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Relevant bibliographies by topics / Next Generation Sequencing / Dissertations / Theses

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Dissertations / Theses on the topic 'Next Generation Sequencing'

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Published: 4 June 2021

Last updated: 25 July 2025

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1

Sundquist, Andreas. "Algorithms for next-generation sequencing /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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2

Espírito, Ana Cláudia Pereira. "Saccharomycotin transcriptomics by next-generation sequencing." Master's thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/15677.

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Mestrado em Biomedicina Molecular<br>The non-standard decoding of the CUG codon in Candida cylindracea raises a number of questions about the evolutionary process of this organism and other species Candida clade for which the codon is ambiguous. In order to find some answers we studied the transcriptome of C. cylindracea, comparing its behavior with that of Saccharomyces cerevisiae (standard decoder) and Candida albicans (ambiguous decoder). The transcriptome characterization was performed using RNA-seq. This approach has several advantages over microarrays and its application is booming. TopH

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3

Qiao, Dandi. "Statistical Approaches for Next-Generation Sequencing Data." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10689.

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During the last two decades, genotyping technology has advanced rapidly, which enabled the tremendous success of genome-wide association studies (GWAS) in the search of disease susceptibility loci (DSLs). However, only a small fraction of the overall predicted heritability can be explained by the DSLs discovered. One possible explanation for this ”missing heritability” phenomenon is that many causal variants are rare. The recent development of high-throughput next-generation sequencing (NGS) technology provides the instrument to look closely at these rare variants with precision and efficiency

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4

Iceton, Gregg. "Next generation sequencing for the water industry." Thesis, University of Newcastle upon Tyne, 2018. http://hdl.handle.net/10443/4187.

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The wastewater industry uses biotechnology to ensure that the discharge of sewage does not have deleterious effects on the environment, yet knowledge of the underlying microbiology is poor. This leads to over engineered and inefficient processes which occasionally and unexpectedly fail. Similarly the impact of sewage on the microbiology of receiving waters is unclear. Recent developments in DNA sequencing have enabled its use where cost was prohibitive. I investigated two applications of Next Generation Sequencing (NGS); activated sludge process monitoring for nitrification, foaming and bulkin

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Odelgard, Anna. "Coverage Analysis in Clinical Next-Generation Sequencing." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-379228.

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With the new way of sequencing by NGS new tools had to be developed to be able to work with new data formats and to handle the larger data sizes compared to the previous techniques but also to check the accuracy of the data. Coverage analysis is one important quality control for NGS data, the coverage indicates how many times each base pair has been sequenced and thus how trustworthy each base call is. For clinical purposes every base of interest must be quality controlled as one wrong base call could affect the patient negatively. The softwares used for coverage analysis with enough accuracy

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6

Clifford, Harry William. "Next generation sequencing in disease-relevant tissues." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:cf2eb0ac-62dd-41c7-896d-35f11f416b82.

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Studies of RNA and the transcriptome are of great importance in providing functional information and unravelling the genetic mechanisms that underlie complex disorders and diseases. With the vast majority of complex disease-associated variants falling outside protein-coding regions of the genome, it is likely that variations in gene expression regulation will be essential to understanding disease aetiology. Information on RNA quantity and splicing isoforms is therefore likely to be crucial for understanding complex pathologies of deleterious genetic variation. The advent of next generation seq

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7

Pyon, Yoon Soo. "Variant Detection Using Next Generation Sequencing Data." Case Western Reserve University School of Graduate Studies / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=case1347053645.

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8

Sala, Claudia. "Ecological modelling for next generation sequencing data." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2013. http://amslaurea.unibo.it/6279/.

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Le tecniche di next generation sequencing costituiscono un potente strumento per diverse applicazioni, soprattutto da quando i loro costi sono iniziati a calare e la qualità dei loro dati a migliorare. Una delle applicazioni del sequencing è certamente la metagenomica, ovvero l'analisi di microorganismi entro un dato ambiente, come per esempio quello dell'intestino. In quest'ambito il sequencing ha permesso di campionare specie batteriche a cui non si riusciva ad accedere con le tradizionali tecniche di coltura. Lo studio delle popolazioni batteriche intestinali è molto importante in quanto

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9

Royall, Ariel. "Next-generation Sequencing Methods for Complex Communities." Thesis, University of Oregon, 2017. http://hdl.handle.net/1794/22682.

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Advances in sequencing technology have opened up the possibility of investigating complex communities, but deviations from homogeneity in a sample create challenges in generating and analyzing sequence data. There are two kinds of heterogeneous populations that are addressed in this dissertation: low-frequency sequence variants in a group of largely homogeneous cells and rare members in complex biological communities. It is important to be able to fully characterize the heterogeneity of a sample, as rare genetic variants may provide fuel for selection and rare members of a complex community ca

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10

Randel, Melissa. "New Technology Development for Next-Generation Sequencing." Thesis, University of Oregon, 2017. http://hdl.handle.net/1794/22704.

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Next-Generation Sequencing (NGS) technologies have been evolving at an unparalleled pace. The ability to generate millions of base pairs of data in a short time and at lower cost than previously has led to a dramatic expansion of technologies within the field. This dissertation discusses the development and validation of new methods for assessing genomic variation, dynamic changes in gene expression, high-accuracy sequencing, and analysis of recombination events. By reducing the cost of analyzing many samples for genetic divergence by genotyping the same region of the genome in multiple samp

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11

BERETTA, STEFANO. "Algorithms for next generation sequencing data analysis." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2013. http://hdl.handle.net/10281/42355.

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Two of the main bioinformatics fields that have been influenced by the introduction of the Next-Generation Sequencing (NGS) techniques are transcriptomics and metagenomics. The adoption of these new methods to sequence DNA/RNA molecules has drastically changed the kind and also the amount of produced data. The effect is that all the developed algorithms and tools working on traditional data cannot be applied on NGS data. For this reason, in this thesis we face two central problems in two fields: transcriptmics and metagenomics. The first one regards the characterization of the Alternative S

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12

Kumar, Sujai. "Next-generation nematode genomes." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/7609.

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The first metazoan to be sequenced was a nematode (Caenorhabditis elegans), and understanding the genome of this model organism has led to many insights about all animals. Although eleven nematode genomes have been published so far and approximately twenty more are under way, the vast majority of the genomes of this incredibly diverse phylum remain unexplored. Next-generation sequencing has made it possible to generate large amounts of genome sequence data in a few days at a fraction of the cost of traditional Sanger-sequencing. However, assembling and annotating these data into genomic resour

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13

Tork, Bassam A. "VIRAL QUASISPECIES RECONSTRUCTION USING NEXT GENERATION SEQUENCING READS." Digital Archive @ GSU, 2013. http://digitalarchive.gsu.edu/cs_diss/77.

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The genomic diversity of viral quasispecies is a subject of great interest, especially for chronic infections. Characterization of viral diversity can be addressed by high-throughput sequencing technology (454 Life Sciences, Illumina, SOLiD, Ion Torrent, etc.). Standard assembly software was originally designed for single genome assembly and cannot be used to assemble and estimate the frequency of closely related quasispecies sequences. This work focuses on parsimonious and maximum likelihood models for assembling viral quasispecies and estimating their frequencies from 454 sequencing data. Ou

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14

Busby, Michele Anne. "Measuring Gene Expression With Next Generation Sequencing Technology." Thesis, Boston College, 2012. http://hdl.handle.net/2345/3145.

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Thesis advisor: Gabor Marth<br>While a PhD student in Dr. Gabor Marth's laboratory, I have had primary responsibility for two projects focused on using RNA-Seq to measure differential gene expression. In the first project we used RNA-Seq to identify differentially expressed genes in four yeast species and I analyzed the findings in terms of the evolution of gene expression. In this experiment, gene expression was measured using two biological replicates of each species of yeast. While we had several interesting biological findings, during the analysis we dealt with several statistical issues t

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15

Laver, Thomas William. "Evaluating metagenomic quantifications from next-generation sequencing data." Thesis, University of Exeter, 2014. http://hdl.handle.net/10871/17439.

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Molecular profiling is exploiting the unprecedented power of next generation DNA sequencing to illuminate the microbial diversity of the natural world. The composition of microbiomes has been implicated as an important factor in human health and the function of ecosystems. It is thus of great importance that measurements of microbiomes are accurate and reliable, and moreover it is essential that the accuracy and reliability of such measurements are well understood. This project sought to provide assessments of the accuracy and precision of measurements made by 16S rDNA amplicon sequencing and

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16

Ljungström, Viktor. "Exploring next-generation sequencing in chronic lymphocytic leukemia." Doctoral thesis, Uppsala universitet, Experimentell och klinisk onkologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-302026.

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Next-generation sequencing (NGS) techniques have led to major breakthroughs in the characterization of the chronic lymphocytic leukemia (CLL) genome with discovery of recurrent mutations of potential prognostic and/or predictive relevance. However, before NGS can be introduced into clinical practice, the precision of the techniques needs to be studied in better detail. Furthermore, much remains unknown about the genetic mechanisms leading to aggressive disease and resistance to treatment. Hence, in Paper I, the technical performance of a targeted deep sequencing panel including 9 genes was eva

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17

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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18

Dupuis, Sandoval Fabien. "Exploring optimal snoRNA profiling using Next Generation Sequencing methods." Mémoire, Université de Sherbrooke, 2018. http://hdl.handle.net/11143/11931.

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Abstract: Recent advances in Next-Generation Sequencing protocols have opened a variety of ways to generate data. However, each newly developed methodology is most suited to represent a certain phenomenon or molecule. The object of this analysis is to identify the most appropriate way to generate and process data to study the snoRNAs, or small nucleolar RNA. Recently, snoRNAs have been revealed as taking part in a variety of unexpected alternative functions such as splicing, resistance to oxidative shock and chromatin unwinding. Finding a method to generate and treat a large quantity of

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19

Forster, Michael [Verfasser]. "Translating Next-Generation-Sequencing into Precision Medicine / Michael Forster." Kiel : Universitätsbibliothek Kiel, 2019. http://d-nb.info/1182989748/34.

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20

Wang, Yi, and 王毅. "Binning and annotation for metagenomic next-generation sequencing reads." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/208040.

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The development of next-generation sequencing technology enables us to obtain a vast number of short reads from metagenomic samples. In metagenomic samples, the reads from different species are mixed together. So, metagenomic binning has been introduced to cluster reads from the same or closely related species and metagenomic annotation is introduced to predict the taxonomic information of each read. Both metagenomic binning and annotation are critical steps in downstream analysis. This thesis discusses the difficulties of these two computational problems and proposes two algorithmic methods,

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21

Bowen, Margot Elizabeth. "Applying Next Generation Sequencing to Skeletal Development and Disease." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11233.

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Next Generation Sequencing (NGS) technologies have dramatically increased the throughput and lowered the cost of DNA sequencing. In this thesis, I apply these technologies to unresolved questions in skeletal development and disease. Firstly, I use targeted re-sequencing of genomic DNA to identify the genetic cause of the cartilage tumor syndrome, metachondromatosis (MC). I show that the majority of MC patients carry heterozygous loss-of-function mutations in the PTPN11 gene, which encodes a phosphatase, SHP2, involved in many signaling pathways. Furthermore, I show that cartilage lesions in MC

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22

Brown, J. R. "Next generation sequencing to understand norovirus in immunocompromised children." Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/1558811/.

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Norovirus is a leading cause of gastroenteritis worldwide, causing self-limited vomiting and diarrhoea in immunocompetent people and chronic infections with significant morbidity in immunocompromised patients. Data presented in this thesis uses deep sequencing to increase our understanding of norovirus in a hospital paediatric population with a large proportion of immunocompromised patients. Real-time PCR reveals that norovirus is the most prevalent gastrointestinal virus in this population, causing infection with a higher viral titre than other gastrointestinal viruses. Norovirus is most comm

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23

Wasylenko, Theresa Anne. "Understanding Huntington's Disease pathogenesis using next generation sequencing analyses." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/103260.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, February 2016.<br>Cataloged from PDF version of thesis. "February 2015."<br>Includes bibliographical references (pages 215-240).<br>Huntington's disease is one of nine expanded (CAG) repeat disorders. The expansion in Huntington's disease lies in the first exon of the huntingtin (HTT) gene and is pathogenic when (CAG)>/= 40 . Individuals with Huntington's disease develop motor, cognitive, and psychiatric symptoms in adulthood. These symptoms progress for approximately 15 years at which time they become fatal. The cli

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24

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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25

Innocenti, Nicolas. "Data Analysis and Next Generation Sequencing : Applications in Microbiology." Doctoral thesis, KTH, Beräkningsbiologi, CB, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-173219.

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Next Generation Sequencing (NGS) is a new technology that has revolutionized the way we study living organisms. Where previously only a few genes could be studied at a time through targeted direct probing, NGS offers the possibility to perform measurements for a whole genome at once. The drawback is that the amount of data generated in the process is large and extracting useful information from it requires new methods to process and analyze it. The main contribution of this thesis is the development of a novel experimental method coined tagRNA-seq, combining 5’tagRACE, a previously developed t

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Shahbazi, Daniel. "Investigating streptococcal biodiversity in sepsis using next-generation sequencing." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-16248.

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Sepsis is one of the leading causes for fatalities in the intensive care unit, and also one of the biggest health problems worldwide. It is a disease caused primarily by bacterial infections but can also be caused by viral or fungal infections. Since it is such a big health problem being associated with increased risk of sepsis, coupled with longer stays in the intensive care unit, the need for fast diagnosis and treatment is very important. Currently, culture is the leading diagnostic method for identification of bacteria, although other methods are currently being tested to improve identific

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27

Yu, Xiaoqing. "Statistical Methods and Analyses for Next-generation Sequencing Data." Case Western Reserve University School of Graduate Studies / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=case1403708200.

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28

Khuder, Basil. "Human Genome and Transcriptome Analysis with Next-Generation Sequencing." University of Toledo Health Science Campus / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=mco1501886695490104.

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29

Lee, Michael. "Next Generation Sequencing Strategies to Investigate Telomeres in Cancer." Thesis, The University of Sydney, 2019. https://hdl.handle.net/2123/21844.

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Telomeres are regions of repetitive DNA at the ends of human chromosomes that function to maintan the integrity of the genome. Telomere attrition is associated with celluar ageing, whilst telomere maintenance is a prerequisite for replicative immortality in cancer. There are two telomere maintenance mechanisms (TMM) that cancer cells can utilize, the enzyme telomerase, or the Alternative Lengthening of Telomeres (ALT) pathway. These two mechanisms synthesise telomeres in very distinct ways leading to differences in their telomere sequence composition and length. The molecular pathways involved

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30

Helmuth, Johannes [Verfasser]. "Robust Normalization of Next Generation Sequencing Data / Johannes Helmuth." Berlin : Freie Universität Berlin, 2017. http://d-nb.info/1136319379/34.

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31

Antanaviciute, Agne. "Novel algorithm development for 'next generation' sequencing data analysis." Thesis, University of Leeds, 2017. http://etheses.whiterose.ac.uk/20734/.

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In recent years, the decreasing cost of ‘Next generation’ sequencing has spawned numerous applications for interrogating whole genomes and transcriptomes in research, diagnostic and forensic settings. While the innovations in sequencing have been explosive, the development of scalable and robust bioinformatics software and algorithms for the analysis of new types of data generated by these technologies have struggled to keep up. As a result, large volumes of NGS data available in public repositories are severely underutilised, despite providing a rich resource for data mining applications. Ind

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32

Li, Zhiwei. "Characterising copy number polymorphisms using next generation sequencing data." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-386050.

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We developed a pipeline to identify the copy number polymorphisms (CNPs) in the Northern Swedish population using whole genome sequencing (WGS) data. Two different methodologies were applied to discover CNPs in more than 1,000 individuals. We also studied the association between the identified CNPs with the expression level of 438 plasma proteins collected in the same population. The identified CNPs were summarized and filtered as a population copy number matrix for 1,021 individuals in 243,987 non-overlapping CNP loci. For the 872 individuals with both WGS and plasma protein biomarkers data,

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Giollo, Manuel. "Computational Approaches to Address the Next-Generation Sequencing Era." Doctoral thesis, Università degli studi di Padova, 2015. http://hdl.handle.net/11577/3424280.

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In this thesis, I propose new algorithms and models to address biological problems. Computer science in fact plays a key role in proteomics and genetics research due to the advent of big datasets. In the context of protein study, I developed new methods for protein function prediction based on information retrieval principles. By using heterogeneous source of knowledge, like graph search and sequence similarity, I designed a tool called INGA that can be used to annotate entire genomes. It has been benchmarked during the Critical Assessment of Function Annotation challenge, and it proved to be

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34

Cui, Hongzhu. "In Silico Edgetic Profiling and Network Analysis of Human Genetic Variants, with an Application to Disease Module Detection." Digital WPI, 2020. https://digitalcommons.wpi.edu/etd-dissertations/596.

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In the past several decades, Next Generation Sequencing (NGS) methods have produced large amounts of genomic data at the exponentially increasing rate. It has also enabled tremendous advancements in the quest to understand the molecular mechanisms underlying human complex traits. Along with the development of the NGS technology, many genetic variation and genotype–phenotype databases and functional annotation tools have been developed to assist scientists to better understand the intricacy of the data. Together, the above findings bring us one step closer towards mechanistic understanding of t

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Nafisinia, Michael. "Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics." Thesis, The University of Sydney, 2017. http://hdl.handle.net/2123/16867.

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The focus of this thesis was the identification of the genetic bases of Mendelian and mitochondrial respiratory chain disorders in a cohort of paediatric patients, to better understand their pathogenesis. Genetic disorders are caused by mutations in the mitochondrial or nuclear genomes and may be influenced to a lesser or greater degree by environmental factors. To date, nearly 3000 genes have been implicated in ~ 4,400 Mendelian phenotypes. However, despite this, the genetic bases for almost 50% of all known Mendelian phenotypes remains to be definitively elucidated. Mitochondrial respiratory

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Khan, Azeem. "Affordable and accesible rolony template preparation for next-generation sequencing." Thesis, Boston University, 2012. https://hdl.handle.net/2144/12443.

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Thesis (M.A.)--Boston University<br>The first draft of the entire human genome was released in 2000, bringing with it the potential for personalized medicine in which there would be customization of health care, with practices and decisions being specially suited to each individual patient by the use of their genetic code. However, the costs and duration of the sequencing with the available technology at that time still left genome analysis out of reach for the majority of people. Since then, there has been an ongoing challenge to lower the cost of sequencing, and to make it more accessible to

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Alshanbari, Huda Mohammed H. "Additive Cox proportional hazards models for next-generation sequencing data." Thesis, University of Leeds, 2017. http://etheses.whiterose.ac.uk/19739/.

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Eighty-Nine Non-Small Cell Lung Cancer (NSCLC) patients experience chromosomal rearrangements called Copy Number Alteration (CNA), where the cells have abnormal number of copies in one or more regions in their genome, this genetic alteration are known to drive cancer development. An important aim of this thesis is to propose a way to combine the clinical covariate as fixed predictors with CNAs genomics windows as smoothing terms using the penalized additive Cox Proportional Hazards (PH) model. Most of the proposed prediction methods assume linearity of the CNAs genomic windows along with the c

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Graham, Joseph (Joseph Arthur). "An analysis of the next generation DNA sequencing technology market." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42360.

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Thesis (S.M.)--Massachusetts Institute of Technology, System Design and Management Program, 2007.<br>Includes bibliographical references (p. 57-60).<br>While there is no shortage of successful and failed biotechnology ventures, it is still very difficult to gage, a priori, how a new company will fare in this industry. In many cases new biotechnology ventures are driven by rapidly evolving technology and emergent customer needs, both unpredictable by nature. Also, the Biotech Industry faces increased public and federal scrutiny as companies attempt to navigate murky ethical and legal waters. Th

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Mayo, Thomas Richard. "Machine learning for epigenetics : algorithms for next generation sequencing data." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/33055.

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The advent of Next Generation Sequencing (NGS), a little over a decade ago, has led to a vast and rapid increase in the generation of genomic data. The drastically reduced cost has in turn enabled powerful modifications that can be used to investigate not just genetic, but epigenetic, phenomena. Epigenetics refers to the study of mechanisms effecting gene expression other than the genetic code itself and thus, at the transcription level, incorporates DNA methylation, transcription factor binding and histone modifications amongst others. This thesis outlines and tackles two major challenges in

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Chen, Xi. "Bayesian Integration and Modeling for Next-generation Sequencing Data Analysis." Diss., Virginia Tech, 2016. http://hdl.handle.net/10919/71706.

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Computational biology currently faces challenges in a big data world with thousands of data samples across multiple disease types including cancer. The challenging problem is how to extract biologically meaningful information from large-scale genomic data. Next-generation Sequencing (NGS) can now produce high quality data at DNA and RNA levels. However, in cells there exist a lot of non-specific (background) signals that affect the detection accuracy of true (foreground) signals. In this dissertation work, under Bayesian framework, we aim to develop and apply approaches to learn the distributi

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Thrush, Mariah A. "Analyzing Algal Diversity in Aquatic Systems Using Next Generation Sequencing." Ohio University Honors Tutorial College / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1366807717.

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

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43

Porter, Ashleigh Fay. "Next generation sequencing to explore microbial diversity, origins and evolution." Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/24919.

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Emerging infectious diseases are major contributors to morbidity and mortality. To prevent such diseases from occurring in the future it is important to understand pathogen evolution and emergence. Unfortunately, we know little about the virosphere outside of clinically significant viruses, leaving the bulk of viral diversity unexplored. A key aim of my thesis was to reveal more of the unknown diversity of viruses, particularly in under-studied animal hosts. To this end I employed bulk RNA sequencing (“meta-transcriptomics”) to identify novel viruses in a range of hosts, including native Austr

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DENTI, LUCA. "Algorithms for analyzing genetic variability from Next-Generation Sequencing data." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2020. http://hdl.handle.net/10281/263551.

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Il DNA contiene l'informazione genetica che è essenziale per il corretto sviluppo di qualsiasi organismo. Essere in grado di analizzare il DNA risulta indispensabile per comprendere le cause di malattie e tumori e per migliorare la qualità delle nostre vite. Lo sviluppo delle tecniche di sequenziamento del DNA ha rivoluzionato il modo in cui queste analisi sono eseguite. A causa dell'immensa quantità di dati biologici disponibili, oggigiorno l'informatica gioca un ruolo fondamentale nella loro analisi. Fortunatamente in molte applicazioni l'informazione biologica contenuta in una molecola di D

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Emelianova, Katie. "Using next generation sequencing to investigate the generation of diversity in the genus Begonia." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/29584.

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Begonia is one of the most diverse genera on the planet, with a species count approaching 2000 and a distribution across tropics in South America, Africa and South East Asia. The genus has occupied a vast range of niches; many highly variable growth forms can be found across the distribution, and species exhibit very diverse morphologies, even in closely related species. A recent study has revealed a putative whole genome duplication (WGD) event in the evolutionary history of Begonia, which has prompted an interest in investigating the impact gene and genome duplication has had on the diversif

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Trujillano, Lidón Daniel 1987. "Mendelian disease gene identification and diagnosis using targeted next generation sequencing." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/295582.

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Les tecnologies de seqüenciació de nova generació (NGS) han emergit com a una poderosa eina per al descobriment de mutacions causals i nous gens per a malalties Mendelianes, i estan tenint un ràpid impacte en l’àmbit del diagnòstic genètic. Les tecnologies de NGS es poden utilitzar en combinació amb mètodes d’enriquiment de l’ADN per a seqüenciar en profunditat regions genòmiques diana, com l’exoma o gens associats a malalties, entregant informació genètica d’una manera ràpida, barata i acurada. Aquesta tesi descriu l’aplicació de la NGS dirigida per a identificar un nou gen per a la hipertens

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47

Köster, Johannes [Verfasser]. "Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis / Johannes Köster." Berlin : epubli GmbH, 2015. http://d-nb.info/1069706299/34.

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48

Otto, Christian. "The mapping task and its various applications in next-generation sequencing." Doctoral thesis, Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-161623.

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The aim of this thesis is the development and benchmarking of computational methods for the analysis of high-throughput data from tiling arrays and next-generation sequencing. Tiling arrays have been a mainstay of genome-wide transcriptomics, e.g., in the identification of functional elements in the human genome. Due to limitations of existing methods for the data analysis of this data, a novel statistical approach is presented that identifies expressed segments as significant differences from the background distribution and thus avoids dataset-specific parameters. This method detects differen

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Huang, Liren [Verfasser]. "Cloud-based Bioinformatics Framework for Next-Generation Sequencing Data / Liren Huang." Bielefeld : Universitätsbibliothek Bielefeld, 2019. http://d-nb.info/1196644020/34.

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50

Saied, Marwa Hanafi Mahmoud. "Next-generation sequencing analysis of DNA methylation in acute myeloid leukaemia." Thesis, Queen Mary, University of London, 2012. http://qmro.qmul.ac.uk/xmlui/handle/123456789/2975.

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DNA methylation has an emerging role in pathogenesis and diagnosis of acute myeloid leukaemia (AML). In order to obtain a global view of the DNA methylation changes in AML genome, we applied methylated DNA immunoprecipitation followed by next-generation sequencing (MeDIP-seq) to AML patients from 4 different cytogenetic subtypes [t(8;21), t(15;17), trisomy 8 and normal karyotype] and normal bone marrows (NBMs). The MeDIP-seq signals were quantified, generating DNA methylation profiles with a 100bp resolution. Whole-genome DNA methylation average was 3% less in AML than NBM. This limited global

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