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Dissertations / Theses on the topic 'High-throughput sequencing of the genome'

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Published: 7 June 2025

Last updated: 2 August 2025

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1

Hoffmann, Steve. "Genome Informatics for High-Throughput Sequencing Data Analysis." Doctoral thesis, Universitätsbibliothek Leipzig, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-152643.

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This thesis introduces three different algorithmical and statistical strategies for the analysis of high-throughput sequencing data. First, we introduce a heuristic method based on enhanced suffix arrays to map short sequences to larger reference genomes. The algorithm builds on the idea of an error-tolerant traversal of the suffix array for the reference genome in conjunction with the concept of matching statistics introduced by Chang and a bitvector based alignment algorithm proposed by Myers. The algorithm supports paired-end and mate-pair alignments and the implementation offers methods fo

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Person, Kerry P. (Kerry Patrick). "Operational streamlining in a high-throughput genome sequencing center." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/37248.

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Thesis (M.B.A.)--Massachusetts Institute of Technology, Sloan School of Management; and, (S.M.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering; in conjunction with the Leaders for Manufacturing Program at MIT, 2006.<br>Includes bibliographical references (p. 83-84).<br>Advances in medicine rely on accurate data that is rapidly provided. It is therefore critical for the Genome Sequencing platform of the Broad Institute of MIT and Harvard to continually strive to reduce cost, improve throughput, and increase the quality of its data output. In the past, new technology in th

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de, Lange Katrina Melanie. "Understanding inflammatory bowel disease using high-throughput sequencing." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/265370.

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For over two decades, the study of genetics has been making significant progress towards understanding the causes of common disease. Across a wide range of complex disorders there have been hundreds of associated loci identified, largely driven by common genetic variation. Now, with the advent of next-generation sequencing technology, we are able to interrogate rare and low frequency variation in a high throughput manner for the first time. This provides an exciting opportunity to investigate the role of rarer variation in complex disease risk on a genome-wide scale, potentially o↵ering novel

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Esteve, Codina Anna. "Characterization of the Iberian pig genome and transcriptome using high throughput sequencing." Doctoral thesis, Universitat Autònoma de Barcelona, 2012. http://hdl.handle.net/10803/134673.

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En aquesta tesis, hem estudiat els patrons de variabilidad nucleotídica del genoma del porc per entendre millor quines forces evolutives l’han afectat. El porc domèstic és una espècie domèstica que presenta una gran variabilitat fenotípica arrel del procés de domesticació i de la formació de races moderna. A més, el porc senglar i altres espècies pròximes encara, avui, estan vives, facilitant, així, la búsqueda de gens candidats que han sofert selecció artificial. El porc, és, també, important en el camp de la biomedicina, com a model de malalties humanes i com a reservori d’organs humans.

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Marticke, Simone Sigrid. "Ultra-high throughput sequencing analysis of FOXP2 occupancy in the human genome /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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6

Roguski, Łukasz 1987. "High-throughput sequencing data compression." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/565775.

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Thanks to advances in sequencing technologies, biomedical research has experienced a revolution over recent years, resulting in an explosion in the amount of genomic data being generated worldwide. The typical space requirement for storing sequencing data produced by a medium-scale experiment lies in the range of tens to hundreds of gigabytes, with multiple files in different formats being produced by each experiment. The current de facto standard file formats used to represent genomic data are text-based. For practical reasons, these are stored in compressed form. In most cases, such storage

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Kamps-Hughes, Nicholas. "Massively Parallel Sequencing-Based Analyses of Genome and Protein Function." Thesis, University of Oregon, 2015. http://hdl.handle.net/1794/19234.

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The advent of high-throughput DNA and RNA sequencing has made possible the assay of millions of nucleic acid molecules in parallel. This allows functional genomic elements to be identified from background in single-tube experiments. This dissertation discusses the development of two such functional screens as well as work implementing a third that was previously developed in my thesis laboratory. Restriction-Associated DNA sequencing (RAD-Seq) is a complexity reduction sequencing method that allows the same subset of genomic sequence to be read across multiple samples. Differences in

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Bysani, Madhusudhan Reddy. "Genome-Wide Studies of Transcriptional Regulation in Human Liver Cells by High-throughput Sequencing." Doctoral thesis, Uppsala universitet, Medicinsk genetik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-198579.

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The human genome contains slightly more than 20 000 genes that are expressed in a tissue specific manner. Transcription factors play a key role in gene regulation. By mapping the transcription factor binding sites genome-wide we can understand their role in different biological processes. In this thesis we have mapped transcription factors and histone marks along with nucleosome positions and RNA levels. In papers I and II, we used ChIP-seq to map five liver specific transcription factors that are crucial for liver development and function. We showed that the mapped transcription factors are i

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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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Moreland, Blythe S. "Genome-wide studies of DNA and RNA with modifications through high-throughput sequencing analysis." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu153452875946939.

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11

Stromberg, Michael Peter. "Enabling high-throughput sequencing data analysis with MOSAIK." Thesis, Boston College, 2010. http://hdl.handle.net/2345/1332.

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Thesis advisor: Gabor T. Marth<br>During the last few years, numerous new sequencing technologies have emerged that require tools that can process large amounts of read data quickly and accurately. Regardless of the downstream methods used, reference-guided aligners are at the heart of all next-generation analysis studies. I have developed a general reference-guided aligner, MOSAIK, to support all current sequencing technologies (Roche 454, Illumina, Applied Biosystems SOLiD, Helicos, and Sanger capillary). The calibrated alignment qualities calculated by MOSAIK allow the user to fine-tune the

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Vokoun, Matthew R. (Matthew Richard). "Operations capability improvement of a molecular biology laboratory in a high throughput genome sequencing center." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/35697.

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Thesis (M.B.A.)--Massachusetts Institute of Technology, Sloan School of Management; and, (S.M.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering; in conjunction with the Leaders for Manufacturing Program at MIT, 2005.<br>This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Vita.<br>Includes bibliographical references (leaves 108-110).<br>The Broad Institute is a research collaboration of MIT, Harvard University and affiliated hospitals, and the Whitehead Institute for Biomedica

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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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Izuno, Ayako. "Ecological and conservation genomics for the tropical tree species Metrosideros polymorpha and Shorea leprosula." Kyoto University, 2016. http://hdl.handle.net/2433/215595.

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Kyoto University (京都大学)<br>0048<br>新制・課程博士<br>博士(農学)<br>甲第19769号<br>農博第2165号<br>新制||農||1040(附属図書館)<br>学位論文||H28||N4985(農学部図書室)<br>32805<br>京都大学大学院農学研究科森林科学専攻<br>(主査)教授井鷺裕司, 教授北山兼弘, 教授神﨑護<br>学位規則第4条第1項該当

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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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Sazinas, Pavelas. "The application of high-throughput sequencing to study the genome composition and transcriptional response of Haemophilus influenzae." Thesis, University of Warwick, 2016. http://wrap.warwick.ac.uk/89145/.

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Haemophilus influenzae is an important human pathogen, responsible for respiratory infections, such as otitis media, bronchitis and epiglottitis, as well as invasive disease. Despite being the first free-‐living organism to have its whole genome sequenced, there have been only a few published studies investigating its transcriptional profile using next-‐generation sequencing (NGS). The work presented in this thesis aimed to use NGS to improve the understanding of how H. influenzae behaves during natural infection and to identify novel RNA structures with potentially important roles in pathog

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Pfeifer, Susanne. "Statistical challenges in the detection of mutation and variation using high throughput sequencing." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:e49ce2fa-aa2c-42d7-bb54-c63e50d14afb.

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The aim of this thesis is to obtain a better understanding of mutation rates within as well as between the genomes of humans and chimpanzees using data generated by high throughput sequencers. I will start with a review of the field and an overview of the technologies and protocols used to generate and analyse high throughput sequencing data. I apply some of the discussed techniques to show that there is evidence of a selective advantage of pathogenic de novo mutations in the Fibroblast Growth Factor Receptor 3 gene in the male germ line of humans. Furthermore, I use some of the methods to gen

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Ballinger, Tracy J. "Analysis of genomic rearrangements in cancer from high throughput sequencing data." Thesis, University of California, Santa Cruz, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3729995.

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<p> In the last century cancer has become increasingly prevalent and is the second largest killer in the United States, estimated to afflict 1 in 4 people during their life. Despite our long history with cancer and our herculean efforts to thwart the disease, in many cases we still do not understand the underlying causes or have successful treatments. In my graduate work, I’ve developed two approaches to the study of cancer genomics and applied them to the whole genome sequencing data of cancer patients from The Cancer Genome Atlas (TCGA). In collaboration with Dr. Ewing, I built a pipel

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Hoffmann, Steve [Verfasser], Peter F. [Gutachter] Stadler, and Rolf [Gutachter] Backofen. "Genome Informatics for High-Throughput Sequencing Data Analysis : Methods and Applications / Steve Hoffmann ; Gutachter: Peter F. Stadler, Rolf Backofen." Leipzig : Universitätsbibliothek Leipzig, 2014. http://d-nb.info/1238789528/34.

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Kung, Johnny Tsun-Yi. "Genome-wide Analysis of Ctcf-RNA Interactions." Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11618.

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Ctcf is a "master regulator" of the genome that plays a role in a variety of gene regulatory functions as well as in genome architecture. Evidence from studying the epigenetic process of X-chromosome inactivation suggests that, in certain cases, Ctcf might carry out its functions through interacting with RNA. Using mouse embryonic stem (ES) cells and a modified protocol for UV-crosslinking and immunoprecipitation followed by high-throughput sequencing (CLIP-seq), Ctcf is found to interact with a multitude of transcripts genome-wide, both protein-coding mRNA (or noncoding transcripts therein) a

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Glaus, Peter. "Bayesian methods for gene expression analysis from high-throughput sequencing data." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/bayesian-methods-for-gene-expression-analysis-from-highthroughput-sequencing-data(cf9680e0-a3f2-4090-8535-a39f3ef50cc4).html.

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We study the tasks of transcript expression quantification and differential expression analysis based on data from high-throughput sequencing of the transcriptome (RNA-seq). In an RNA-seq experiment subsequences of nucleotides are sampled from a transcriptome specimen, producing millions of short reads. The reads can be mapped to a reference to determine the set of transcripts from which they were sequenced. We can measure the expression of transcripts in the specimen by determining the amount of reads that were sequenced from individual transcripts. In this thesis we propose a new probabilist

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González-Vallinas, Rostes Juan 1983. "Software development and analysis of high throughput sequencing data for genomic enhancer prediction." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/283480.

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High Throughput Sequencing technologies (HTS) are becoming the standard in genomic regulation analysis. During my thesis I developed software for the analysis of HTS data. Through collaborations with other research groups, I specialized in the analysis of ChIP-Seq short mapped reads. For instance, I collaborated in the analysis of the effect of Hog1 stress induced response in Yeast and helped in the design of a multiple promoter-alignment method using ChIP-Seq data, among other collaborations. Making use of expertise and the software developed during this time, I analyzed ENCODE datasets

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Hutt, Kasey Robert. "High-throughput genomic assays applications and analysis of DSL technology and next-generation sequencing /." Diss., [La Jolla, Calif.] : University of California, San Diego, 2009. http://wwwlib.umi.com/cr/ucsd/fullcit?p3337194.

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Thesis (Ph. D.)--University of California, San Diego, 2009.<br>Title from first page of PDF file (viewed Jan. 9, 2009). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 117-130).

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Tan, Cong. "Exploring genomic diversity in wild and cultivated barley using high throughput DNA sequencing technology." Thesis, Tan, Cong (2018) Exploring genomic diversity in wild and cultivated barley using high throughput DNA sequencing technology. PhD thesis, Murdoch University, 2018. https://researchrepository.murdoch.edu.au/id/eprint/41577/.

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Barley (Hordeum vulgare L.) was domesticated from wild barley (Hordeum spontaneum L.) around 10,000 years ago in the Fertile Crescent. It has been widely used as a model organism to research plant adaptive evolutionary processes as well as a vital genetic repository to explore plant abiotic and biotic stress tolerance. This thesis used the recent barley genome sequence as a reference to characterise the genomic evolution of wild barley, explore genomic diversity, and created a database of barley genomic variation. Wild barley accessions from oppos ite slopes of the ‘Evolution Canyon’ in Is

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Das, Samarendra. "Statistical Approaches of Gene Set Analysis with Quantitative Trait Loci for High-throughput Genomic Studies." Dissertation/Thesis, University of Louisville, 2020. http://krishi.icar.gov.in/jspui/handle/123456789/74070.

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Ph.D. Dissertation Thesis<br>Recently, gene set analysis has become the first choice for gaining insights into the underlying complex biology of diseases through high-throughput genomic studies, such as Microarrays, bulk RNA-Sequencing, single cell RNA-Sequencing, etc. It also reduces the complexity of statistical analysis and enhances the explanatory power of the obtained results. Further, the statistical structure and steps common to these approaches have not yet been comprehensively discussed, which limits their utility. Hence, a comprehensive overview of the available gene set analysis app

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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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Wegner, Fanny. "Genomic studies on the impact of host/virus interaction in EBV infection using massively parallel high throughput sequencing." Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/1570481/.

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Epstein-Barr virus is one of the most common viral infections in humans and, once acquired, persists within its host throughout their life. EBV therefore represents an ex- tremely successful virus, having evolved complex strategies to evade the host’s innate and adaptive immune response during both initial and persistent stages of infection. While infection is mostly harmless in the majority of cases, EBV has the ability to be oncogenic in some individuals, and is associated with a wide range of malignancies as well as non-cancerous diseases. To generate new and useful insights into the evolut

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Morlot, Jean-Baptiste. "Annotation of the human genome through the unsupervised analysis of high-dimensional genomic data." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066641/document.

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Le corps humain compte plus de 200 types cellulaires différents possédant une copie identique du génome mais exprimant un ensemble différent de gènes. Le contrôle de l'expression des gènes est assuré par un ensemble de mécanismes de régulation agissant à différentes échelles de temps et d'espace. Plusieurs maladies ont pour cause un dérèglement de ce système, notablement les certains cancers, et de nombreuses applications thérapeutiques, comme la médecine régénérative, reposent sur la compréhension des mécanismes de la régulation géniques. Ce travail de thèse propose, dans une première partie,

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Caporossi, Alban. "Apport du séquençage haut débit dans l'analyse bioinformatique du génome du virus de l'hépatite C." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAS021/document.

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Le séquençage haut débit a été utilisé dans ce travail pour reconstruire avec des méthodes adaptées le génomeviral entier du virus de l’hépatite C (VHC) notamment pour le typer avec précision. Une étude a ainsi permisde mettre en évidence la présence d’une forme recombinante du VHC chez un patient. Une autre a permisde typer et détecter les mutations de résistance de plusieurs souches de VHC de génotypes différents. Enfin,une dernière étude basée sur cette approche a permis de découvrir une souche VHC appartenant à un nouveausous-type. Le séquençage haut débit a aussi été utilisé dans ce trava

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Gurjav, Ulziijargal. "Molecular epidemiology of tuberculosis in low and high incidence settings." Thesis, The University of Sydney, 2016. http://hdl.handle.net/2123/16481.

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Tuberculosis (TB) surpassed HIV/AIDS in 2015 to become the greatest infectious disease killer on the planet, while the inexorable rise of drug-resistant TB adds another layer of complexity to TB control challenges in both high and low incidence settings. The advances in molecular genotyping of Mycobacterium tuberculosis has promised new but yet validated evidence and performance indicators to inform jurisdictional TB control programs. The overall aim of this thesis was to improve our understanding of the epidemiology of M. tuberculosis through integration of traditional genotyping and geospati

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Li, Yanhui. "Construction and Analysis of a Genome-Wide Insertion Library in Schizosaccharomyces pombe Reveals Novel Aspects of DNA Repair." Case Western Reserve University School of Graduate Studies / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=case1413927620.

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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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Kranz, Angela [Verfasser], Michael [Akademischer Betreuer] Bott, and Michael [Gutachter] Bott. "High-resolution genome and transcriptome analysis of Gluconobacter oxydans 621H and growth-improved strains by next-generation sequencing / Angela Kranz ; Gutachter: Michael Bott ; Betreuer: Michael Bott." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2018. http://d-nb.info/1169393349/34.

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Pavinato, Vitor Antonio Corrêa 1983. "Estudo da variabilidade genética, estruturação populacional e busca de variação alélica em locos associados à adaptação inseto-planta em Diatraea saccharalis (Fabr. 1794) (Lepidoptera: Crambidae) = Genetic variability, population structure and genome scan for host-plant association in Diatraea saccharalis (Fabr. 1794) (Lepidoptera: Crambidae)." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/317087.

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Orientadores: Maria Imaculada Zucchi, Anete Pereira de Souza<br>Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia<br>Made available in DSpace on 2018-08-27T12:00:33Z (GMT). No. of bitstreams: 1 Pavinato_VitorAntonioCorrea_D.pdf: 6829608 bytes, checksum: 7fdb8c74593eb4dc2fe78e2302d3995f (MD5) Previous issue date: 2014<br>Resumo: A associação entre subpopulações de insetos e plantas-hospedeiras pode ocorrer por adaptação e esta, pode ser uma etapa anterior ao surgimento de raças-hospedeiras e especialização. Pouco se sabe sobre o papel da mudança da composição da pais

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Mozere, M. "High-throughput sequencing analysis pipeline." Thesis, University College London (University of London), 2016. http://discovery.ucl.ac.uk/1528797/.

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High-throughput sequencing methods were developed to increase the productivity of processing data from genomic DNA. Sequencing platforms are generating massive amounts of genetic variation data which makes it difficult to pinpoint a small subset of functionally important variants. The focus has now shifted from generating sequences to searching for the critical differences that separate normal variants from disease ones. Our High-throughput Sequencing Analysis Pipeline (HSAP) is a multistep analysis software designed to annotate and filter variants in a top-down fashion from Variant Calling Fo

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Durif, Ghislain. "Multivariate analysis of high-throughput sequencing data." Thesis, Lyon, 2016. http://www.theses.fr/2016LYSE1334/document.

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L'analyse statistique de données de séquençage à haut débit (NGS) pose des questions computationnelles concernant la modélisation et l'inférence, en particulier à cause de la grande dimension des données. Le travail de recherche dans ce manuscrit porte sur des méthodes de réductions de dimension hybrides, basées sur des approches de compression (représentation dans un espace de faible dimension) et de sélection de variables. Des développements sont menés concernant la régression "Partial Least Squares" parcimonieuse (supervisée) et les méthodes de factorisation parcimonieuse de matrices (non s

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Macêdo, Francisca Delanie Bulcão de. "Mutações inativadoras no gene MKRN3 são causa de puberdade precoce central familial." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/5/5135/tde-30062016-163440/.

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A maioria dos casos de puberdade precoce central (PPC) em meninas permanece idiopática. A hipótese de uma causa genética vem se fortalecendo após a descoberta de alguns genes associados a este fenótipo, sobretudo aqueles implicados com o sistema kisspeptina (KISS1 e KISS1R). Entretanto, apenas casos isolados de PPC foram relacionados à mutação na kisspeptina ou em seu receptor. Até recentemente, a maioria dos estudos genéticos em PPC buscava genes candidatos selecionados com base em modelos animais, análise genética de pacientes com hipogonadismo hipogonadotrófico, ou ainda, nos estudos de ass

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Langenberger, David. "High-throughput sequencing and small non-coding RNAs." Doctoral thesis, Universitätsbibliothek Leipzig, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-112876.

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In this thesis the processing mechanisms of short non-coding RNAs (ncRNAs) is investigated by using data generated by the current method of high-throughput sequencing (HTS). The recently adapted short RNA-seq protocol allows the sequencing of RNA fragments of microRNA-like length (∼18-28nt). Thus, after mapping the data back to a reference genome, it is possible to not only measure, but also visualize the expression of all ncRNAs that are processed to fragments of this specific length. Short RNA-seq data was used to show that a highly abundant class of small RNAs, called microRNA-offset-RNAs

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Zhang, Xuekui. "Mixture models for analysing high throughput sequencing data." Thesis, University of British Columbia, 2011. http://hdl.handle.net/2429/35982.

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The goal of my thesis is to develop methods and software for analysing high-throughput sequencing data, emphasizing sonicated ChIP-seq. For this goal, we developed a few variants of mixture models for genome-wide profiling of transcription factor binding sites and nucleosome positions. Our methods have been implemented into Bioconductor packages, which are freely available to other researchers. For profiling transcription factor binding sites, we developed a method, PICS, and implemented it into a Bioconductor package. We used a simulation study to confirm that PICS compares favourably to riva

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Roberts, Adam. "Ambiguous fragment assignment for high-throughput sequencing experiments." Thesis, University of California, Berkeley, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3616509.

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<p> As the cost of short-read, high-throughput DNA sequencing continues to fall rapidly, new uses for the technology have been developed aside from its original purpose in determining the genome of various species. Many of these new experiments use the sequencer as a digital counter for measuring biological activities such as gene expression (RNA-Seq) or protein binding (ChIP-Seq). </p><p> A common problem faced in the analysis of these data is that of sequenced fragments that are "ambiguous", meaning they resemble multiple loci in a reference genome or other sequence. In early analyses, su

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Duggett, Nicholas A. "High-throughput sequencing of the chicken gut microbiome." Thesis, University of Birmingham, 2016. http://etheses.bham.ac.uk//id/eprint/6678/.

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The chicken (\(Gallus\) \(gallus\) \(domesticus\)) is the most abundant and widely distributed livestock animal with a global population of over 21 bill ion. A newly hatched broiler chick increases its body weight by 25% overnight and 50-fold over five weeks. The symbiotic, complex and variable community of the microbiome forms an important part of the gastrointestinal tract (gut). It is involved in gut development, biochemistry, immunology, physiology and non-specific resistance to infection. This study investigated the chicken gut microbiota using high-throughput 16S rRNA sequencing and cult

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Chiang, HyoJin Rosaria. "Examination of mammalian microRNAs by high-throughput sequencing." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/65289.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2011.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>Small non-coding RNAs play an important role in a wide range of cellular events. MicroRNAs (miRNAs) are an abundant class of small RNAs that post-transcriptionally repress expression of their target genes. Since miRNA targeting is based on its sequence, accurate and comprehensive annotation of miRNA genes is fundamental to understanding miRNA gene regulation. Advances in high-throughput sequencing technology have led to discoveries

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Xing, Zhengrong. "Poisson multiscale methods for high-throughput sequencing data." Thesis, The University of Chicago, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10195268.

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<p> In this dissertation, we focus on the problem of analyzing data from high-throughput sequencing experiments. With the emergence of more capable hardware and more efficient software, these sequencing data provide information at an unprecedented resolution. However, statistical methods developed for such data rarely tackle the data at such high resolutions, and often make approximations that only hold under certain conditions. </p><p> We propose a model-based approach to dealing with such data, starting from a single sample. By taking into account the inherent structure present in such dat

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Schwartz, Jerrod Joseph. "Technologies for high throughput single molecule DNA sequencing /." May be available electronically:, 2009. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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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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Siragusa, Enrico [Verfasser]. "Approximate string matching for high-throughput sequencing / Enrico Siragusa." Berlin : Freie Universität Berlin, 2015. http://d-nb.info/1074404882/34.

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Keebler, Jonathan Edward Myers. "Spontaneous Mutation Discovery via High-Throughput Sequencing of Pedigrees." NCSU, 2010. http://www.lib.ncsu.edu/theses/available/etd-03312010-151914/.

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Recent technological advances have made high-throughput DNA sequencing a routine laboratory experiment. This progression in technology has been made possible by the parallel production of millions of short fragments of sequence. The responsibility of garnering biological information from these DNA fragments has shifted from the wet-lab to the bioinformatician. As sequencing technology is applied to a growing number of individual human genomes, entire families are now being sequenced. Information contained within the pedigree of a sequenced family can be leveraged when inferring the donorsâ gen

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Weese, David [Verfasser]. "Indices and Applications in High-Throughput Sequencing / David Weese." Berlin : Freie Universität Berlin, 2013. http://d-nb.info/1036130150/34.

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Woolford, Julie Ruth. "Statistical analysis of small RNA high-throughput sequencing data." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610375.

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Kothe, Caroline. "Diversité des bactéries halophiles dans l'écosystème fromager et étude de leurs impacts fonctionnels." Thesis, université Paris-Saclay, 2021. http://www.theses.fr/2021UPASB014.

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Les bactéries halophiles et halotolérantes sont généralement isolées dans des environnements naturels, bien qu'elles soient également présentes dans les aliments, comme les croûtes de fromage et les fruits de mer. Cependant, les études sur leurs fonctions écologiques et technologiques dans le fromage sont encore peu développées. Afin de combler le manque de données dans la littérature sur ce sujet, nous avons utilisé des approches culturales, génomiques et métagénomiques pour déconstruire ces écosystèmes dans les croûtes de fromages. L’approche culturale, assistée par le développement de strat

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