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Dissertations / Theses on the topic 'Whole genome sequencing PacBio'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Anson, Eric Lance. "Algorithms for whole genome shotgun sequencing." Diss., The University of Arizona, 2000. http://hdl.handle.net/10150/289091.

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A monumental achievement in the history of science, the sequencing of the entire human genome, will soon be reached. The Human Genome Project (HGP) has been working toward this goal since 1990 using a two-tiered strategy. Recently it was proposed that using a whole-genome shotgun approach to sequence the genome would be faster and less costly. This thesis expands on that proposal by presenting two algorithms that can be used in whole-genome shotgun sequencing. These algorithms were implemented and tested on simulated data. Essential to this approach is the availability of pairs of short, uniqu

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2

Farmery, James Henry Royston. "Estimating telomere length from whole genome sequencing data." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/275827.

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This thesis details the development of two computational tools, Telomerecat and Parabam, as well as their applications to whole genome sequencing (WGS) data. Telomerecat is a tool for estimating telomere length from WGS data. The strength of Telomerecat lies in its applicability. This applicability is due to a number of advantages over previous attempts to estimate telomere length from WGS. Chief amongst these advantages is that it makes no assumption about the underlying chromosome count or size of the genome within input samples. This means that Telomerecat lends itself well to analysing can

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3

Huang, Jie. "Whole-genome sequencing-based association studies of cardiovascular biomarkers." Thesis, University of Cambridge, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708994.

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4

Li, Karen Christine. "Supporting decision-making in whole genome/exome sequencing : parents' perspectives." Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/50835.

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Whole genome sequencing/exome sequencing (WGS/ES) technology is becoming more affordable and accessible, and will become more frequently used in various clinical settings, including for diagnosing rare childhood diseases. However, its use means that parents face decisions that could uncover life-altering information, unrelated to their child’s illness that may also have personal and ethical implications for their families. The purpose of this study is to explore and describe parents’ perceptions of their decisional needs when deciding on WGS/ES for their child. The qualitative methodological

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5

Mattisson, Jonas. "Identifying esophageal atresi associated variants from whole genome sequencing data." Thesis, Uppsala universitet, Institutionen för immunologi, genetik och patologi, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-345329.

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Knowing the underlying cause of a genetic disorder could not only further our understanding of the disease itself, and the otherwise healthy mechanism that is disrupted. It could potentially improve people’s lives. Even if whole genome sequencing has drastically improved the potential of discovering the cause, a comparison of two non-related individual’s genome will find several million sequence variations. While most variants have no significant impact, it is enough for only one to functionally impact a gene, for it to cause a genetic disorder. This project therefore focused on the filtering

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6

Kolicheski, Ana Leticia. "Discovering Disease Causing Variants in Dogs Through Whole Genome Sequencing." Thesis, University of Missouri - Columbia, 2019. http://pqdtopen.proquest.com/#viewpdf?dispub=13877152.

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<p> This dissertation focuses on the use of whole genome sequencing (WGS) for the identification of disease causing variants in canine genomes. A brief review on the historical milestones of genetics, the creation and popularization of the fast throughput DNA sequencing technologies and their advantages and potential problems and biases, the importance of the study of canine genetics and the current state of the canine genome assembly is presented. Our lab sequenced ~100 dogs in the attempt to discover disease-causing variants. So far 20 such variants have been identified. This dissertation co

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7

Wong, Tse Hua Nicholas. "Investigation of in-hospital norovirus transmission using whole genome sequencing." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:0c059680-337e-4a70-aab7-5b7d7e483962.

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Norovirus is the commonest cause of viral gastroenteritis, affecting all age groups worldwide. Outbreaks frequently occur in semi-closed communities such as schools, cruise ships, prisons and hospitals. Within the healthcare environment, the economic and logistical burdens and the inconvenience caused by norovirus is significant, since ward closure remains central to infection control. The aim of this study was to investigate norovirus transmission dynamics during hospital outbreaks. The ultimate goal was to provide information that could, in future, lead to the development of novel, less disr

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8

Colombini, Lorenzo. "Whole genome sequencing and comparative genomics in lactic acid bacteria." Doctoral thesis, Università di Siena, 2022. http://hdl.handle.net/11365/1182475.

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In the present thesis, the genomes of different microbial species, belonging to the lactic acid bacteria and including Lactobacillus crispatus, Streptococcus pneumoniae and Enterococcus faecalis, were obtained and analyzed using comparative genomics tools. In the first part of the thesis was described the genome of the probiotic L. crispatus strain M247, which contains a novel integrative and mobilizable element named Tn7088. Tn7088 carries a biosynthetic gene cluster coding for a class I bacteriocin which is homologous to the listeriolysin S gene cluster of Listeria monocytogenes and may conf

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9

Clouse, Jared William. "The Amaranth (Amaranthus Hypochondriacus) Genome: Genome, Transcriptome and Physical Map Assembly." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/5916.

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Amaranthus hypochondriacus is an emerging pseudo-cereal native to the New World which has garnered increased attention in recent years due to its nutritional quality, in particular its seed protein, and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleotetraploid that shows amphidiploid inheritance (2n=32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth A. hypochondriacus. The genome assembly consisted of 377 Mb in 3,518 scaffolds with an N50 of

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10

Ramos, Alexis. "Cancer Genome Characterization with SNP Array and Whole-Exome Sequencing Analysis." Thesis, Harvard University, 2011. http://dissertations.umi.com/gsas.harvard:10036.

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Cancer, the uncontrolled growth of morphologically and genetically abnormal cells in the body, is a major worldwide public health problem and there is a great need for novel insights into this disease. The majority of tumors arise from the acquisition of somatic alterations leading to changes in gene function and expression. The clinical success of targeted therapeutics in molecularly defined subsets of patients has highlighted the need for comprehensive characterization of the somatic alterations in individual cancer types. Copy number profiling using SNP arrays is a common approach for profi

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11

Cartwright, Edward John Philip. "Whole genome sequencing and applied epidemiology for the control of MRSA." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708973.

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12

Yang, Li. "A Goodness-of-fit Association Test for Whole Genome Sequencing Data." Digital WPI, 2013. https://digitalcommons.wpi.edu/etd-theses/296.

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Although many genetic factors have been successfully identified for human diseases in genome-wide association studies (GWAS), genes discovered to date only account for a small proportion of overall genetic contributions to many complex traits. Association studies have difficulty in detecting the remaining true genetic variants that are either common variants with weak allelic effects, or rare variants that have strong allelic effects but are weakly associated at the population level. In this work we applied a goodness-of-fit test for detecting sets of common and rare variants associated with q

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13

Jones, Rhys C. "Use of whole genome sequencing in understanding transmission dynamics of tuberculosis." Thesis, Swansea University, 2018. https://cronfa.swan.ac.uk/Record/cronfa44995.

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Mycobacterium tuberculosis is the leading cause of death from an infectious disease worldwide. An understanding of tuberculosis transmission dynamics in outbreak settings is vital for its control. The advent of affordable whole genome sequencing (WGS) has provided scope for superior resolution of tuberculosis outbreaks, compared to previous methods. However, the challenge lies in standardising the vast quantities of resulting data in a structured manner which lends itself to easy comparison of isolates. Gene-by-gene Multi-Locus Sequence Typing (MLST) methods of analysing WGS data, as opposed t

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14

Naghra, H. "Application of whole genome sequencing to the study of Pseudomonas aeruginosa." Thesis, University of Nottingham, 2016. http://eprints.nottingham.ac.uk/33329/.

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The reduction in cost and increase in throughput of whole genome sequencing (WGS) technologies, and the advent of benchtop WGS instruments such as the Illumina MiSeq, means that WGS is no longer restricted to large genome centres and consortia. The number of microbial genomes in public repositories is ever increasing due to the availability of WGS technologies to research groups, with individual genera having their own dedicated genome databases. Pseudomonas aeruginosa is an opportunistic pathogen and a major cause of healthcare associated infection in immunocompromised individuals and cystic

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15

Bao, Teng. "Deciphering and Expending Clostridium formicoaceticum Metabolism Based on Whole Genome Sequencing." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1480631398782307.

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16

Hottel, Wesley Johnathan. "Whole genome sequencing analysis of Legionella in hospital premise plumbing systems." Diss., University of Iowa, 2019. https://ir.uiowa.edu/etd/6767.

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Legionella bacteria, the causative agent of Legionaries’ disease and Pontiac fever, are ubiquitous in fresh-water environments including man-made water systems. Incidence of legionellosis is increasing in the United States resulting in thousands of cases every year. Infection via aerosols generated by showers, faucets, cooling towers, spas, fountains, and other water fixtures has been identified as the primary source of transmission. Legionella bacteria pose a significant public health threat, particularly in health care and long term care settings as Legionella can readily colonize the plumbi

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17

Fujimoto, Masaki Stanley. "Graph-Based Whole Genome Phylogenomics." BYU ScholarsArchive, 2020. https://scholarsarchive.byu.edu/etd/8461.

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Understanding others is a deeply human urge basic in our existential quest. It requires knowing where someone has come from and where they sit amongst peers. Phylogenetic analysis and genome wide association studies seek to tell us where we’ve come from and where we are relative to one another through evolutionary history and genetic makeup. Current methods do not address the computational complexity caused by new forms of genomic data, namely long-read DNA sequencing and increased abundances of assembled genomes, that are becoming evermore abundant. To address this, we explore specialized dat

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18

Niemiec, Emilia <1987&gt. "Ethical, legal and social issues related to the offer of whole exome and whole genome sequencing." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2018. http://amsdottorato.unibo.it/8295/1/NIEMIEC_EMILIA_tesi.pdf.

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Whole genome and exome sequencing (WGS and WES) raise numerous ethical, legal and social issues (ELSI), such as related to informed consent and usage of sequencing data in research. These concerns may be amplified when genomic sequencing is offered direct-to-consumer (DTC) bypassing the traditional heathcare system. This thesis discusses ELSI related to WES/WGS and DTC genetic testing, provides an overview of current DTC genetic testing market, and analyses the impact of the recently adopted Regulation of the European Parliament and of the Council on in vitro diagnostic medical devices on DTC

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19

Anscombe, C. J. "Multiple displacement amplification and whole genome sequencing for the diagnosis of infectious diseases." Thesis, Queen Mary, University of London, 2016. http://qmro.qmul.ac.uk/xmlui/handle/123456789/18409.

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Next-generation sequencing technologies are revolutionising our ability to characterise and investigate infectious diseases. Utilising the power of high throughput sequencing, this study reports, the development of a sensitive, non-PCR based, unbiased amplification method, which allows the rapid and accurate sequencing of multiple microbial pathogens directly from clinical samples. The method employs Φ29 DNA polymerase, a highly efficient enzyme able to produce strand displacement during the polymerisation process with high fidelity. Problems with DNA secondary structure were overcome and the

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20

Gerbig, Gracen Renee. "Characterization and Whole-Genome Sequencing of Staphylococcus aureus Collected from Boston Rats." Kent State University Honors College / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors158834219326593.

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21

Cimmino, Teresa. "Whole genome sequencing to decipher the resistome of clinical multidrug-resistant bacteria." Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM5068/document.

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WGS permet d'analyser et de déchiffrer l'étude de résistances de bactéries multirésistantes(MDR), en comprenant les différents mécanismes de résistance, les annuaires génétiques. Au cours de ma thèse de doctorat, j'ai réalisé: 1 revue de la littérature sur l'utilisation de nouveaux outils de diagnostic contemporains et les capacités dans la détection des foyers dans les maladies infectieuses causées par MDR. L'identification et l'analyse de résistances de bactéries multirésistantes Comme étant des Shewanellalgae, normalement de l'environnement marin, dans notre cas une souche clinique isolée d

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22

Borgström, Erik. "Technologies for Single Cell Genome Analysis." Doctoral thesis, KTH, Genteknologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-181059.

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During the last decade high throughput DNA sequencing of single cells has evolved from an idea to one of the most high profile fields of research. Much of this development has been possible due to the dramatic reduction in costs for massively parallel sequencing. The four papers included in this thesis describe or evaluate technological advancements for high throughput DNA sequencing of single cells and single molecules. As the sequencing technologies improve, more samples are analyzed in parallel. In paper 1, an automated procedure for preparation of samples prior to massively parallel sequen

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23

Petzold, Markus. "Array hybridization and whole genome sequencing as new typing tools for Legionella pneumophila." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-233546.

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To understand transmissible human diseases, disciplines such as epidemiology and the surveillance of affected cases are as essential as the knowledge about the pathogenesis and the course of a disease. Epidemiologists categorize and estimate factors for public health risks by taking metadata into account including geographic aspects, health and social states to study a disease transmission and prevent further cases. In addition, a focus on the causative agents itself is necessary in order to understand their ecology and hence their virulence traits. The causative agents for a severe pneumonia

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24

Ciferri, Brianne. "Utilization of whole genome sequencing to determine Clostridium difficile diversity and transmission potential." Thesis, Icahn School of Medicine at Mount Sinai, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=1606872.

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<p> Objective: To identify genomic variance of C. difficile strains to determine diversity and transmission potential which can guide future directions in clinical care and hospital policy. Study Design: We analyzed epidemiological and genomic data from 35 patients with laboratory confirmed C. difficile infection (CDI) in two three-month periods in 2011 and 2014 at a large urban hospital. Whole genome sequencing was conducted on all isolates; further analysis was conducted for 13 cases of CDI with the highly virulent NAP1 strain. Results: Overall strain diversity within the hospital was anal

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25

Muzondiwa, Dillon. "Exploring the evolution of drug resistance in mycobacterium using whole genome sequencing data." Diss., University of Pretoria, 2019. http://hdl.handle.net/2263/77865.

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Mycobacterium tuberculosis (Mtb) remains a global challenge that has been worsened by the emergence of drug resistant strains of Mtb. We used publicly available Next Generation Sequencing (NGS) and drug susceptibility (DST) data to develop “Resistance sniffer”, an online software program for the rapid prediction of lineage and Mtb drug resistance. Based on the distribution of polymorphisms in the genomes of Mtb, we calculated the power of association between the polymorphisms in different clades of Mtb and resistance to 13 anti-TB drugs. Our data suggests that the development of drug resistanc

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Baldwin-Brown, James. "Identifying selection in differentiated populations through simulation, experimental evolution, and whole genome sequencing." Thesis, University of California, Irvine, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10245933.

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<p>Population differentiation is both one of the central processes underlying the diversity that we observe in the natural world, and a mechanism that can be used to differentiate between evolutionary forces both at the level of the polymorphism, and at the level of the entire genome. Here, I use simulated evolution to analyze the statistical power to detect signals of selection in artificially selected laboratory populations, and use genomic data from wild populations of the clam shrimp Eulimnadia texana to identify genomic signals of selection in wild populations. Several loci in the wild po

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27

Price, James Richard. "Application of whole-genome sequencing to understand transmission of healthcare-associated Staphylococcus aureus." Thesis, University of Brighton, 2014. https://research.brighton.ac.uk/en/studentTheses/f357a873-49b6-4269-9b39-df2dc24ef3ee.

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Staphylococcus aureus is a leading cause of healthcare associated infection. Efforts to reduce the burden of S. aureus infections in healthcare settings have targeted patient carriage and preventing person-to-person transmission. These measures have only been partially successful. Our understanding of S. aureus transmission is limited by low discrimination of currently available typing techniques. The high resolution offered by whole-genome sequencing (WGS) has the potential to overcome these limitations. Work undertaken in this thesis exploits recent advances in WGS to understand S. aureus tr

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Rieber, Nora [Verfasser], and Roland [Akademischer Betreuer] Eils. "Performance comparison of four human whole-genome sequencing technologies / Nora Rieber. Betreuer: Roland Eils." Heidelberg : Universitätsbibliothek Heidelberg, 2013. http://d-nb.info/1061054527/34.

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29

Crispell, Joseph. "Using whole genome sequencing to investigate the inter-species transmission dynamics of Mycobacterium bovis." Thesis, University of Glasgow, 2017. http://theses.gla.ac.uk/8254/.

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30

Khan, Hamza. "De novo annotation of non-model organisms using whole genome and transcriptome shotgun sequencing." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/60152.

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31

Chen, Taoye. "A Multi-level Model for Analysing Whole Genome Sequencing Family Data with Longitudinal Traits." Digital WPI, 2013. https://digitalcommons.wpi.edu/etd-theses/271.

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Compared to microarray-based genotyping, next-generation whole genome-sequencing (WGS) studies have the strength to provide greater information for the identification of rare variants, which likely account for a significant portion of missing heritability of common human diseases. In WGS, family-based studies are important because they are likely enriched for rare disease variants that segregate with the disease in relatives. We propose a multilevel model to detect disease variants using family-based WGS data with longitudinal measures. This model incorporates the correlation structure from fa

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32

Park, Doori, Je Won Jung, Beom-Soon Choi, et al. "Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing." BioMed Central Ltd, 2015. http://hdl.handle.net/10150/610288.

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BACKGROUND: The honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey bee, Apis mellifera, has served as a model species, and its genome sequence has been published. In contrast, the genome of the Asian honey bee, Apis cerana, has not yet been sequenced. A. cerana has been raised in Asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. A cerana has divergent biological traits compared

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33

Eyre, David William. "Quantitative study of Clostridium difficile transmission using extensive epidemiological data and whole genome sequencing." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:a7197605-6da6-4dbc-9bec-171d6e683eb1.

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Clostridium difficile is a leading healthcare-associated infection, which causes diarrhoea, and is almost exclusively precipitated by antibiotic exposure. Traditionally C. difficile infection (CDI) has been considered predominantly transmitted within hospitals. However, endemic spread hampers identification of the source of infections, and therefore control and prevention of disease. A cohort of consecutive hospital and community CDI cases in Oxfordshire from September 2007 to March 2011 was investigated. For each case hospital admission, ward movement and demographic data were available allow

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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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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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Young, Bernadette. "Investigating the variability of virulence in natural populations of Staphylococcus aureus using whole genome sequencing." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:f76d1478-10c2-4267-9f6b-c3613e4aa71e.

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Invasive Staphylococcus aureus disease is an important cause of morbidity and mortality, but is much rarer than asymptomatic carriage. The contribution of the bacterial genome to S. aureus infection is incompletely understood, and molecular epidemiology provides conflicting evidence. This thesis aims to improve our understanding of this contribution using the resolution afforded by whole-genome sequencing. In a systematic study of S. aureus evolution in 105 hosts during invasive S. aureus disease, I demonstrate extensive within-host diversity, with evidence for varying selective pressures and

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Dunckel, Sandra Margarita. "Whole genome approaches for characterizing and utilizing synthetic wheat." Diss., Kansas State University, 2015. http://hdl.handle.net/2097/20518.

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Doctor of Philosophy<br>Genetics - Plant Pathology<br>Jesse A. Poland<br>The global population is estimated to reach 9.1 billion by 2050. Together with climate change, insuring food security for this population presents a significant challenge to agriculture. In this context, a large number of breeding objectives must be targeted. The focus of the work presented here is to explore genomic approaches for tapping exotic germplasm for valuable alleles to increased yield, disease resistance and abiotic stress tolerance. The loss of genetic diversity in bread wheat (Triticum aestivum L.) due to bo

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Pintara, Alexander P. "Understanding STEC epidemiology and predominance of O157:H-negative in Australia: Genetic characterisation and virulence assessment of STEC isolates." Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/229023/8/Alexander%20Pintara%20Thesis.pdf.

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This research investigated the epidemiology of Australian Shiga toxin-producing Escherichia coli (STEC). STEC cause mild to severe disease in humans. Australian STEC are non-motile and mis-characterised as O157:H7 that cause severe disease and outbreaks globally. Using comparative genomics, a genetic mutation was found only in Australian STEC. This discovery enables differentiation of Australian STEC from severe disease-causing strains. In addition, Australian STEC strains lack stx2a, unlike international strains. This difference could define why Australian O157 STEC cause mild disease. This r

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Haimel, Matthias. "Development of computational approaches for whole-genome sequence variation and deep phenotyping." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/283563.

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The rare disease pulmonary arterial hypertension (PAH) results in high blood pressure in the lung caused by narrowing of lung arteries. Genes causative in PAH were discovered through family studies and very often harbour rare variants. However, the genetic cause in heritable (31%) and idiopathic (79%) PAH cases is not yet known but are speculated to be caused by rare variants. Advances in high-throughput sequencing (HTS) technologies made it possible to detect variants in 98% of the human genome. A drop in sequencing costs made it feasible to sequence 10,000 individuals including 1,250 subject

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Cox, Brian James. "EMS Mutagenesis in Quinoa: Developing a Genetic Resource." BYU ScholarsArchive, 2020. https://scholarsarchive.byu.edu/etd/9080.

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Chenopodium quinoa, a South American pseudocereal, has valuable agricultural traits such as salt tolerance and drought tolerance, and it has beneficial nutritional properties such as high protein content and a complete amino acid profile. However, problems including disease susceptibility, low harvest index, lodging, seed shattering, low heat tolerance, and saponin content plague quinoa. Genetic resources for quinoa are needed to fix these problems and make quinoa more available throughout the world. We used ethyl methanesulfonate (EMS) to create a mutant population of QQ74 quinoa (USDA GRIN P

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Mackley, Michael. "A clinical and ethical evaluation of secondary findings in the era of clinical whole-genome sequencing." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:aefaaed4-42e9-4313-8354-c8526491b0eb.

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With transformative initiatives like the UK's 100,000 Genomes Project underway, vast amounts of data from genome sequencing are being generated. Genomic results are being actively returned to participants, although policies around their management remain inconsistent and a subject of debate. Secondary findings (SF) have been of particular concern - variants associated with health conditions other than the indication for sequencing, which may or may not be medically actionable. I have conducted a mixed methods study to explore the current transitional period and the issue of secondary findings,

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Walker, Timothy M. "The role of whole-genome sequencing technology in the control and treatment of Mycobacterium tuberculosis infection." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:f523d3d5-635b-4ae6-8c97-1e52b2cb2537.

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In 2013 an estimated 9 million patients were diagnosed with tuberculosis across the globe, leading to 1.5 million deaths. In the UK, just under 8,000 cases were notified. Where resources allow, tuberculosis control is based on the identification of outbreaks, and the timely diagnosis and appropriate treatment of infected patients. However, current methods for identifying tuberculosis outbreaks are limited in their specificity, whilst the definitive diagnostic tests remain culture-dependent and can hence take weeks before producing a result. Whole-genome sequencing (WGS) technology is now affor

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Anahtar, Melis N. "Rapid and Comprehensive Bacterial Identification and Antimicrobial Resistance Determination Using Microfluidic Enrichment and Whole-Genome Sequencing." Thesis, Harvard University, 2017. http://nrs.harvard.edu/urn-3:HUL.InstRepos:32676117.

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Sepsis and other severe bacterial infections affect over 750,000 Americans annually, resulting in a 28% mortality rate and $16 billion in health care costs due to delays in proper diagnosis. The current gold-standard method for determining the species identification (ID) and antimicrobial resistance (AMR) profile of a clinical pathogen relies on the century-old method of growing bacteria in culture media, which takes 2-5 days, and frequently fails to cultivate the causative pathogen. In the absence of microbiologic data, physicians are forced to treat suspected infections with broad-spectrum e

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Croce, Roberta. "Identification of new variants in patients with neurodegenerative disorders by whole genome sequencing data and development of a bioinformatic pipeline." Doctoral thesis, Università del Piemonte Orientale, 2021. http://hdl.handle.net/11579/127934.

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We explored the missing heritability in a cohort of 140 patients affected by Neurodegenerative disorders (NDDs), including Amyotrophic Lateral Sclerosis (ALS), Frontotemporal dementia (FTD)) Parkinson disease (PD) and Spinocerebellar Ataxia (SCA). We performed Whole Genome Sequencing (WGS) after excluding pathogenic variants in the main disease-relevant causative genes and investigated 3 classes of potentially pathogenic variants: a)Coding/non-coding SNV/Indels in a panel of 696 genes involved in NODs. Using standard annotation, we identified pathogenic/likely pathogenic variants (ACMG) in gen

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Hunt, Spencer Philip. "Whole-Genome Assembly of Atriplex hortensis L. Using OxfordNanopore Technology with Chromatin-Contact Mapping." BYU ScholarsArchive, 2019. https://scholarsarchive.byu.edu/etd/8580.

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Atriplex hortensis (2n = 2x = 18, 1C genome size ~1.1 gigabases), also known as garden orach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae family that has spread from its native Eurasia to other temperate and subtropical environments worldwide. Atriplex is a highly complex and polyphyletic genus of generally halophytic and/or xerophytic plants, some of which have been used as food sources for humans and animals alike. Although there is some literature describing the taxonomy and ecology of orach, there is a lack of genetic and genomic data that would otherwise h

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Farrell, Andrew R. "Expanding the horizons of next generation sequencing with RUFUS." Thesis, Boston College, 2014. http://hdl.handle.net/2345/bc-ir:104176.

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Thesis advisor: Gabor T. Marth<br>To help improve the analysis of forward genetic screens, we have developed an efficient and automated pipeline for mutational profiling using our reference guided tools including MOSAIK and FREEBAYES. Studies using next generation sequencing technologies currently employ either reference guided alignment or de novo assembly to analyze the massive amount of short read data produced by second generation sequencing technologies; the far more common approach being reference guided alignment due to the massive computational and sequencing costs associated with de n

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Forst, Jannine. "Detecting and sequencing Mycobacterium tuberculosis aDNA from archaeological remains." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/detecting-and-sequencing-mycobacterium-tuberculosis-adna-from-archaeological-remains(a806f3a9-8d22-4395-a1ff-a3ffbcb1c8cc).html.

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Tuberculosis has been an important disease throughout human history, shaping countless past populations. The archaeological study of the causative agents of tuberculosis, members of the Mycobacterium tuberculosis Complex (MTBC), is hindered by the non-diagnostic nature of tuberculosis-associated skeletal changes. As such, ancient DNA (aDNA) or palaeogenetic analyses have become an important tool for identifying tuberculosis in past populations. However, due to the age and variable preservation of aDNA, there are often issues with sporadic results and false negatives. The overall aim of the wor

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Rashkin, Misha Dmitry Shepard. "Attitudes toward Whole Genome Sequencing among Parents of Children with Autism Spectrum Disorder| A Qualitative Interview Study." Thesis, Icahn School of Medicine at Mount Sinai, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=1537181.

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<p> <b>Background:</b> Whole genome sequencing (WGS) is increasingly used for research and clinical purposes. This study explored attitudes of parents of children with a suspected autism spectrum disorder (ASD) toward WGS. <b>Methods:</b> A topic guide informed by the Theory of Planned Behavior was developed covering perceived benefits, concerns, barriers, and facilitators regarding WGS. Participants also summarized likely major factors in their decision. Interviews were audio-recorded, transcribed and analyzed for themes using framework analysis. <i><b>Results:</b></i> Participants (n=

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Dadi, Temesgen Hailemariam [Verfasser]. "Whole Genome Shotgun Sequencing Based Taxonomic Profiling Methods for Comparative Study of Microbial Communities / Temesgen Hailemariam Dadi." Berlin : Freie Universität Berlin, 2019. http://d-nb.info/1185485856/34.

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Gordon, Nicola. "Whole genome sequencing (WGS) as a unified platform for outbreak identification and resistance prediction in Staphylococcus aureus." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:7d705b89-c5ed-4103-98fb-3f8637e88d32.

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Staphylococcus aureus continues to present challenges to modern healthcare, due to its acquisition of antimicrobial resistance factors, its ability to cause invasive infections associated with significant morbidity and mortality, and its propensity for person-to-person transmission resulting in outbreaks. For outbreak investigation, current typing methods lack resolution, and the relatively slow turnaround times may hinder effective infection control intervention. Whole-genome sequencing (WGS) is rapidly becoming faster and more affordable, offering increased resolution in a comparable timefra

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