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Relevant bibliographies by topics / DNA nucleotide sequencing / Dissertations / Theses

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Dissertations / Theses on the topic 'DNA nucleotide sequencing'

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Published: 10 September 2021

Last updated: 17 July 2025

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1

Boufounos, Petros T. 1977. "Signal processing for DNA sequencing." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/17536.

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Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.<br>Includes bibliographical references (p. 83-86).<br>DNA sequencing is the process of determining the sequence of chemical bases in a particular DNA molecule-nature's blueprint of how life works. The advancement of biological science in has created a vast demand for sequencing methods, which needs to be addressed by automated equipment. This thesis tries to address one part of that process, known as base calling: it is the conversion of the electrical signal-the electro

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2

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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3

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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4

Musgrave-Brown, Esther. "Development and application of methods for targeted DNA sequencing of pooled samples." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648613.

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5

Andrews, Daniel James. "Statistical models of PCR for quantification of target DNA by sequencing." Thesis, University of Cambridge, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708581.

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6

Lin, Cheng-Hsien Kenny. "An ASIC application for DNA sequencing by Smith-Waterman algorithm (DNASSWA) /." [St. Lucia, Qld.], 2004. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe18716.pdf.

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7

Wang, Yikang. "Synthesis of some novel phospholipids, and nucleotide analogues, as potential chemotherapeutic agents and for DNA sequencing." Thesis, University of Southampton, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.295106.

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8

Stranneheim, Henrik. "Enabling massive genomic and transcriptomic analysis." Doctoral thesis, KTH, Genteknologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-45957.

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In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid advances have enormously expanded sequencing opportunities and applications, but also imposed heavy strains on steps prior to sequencing, as well as the subsequent handling and analysis of the massive amounts of sequence data that are generated, in order to exploit the full capacity of these novel platforms. The work presented in this the

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9

Fletcher, Jeremy Charles. "THE USE OF PYROSEQUENCING FOR THE ANALYSIS OF Y CHROMOSOME SINGLE NUCLEOTIDE POLYMORPHISMS." Master's thesis, University of Central Florida, 2004. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4487.

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The potential value of the Y chromosome for forensic applications has been recognized for some time with the current work dedicated to Short Tandem Repeat analysis and Single Nucleotide Polymorphism (SNP) discovery. This study examined the ability of two different SNP analysis methods to determine if they could be utilized in forensic applications and ultimately be developed into an established system for Y chromosome SNP analysis. This study examined two principle SNP analysis systems: single base extension and Pyrosequencing. Pyrosequencing was determined to be superior to single base extens

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10

Hasmats, Johanna. "Analysis of genetic variations in cancer." Doctoral thesis, KTH, Genteknologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-104438.

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The aim of this thesis is to apply recently developed technologies for genomic variation analyses, and to ensure quality of the generated information for use in preclinical cancer research. Faster access to a patients’ full genomic sequence for a lower cost makes it possible for end users such as clinicians and physicians to gain a more complete understanding of the disease status of a patient and adjust treatment accordingly. Correct biological interpretation is important in this context, and can only be provided through fast and simple access to relevant high quality data. Therefore, we here

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11

Baudet, Christian. "Uma abordagem para detecção e remoção de artefatos em sequencias ESTs." [s.n.], 2006. http://repositorio.unicamp.br/jspui/handle/REPOSIP/276264.

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Orientador: Zanoni Dias<br>Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Computação<br>Made available in DSpace on 2018-08-08T07:27:54Z (GMT). No. of bitstreams: 1 Baudet_Christian_M.pdf: 13612079 bytes, checksum: 648d18039dc13dcd5a2f422cc7863666 (MD5) Previous issue date: 2006<br>Resumo: O sequenciamento de ESTs (Expressed Sequence Tag) [2] e uma tecnica que trabalha com bibliotecas de cDNAs tendo como objetivo a obtençao de uma boa aproximaçao para o ?ndice genico, que e a listagem de genes existentes no genoma do organismo estudado. Antes da serem analisadas, as

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12

Ståhl, Patrik L. "Methods for Analyzing Genomes." Doctoral thesis, KTH, Genteknologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-12407.

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The human genome reference sequence has given us a two‐dimensional blueprint of our inherited code of life, but we need to employ modern‐day technology to expand our knowledge into a third dimension. Inter‐individual and intra‐individual variation has been shown to be larger than anticipated, and the mode of genetic regulation more complex. Therefore, the methods that were once used to explain our fundamental constitution are now used to decipher our differences. Over the past four years, throughput from DNA‐sequencing platforms has increased a thousand‐fold, bearing evidence of a rapid develo

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Dordio, Ana Mafalda Duarte. "Deteção e caracterização molecular de Babesia spp. em Canis familiaris e de outros agentes transmitidos por ixodídeos na Área Metropolitana de Lisboa e Oeste, Portugal." Master's thesis, Universidade de Lisboa, Faculdade de Medicina Veterinária, 2018. http://hdl.handle.net/10400.5/14764.

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Dissertação de Mestrado Integrado em Medicina Veterinária<br>As doenças dos canídeos cujos agentes são transmitidos por vetores (DCTV), são causadas por um número abrangente de agentes patogénicos transmitidos por artrópodes e são um problema crescente no mundo nos últimos anos. A Babesiose canina faz parte dessas doenças, sendo causada por diversas espécies pertencentes ao género Babesia. Até ao momento sabe-se que a Babesiose canina é provocada pelas espécies Babesia canis e Babesia microti-like no Norte e Babesia vogeli em todas as regiões de Portugal. No entanto, as informações relativas à

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Syaifudin, Mochamad. "Species-specific DNA markers for improving the genetic management of tilapia." Thesis, University of Stirling, 2015. http://hdl.handle.net/1893/22624.

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The tilapias are a group of African and Middle Eastern cichlid fish that are widely cultured in developed and developing countries. With many different species and sub-species, and extensive use of interspecies hybrids, identification of tilapia species is of importance in aquaculture and in wild populations where introductions occur. This research set out to distinguish between tilapia species and sub-species by retrieving species-specific nuclear DNA markers (SNPs) using two approaches: (i) sequencing of the coding regions of the ADA gene; and (ii) next-generation sequencing, both standard R

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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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Wang, Wei. "Unveiling Molecular Mechanisms of piRNA Pathway from Small Signals in Big Data: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/805.

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PIWI-interacting RNAs (piRNA) are a group of 23–35 nucleotide (nt) short RNAs that protect animal gonads from transposon activities. In Drosophila germ line, piRNAs can be categorized into two different categories— primary and secondary piRNAs— based on their origins. Primary piRNAs, generated from transcripts of specific genomic regions called piRNA clusters, which are enriched in transposon fragments that are unlikely to retain transposition activity. The transcription and maturation of primary piRNAs from those cluster transcripts are poorly understood. After being produced, a group of prim

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Wang, Wei. "Unveiling Molecular Mechanisms of piRNA Pathway from Small Signals in Big Data: A Dissertation." eScholarship@UMMS, 2010. http://escholarship.umassmed.edu/gsbs_diss/805.

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PIWI-interacting RNAs (piRNA) are a group of 23–35 nucleotide (nt) short RNAs that protect animal gonads from transposon activities. In Drosophila germ line, piRNAs can be categorized into two different categories— primary and secondary piRNAs— based on their origins. Primary piRNAs, generated from transcripts of specific genomic regions called piRNA clusters, which are enriched in transposon fragments that are unlikely to retain transposition activity. The transcription and maturation of primary piRNAs from those cluster transcripts are poorly understood. After being produced, a group of prim

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Castro, Lara Reinel de. "Análise exômica em pacientes portadores de cardiomiopatia hipertrófica." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/98/98131/tde-26042016-090654/.

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A cardiomiopatia hipertrófica (CMH) é uma doença geneticamente determinada, caracterizada por hipertrofia ventricular primária, com prevalência estimada de 0.2% na população geral. Qualquer portador tem 50% de chance de transmitir esta doença para seus filhos, o que torna cada vez mais relevante a importância do estudo genético dos indivíduos acometidos e de seus familiares. Já foram descritas diversas mutações genéticas causadoras de CMH, a maioria em genes que codificam proteínas do sarcômero, e algumas mutações mais raras em genes não sarcoméricos. O objetivo desse estudo é sequencia

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Cappi, Carolina. "Variações raras no genoma de pacientes com transtorno obsessivo-compulsivo." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/5/5142/tde-09092013-160344/.

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Estudos de variações genéticas raras têm caracterizado com sucesso regiões do genoma e processos biológicos envolvidos no risco de desenvolver transtornos psiquiátricos. Dentro deste contexto, o sequenciamento de nucleotídeos em larga escala de exons do genoma inteiro para a observação de variações raras, conhecidas em inglês como single-nucleotide variation (SNV), e mutações espontâneas (\"de novo\" - DNM) tornou-se uma abordagem essencial na descoberta de novos genes de risco para transtornos psiquiátricos. Até o presente momento, nenhum estudo de SNV e variações de novo com sequenciamento d

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21

Silva, Artur Guazzelli Leme. "A influência de polimorfismos de base única na metilação de DNA em genes de receptores olfatórios." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-19072018-104722/.

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Os genes de receptores olfatórios (OR) pertencem a uma família de proteínas de membrana formada por cerca de 1000 genes no genoma de camundongo. Os genes OR são expressos de forma monogênica e monoalélica nos neurônios olfatórios (OSNs). No entanto, ainda não está claro o mecanismo que permite essa forma de expressão peculiar, sobretudo, qual o papel da metilação de DNA nesse processo. Nosso estudo determinou o padrão de metilação de DNA da região promotora e codificadora do gene Olfr17. Em células de epitélio olfatório (MOE) de camundongos adultos, observamos na região codificadora (CDS) do g

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22

Reis, Viviane Neri de Souza. "Variações de novo e raras no genoma de pacientes com transtornos do espectro do autismo verbais e não verbais." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/5/5142/tde-08122014-121628/.

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Estudos de gêmeos e famílias demonstram que os transtornos do espectro do autismo (TEA) apresentam um grande componente genético (~50%), porém sua etiologia ainda é desconhecida, possivelmente devido aos TEA serem caracterizados como doenças complexas, poligênicas e multifatoriais. Recentemente, variações no número de cópias (CNVs, do inglês Copy Number Variations) e mutações pontuais (SNV, do inglês Single Nucleotide Variant) raras, de novo e herdadas foram associadas com TEA, sugerindo novos loci e genes candidatos. No entanto, a grande maioria das alterações descritas são individuais, de fo

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23

Lopalco, Maria. "A new class of enzymatically cleavable nucleotides for DNA sequencing by synthesis." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/15233.

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A new family of nucleotides has been designed, synthesised and evaluated for DNA sequencing by synthesis. Each of the nucleotide analogues had a free 3’-OH group and a fluorophore attached to the base through a small peptide linkage that was designed to stop multiple base additions. Analysis by HPLC and MALDI-TOF proved the modified nucleotides were incorporated into a growing DNA strand by a DNA polymerase and that the peptide linker was cleaved with high efficiency after incubation of the extended primer with a protease. Enzymatically cleavable nucleotides were successfully applied to chip-b

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Hansen, Tarrant William. "Evaluation of molecular methods used for the rapid detection of multi-drug resistant Mycobacterium tuberculosis." Thesis, Queensland University of Technology, 2008. https://eprints.qut.edu.au/20723/1/Tarrant_Hansen_Thesis.pdf.

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Tuberculosis remains a major public health issue globally, with an estimated 9.2 million new cases in 2006. A new threat to TB control is the emergence of drug resistant strains. These strains are harder to cure as standard anti-tuberculosis first line treatments are ineffective. Multi Drug Resistant Tuberculosis (MDR-TB) is defined as Mycobacterium tuberculosis that has developed resistance to at least rifampicin and isoniazid, and these strains now account for greater than 5% of worldwide cases. Mutations within the Rifampicin Resistance Determining Region (RRDR) of the rpoB gene are pre

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Hansen, Tarrant William. "Evaluation of molecular methods used for the rapid detection of multi-drug resistant Mycobacterium tuberculosis." Queensland University of Technology, 2008. http://eprints.qut.edu.au/20723/.

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Tuberculosis remains a major public health issue globally, with an estimated 9.2 million new cases in 2006. A new threat to TB control is the emergence of drug resistant strains. These strains are harder to cure as standard anti-tuberculosis first line treatments are ineffective. Multi Drug Resistant Tuberculosis (MDR-TB) is defined as Mycobacterium tuberculosis that has developed resistance to at least rifampicin and isoniazid, and these strains now account for greater than 5% of worldwide cases. Mutations within the Rifampicin Resistance Determining Region (RRDR) of the rpoB gene are pre

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Yamamoto, Guilherme Lopes. "Aplicabilidade clínica da técnica de sequenciamento de nova geração com enfoque em displasias esqueléticas." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/5/5141/tde-18122017-091713/.

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INTRODUÇÃO: Na última década surgiu uma nova técnica, o sequenciamento de nova geração, que, contrário ao método tradicional de Sanger, permite o sequenciamento em paralelo e em larga escala de múltiplos genes, ou até mesmo todos os genes humanos, a menor custo e com uma análise mais acelerada. Essa técnica possibilitou a descoberta de novos genes responsáveis por diversas doenças mendelianas, sendo rapidamente incorporada no contexto clínico. OBJETIVOS: comparar os resultados das técnicas de Sanger e sequenciamento de nova geração em amostras controle; introduzir a técnica de sequenciamento d

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Benazir, Katarina Marquez. "Molecular Marker Applications in Oat (Avena Sativa L.) Breeding and Germplasm Diagnostics." Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31148.

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The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selectio

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28

Baratela, Wagner Antonio da Rosa. "Estudo genético-clínico das displasias esqueléticas, com enfoque nas osteocondrodisplasias com acometimento do esqueleto axial, associado ao envolvimento epifisário e/ou metafisário." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/5/5141/tde-02072018-120400/.

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INTRODUÇÃO: As osteocondrodisplasias constituem um grupo heterogêneo de doenças que comprometem a formação, crescimento e desenvolvimento do sistema esquelético. O diagnóstico definitivo, principalmente nas formas com acometimento de coluna, epífise e/ou metáfise, é desafiador, devido à heterogeneidade genética, raridade de algumas formas específicas e da sobreposição de fenótipos clínico-radiológicos. OBJETIVOS: avaliar as características clínico-radiológicas e as bases moleculares de um grupo de pacientes com osteocondrodisplasias com envolvimento do esqueleto axial associado a anomalias epi

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29

Piazza, João Paulo. "Uma metodologia para determinação do organismo de origem de sequencias de DNA com aplicação em projetos EST." [s.n.], 2004. http://repositorio.unicamp.br/jspui/handle/REPOSIP/275787.

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Orientador: João Carlos Setubal<br>Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Computação<br>Made available in DSpace on 2018-08-31T09:21:06Z (GMT). No. of bitstreams: 1 Piazza_JoaoPaulo_M.pdf: 1307969 bytes, checksum: 885944b1beb24b7a3979738e217bfb50 (MD5) Previous issue date: 2004<br>Resumo: Este trabalho apresenta uma nova metodologia para a determinação computacional do organismo de origem de seqüência de DNA, implementada na forma de um programa chamado QUEST. O QUEST é baseado em dois princípios: a extração de informações intrínsecas a cada seqüência, chama

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Silva, Amanda Santiago Ferreira Lantyer. "Filogeografia e genômica populacional de anuros neotropicais : estruturação, diversidade e demografia histórica /." Rio Claro, 2019. http://hdl.handle.net/11449/182576.

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Orientador: Célio Fernando Baptista Haddad<br>Resumo: Nesta tese exploramos a diversificação de espécies de anuros da Tribo Lophyohylini distribuídas na Mata Atlântica (MA) e Caatinga, biomas do Brasil. Para tanto, utilizamos dados genômicos e métodos de filogeografia estatística para analisá-los, uma abordagem robusta e até então ainda escassa na filogeografia dos organismos sul-americanos. Através do sequenciamento Sanger amostramos trechos de DNA mitocondrial (mtDNA) e através do sequenciamento de alto rendimento obtivemos polimorfismos de nucleotídeo único (SNPs) do DNA nuclear (nDNA). No

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Guo, Wenjing. "Design and synthesis of novel nucleotide analogs and protein conjugates for DNA sequencing." Thesis, 2016. https://doi.org/10.7916/D8ZP4686.

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Sequencing by Synthesis (SBS), a DNA sequencing methodology based on the DNA polymerase reaction, is a promising paradigm for deciphering large-scale genomes. This thesis describes the design and synthesis of a variety of nucleotide reversible terminators (NRTs) with different characteristics. One set of NRTs possesses a phosphate moiety attached to the 2’ position of the sugar to block further incorporation in polymerase reaction, with the potential for fluorescent tag attachment at the same site or on the base through a cleavable linker for detection. The other set of NRTs possesses a

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Payne, Christina M. "Molecular dynamics simulation of a nanoscale device for fast sequencing of DNA." Diss., 2007. http://etd.library.vanderbilt.edu/ETD-db/available/etd-11282007-144800/.

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"Bioinformatics analyses for next-generation sequencing of plasma DNA." 2012. http://library.cuhk.edu.hk/record=b5549423.

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1997年，Dennis等證明胚胎DNA在孕婦母體中存在的事實開啟了產前無創診斷的大門。起初的應用包括性別鑒定和恒河猴血型系統的識別。隨著二代測序的出現和發展，對外周血游離DNA更加成熟的分析和應用應運而生。例如當孕婦懷孕十二周時，應用二代測序技術在母體外周血DNA中預測胎兒21號染色體是否是三倍體，其準確性達到98%。本論文的第一部分介紹如何應用母體外周血DNA構建胎兒的全基因組遺傳圖譜。這項研究極具挑戰，原因是孕後12周，胎兒對外周血DNA貢獻很小，大多數在10%左右，另外外周血中的胎兒DNA大多數短於200 bp。目前的演算法和程式都不適合於從母體外周血DNA中構建胎兒的遺傳圖譜。在這項研究中，根據母親和父親的基因型，用生物資訊學手段先構建胎兒可能有的遺傳圖譜，然後將母體外周血DNA的測序資訊比對到這張可能的遺傳圖譜上。如果在母親純和遺傳背景下，決定父親的特異遺傳片段，只要定性檢測父親的特異遺傳片段是否在母體外周血中存在。如果在母親雜合遺傳背景下，決定母親的遺傳特性，就要進行定量分析。我開發了單倍型相對劑量分析方案，統計學上判斷母親外周血中的兩條單倍型相對劑量水準，顯著增加的單倍型即為最大可能地遺傳給胎兒的單倍型。單倍型相對劑量分析方案可以加強測序資訊的分析效率，降低測序數據波動，比單個位點分析更加穩定，強壯。<br>隨著靶標富集測序出現，測序價格急劇下降。第一部分運用母

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Erturk, Ece. "Photochemical and Enzymatic Method for DNA Methylation Profiling and Walking Approach for Increasing Read Length of DNA Sequencing by Synthesis." Thesis, 2018. https://doi.org/10.7916/D88W4WQ5.

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The first half of this dissertation demonstrates development of a novel method for DNA methylation profiling based on site specific conversion of cytosine in CpG sites catalyzed by DNA methyltransferases. DNA methylation, a chemical process by which DNA bases are modified by methyl groups, is one of the key epigenetic mechanisms used by cells to regulate gene expression. It predominantly occurs at the 5-position of cytosines in CpG sites and is essential in normal development. Aberrant methylation is associated with many diseases including cancer. Bisulfite Genomic Sequencing (BGS), the gold s

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Hsieh, Min-Kang. "Design and Synthesis of 3'-Oxygen-Modified Cleavable Nucleotide Reversible Terminators for Scarless DNA Sequencing by Synthesis." Thesis, 2018. https://doi.org/10.7916/D8XD2HST.

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This dissertation describes the design and synthesis of novel cleavable fluorescent/anchor modified nucleotide reversible terminators using 3’-O-dithiomethyl (3’-O-DTM; 3’-O-SS) as a linker to directly or indirectly attach a fluorescent reporter to achieve scarless DNA Sequencing by Synthesis (SBS). To develop these nucleotide analogues for four-color SBS, two nucleotide analogues (3’-O-ROX-SS-dATP and 3’-O-BodipyFL-SS-dTTP) with directly attached fluorescent dyes and two other nucleotide analogues with directly attached biotin or trans-cyclooctene (TCO) as anchors (3’-O-Biotin-SS-dCTP and 3’-

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Ren, Jianyi. "Design and Synthesis of Novel Cleavable Fluorescent Nucleotide Reversible Terminators Using Disulfide Linkers for DNA Sequencing by Synthesis." Thesis, 2018. https://doi.org/10.7916/D82R544K.

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High-throughput DNA sequencing technology has advanced rapidly in the past few decades and is the driving force for personalized precision medicine. In this Thesis, a set of novel disulfide linker-based nucleotide reversible terminators (NRTs) has been designed and synthesized for application in DNA sequencing by synthesis (SBS), which is the dominant sequencing platform. The design and synthesis principles are outlined as follows. Four nucleotides (A, C, G, T) are modified as NRTs for the DNA extension reaction catalyzed by polymerase by attaching a cleavable fluorophore to a specific locatio

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Fox, Samuel E. "Transcriptomic analysis using high-throughput sequencing and DNA microarrays." Thesis, 2011. http://hdl.handle.net/1957/23741.

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Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental cues. Two major methods are utilized for the study of transcriptomes, high-throughput sequencing and microarray analysis. High-throughput sequencing technologies such as the Illumina platform are relatively new and protocols must be

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"Plasma DNA sequencing: a tool for noninvasive prenatal diagnosis and research into circulating nucleic acids." Thesis, 2010. http://library.cuhk.edu.hk/record=b6075311.

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In the first part of this thesis, two chromosome Y specific genes ( SRYand TSPY) were chosen as the molecular targets to investigate the characteristics of fetal-specific DNA fragments in maternal plasma. By employing the touch down ligation-mediated PCR coupled with cloning and sequencing, the end property and the fragment species of fetal DNA were studied.<br>Noninvasive prenatal detection of fetal chromosomal aneuploidies is a much sought-after goal in fetomaternal medicine. The discovery of fetal DNA in the plasma of pregnant women has offered new opportunities for this purpose. However, t

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Wang, Xuanting. "Identification of SARS-CoV-2 Polymerase and Exonuclease Inhibitors and Novel Methods for Single-Color Fluorescent DNA Sequencing by Synthesis." Thesis, 2021. https://doi.org/10.7916/d8-n6ah-nt76.

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This dissertation is divided into two main sections describing major portions of my Ph.D. research: (1) development of two enzymatic assays for identifying inhibitors of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and the associated proofreading exonuclease complexes, two key enzymatic activities of SARS-CoV-2, the virus responsible for the COVID-19 pandemic and (2) the design and implementation of four novel single-color fluorescent DNA sequencing by synthesis (SBS) methods, including the synthesis of many of the key nucleotide analogues required for these studies. In response to the COV

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"Development of bioinformatics algorithms for trisomy 13 and 18 detection by next generation sequencing of maternal plasma DNA." 2011. http://library.cuhk.edu.hk/record=b5894869.

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Chen, Zhang.<br>Thesis (M.Phil.)--Chinese University of Hong Kong, 2011.<br>Includes bibliographical references (p. 109-114).<br>Abstracts in English and Chinese.<br>ABSTRACT --- p.I<br>摘要 --- p.III<br>ACKNOWLEDGEMENTS --- p.IV<br>PUBLICATIONS --- p.VI<br>CONTRIBUTORS --- p.VII<br>TABLE OF CONTENTS --- p.VIII<br>LIST OF TABLES --- p.XIII<br>LIST OF FIGURES --- p.XIV<br>LIST OF ABBREVIATIONS --- p.XVI<br>Chapter SECTION I : --- BACKGROUND --- p.1<br>Chapter CHAPTER 1: --- PRENATAL DIAGNOSIS OF FETAL TRISOMY BY NEXT GENERATION SEQUENCING TECHNOLOGY --- p.2<br>Chapter 1.1 --- FETAL T

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Andere, Anne A. "De novo genome assembly of the blow fly Phormia regina (Diptera: Calliphoridae)." Thesis, 2014. http://hdl.handle.net/1805/5630.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>Phormia regina (Meigen), commonly known as the black blow fly is a dipteran that belongs to the family Calliphoridae. Calliphorids play an important role in various research fields including ecology, medical studies, veterinary and forensic sciences. P. regina, a non-model organism, is one of the most common forensically relevant insects in North America and is typically used to assist in estimating postmortem intervals (PMI). To better understand the roles P. regina plays in the numerous research fields, we re-constructed its genome

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