/3731.

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Submitted by Maria Beatriz Vieira (mbeatriz.vieira@gmail.com) on 2017-10-18T11:53:11Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) tese_marcus_redu_eslabao.pdf: 2744083 bytes, checksum: 5950b0ffa159bbf193a91d88276a5e49 (MD5)<br>Approved for entry into archive by Aline Batista (alinehb.ufpel@gmail.com) on 2017-10-23T11:08:52Z (GMT) No. of bitstreams: 2 tese_marcus_redu_eslabao.pdf: 2744083 bytes, checksum: 5950b0ffa159bbf193a91d88276a5e49 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)<br>Approved for entry into archive

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Xu, Guang. "Identification of Novel Genetic Variations for Amyotrophic Lateral Sclerosis (ALS)." eScholarship@UMMS, 2018. https://escholarship.umassmed.edu/gsbs_diss/958.

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A list of genes have been identified to carry mutations causing familial ALS such as SOD1, TARDBP, C9orf72. But for sporadic ALS, which is 90% of all ALS cases, the underlying genetic variants are still largely unknown. There are multiple genome-wide association study (GWAS) for sporadic ALS, but usually a large number nominated SNP can hardly be replicated in larger cohort analysis. Also majority of GWAS SNP lie within noncoding region of genome, imposing a huge challenge to study their biological role in ALS pathology. With the rapid development of next-generation sequencing technology, we a

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Driscoll, Timothy. "Host-Microbe Relations: A Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data." Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/50921.

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Plants and animals are characterized by intimate, enduring, often indispensable, and always complex associations with microbes. Therefore, it should come as no surprise that when the genome of a eukaryote is sequenced, a medley of bacterial sequences are produced as well. These sequences can be highly informative about the interactions between the eukaryote and its bacterial cohorts; unfortunately, they often comprise a vanishingly small constituent within a heterogeneous mixture of microbial and host sequences. Genomic analyses typically avoid the bacterial sequences in order to obtain a geno

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Evenstone, Lauren. "Employing Limited Next Generation Sequence Data for the Development of Genetic Loci of Phylogenetic and Population Genetic Utility." FIU Digital Commons, 2015. http://digitalcommons.fiu.edu/etd/2191.

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Massively parallel high throughput sequencers are transforming the scientific research by reducing the cost and time necessary to sequence entire genomes. The goal of this project is to produce preliminary genome assemblies of calliphorid flies using Life Technologies’ Ion Torrent sequencing and Illumina’s MiSeq sequencing. I located, assembled, and annotated a novel mitochondrial genome for one such fly, the little studied Chrysomya pacifica that is central to one hypothesis about blow fly evolution. With sequencing data from Chrysomya megacephala, its forensically relevant sister species, mu

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