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Relevant bibliographies by topics / Salmonella ; Next-generation sequencing ; Bioinformatics / Dissertations / Theses

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Dissertations / Theses on the topic 'Salmonella ; Next-generation sequencing ; Bioinformatics'

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Published: 4 June 2021

Last updated: 1 February 2022

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1

Richardson, Emily Jane. "Next-generation bioinformatics analysis of bacterial genomes, with a focus on serovar host specificity and pathogenicity in Salmonella." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/8793.

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Salmonella is one of the most important pathogens of mankind and animals alike, causing several billion pounds worth of damage worldwide each year. We have sequenced, annotated and published 4 genomes of Salmonella of well-defined virulence in farm animals. This provides valuable measures of intraserovar diversity and opportunities to formally link genotypes to phenotypes in target animals. Specifically, we have examined pathway detrition and mutagenesis and linked this to host specificity of the serovars. With the advent of next generation sequencing there has been a boom in genomic sequence

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2

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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3

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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4

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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5

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

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

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6

Fedewa, Gregory. "Quantifying Nucleotide Variation in RNA Virus Populations by Next-generation Sequencing." Thesis, University of California, San Francisco, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10936274.

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<p> RNA viruses include several notable human pathogens including HIV, hepatitis C virus, West Nile virus, influenza, and Ebola virus. This group of viruses includes viruses with incredibly diverse genome structures, such as single-stranded genomes, double-stranded genomes, multipart genomes, negative-stranded genomes, and positive-stranded genomes. They also exist as heterogeneous populations that can mutate and rapidly evolve due to their error-prone polymerases. These errors then accumulate as they are passed down through generation. They can, therefore, be used as a historical marker for g

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7

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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8

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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9

Ramsay, Trevor. "A Motif Discovery and Analysis Pipeline for Heterogeneous Next-Generation Sequencing Data." Thesis, University of California, Davis, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=1599520.

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<p> Bioinformatics has made great strides in understanding the regulation of gene expression, but many of the tools developed for this purpose depend on data from a limited number of species. Despite their unique genetic attributes, there remains a dearth of research into undomesticated trees. The poplar tree, <i> Populus trichocarpa</i>, has undergone multiple rounds of genome duplication during its evolution. In addition its life cycle varies from other annual crop and model plants previously studied, leading to significant technical challenges to understand the unique biology of these trees

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10

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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11

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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12

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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13

Menelaou, Androniki. "LD-based SNP and genotype calling from next-generation sequencing reads." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:2093d498-3e7f-4648-9fde-fcdb311849de.

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Next-generation sequencing is revolutionising in genetics, where base-by base information for the whole genome is available for a large sample of individuals. This type of data is becoming commonly used and will continue to be in the near future. One of the first questions arising is the identification of novel variants and subsequently genotype calling of the individuals in the sample. However, given the cost of sequencing, so far most projects are sequencing individuals in low to medium coverage. In this thesis, we present two distinct methods for SNP and genotype calling from low-coverage s

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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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15

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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Chikhi, Rayan. "Computational methods for de novo assembly of next-generation genome sequencing data." Phd thesis, École normale supérieure de Cachan - ENS Cachan, 2012. http://tel.archives-ouvertes.fr/tel-00752033.

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In this thesis, we discuss computational methods (theoretical models and algorithms) to perform the reconstruction (de novo assembly) of DNA sequences produced by high-throughput sequencers. This problem is challenging, both theoretically and practically. The theoretical difficulty arises from the complex structure of genomes. The assembly process has to deal with reconstruction ambiguities. The output of sequencing predicts up to an exponential number of reconstructions, yet only one is correct. To deal with this problem, only a fragmented approximation of the genome is returned. The practica

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Saxenborn, Patricia. "Sepsis : Genotypic analysis of clinical Klebsiella spp. using next-generation sequencing." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-15842.

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Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response system and can occur when the immune system over- or under- reacts to an infection. Klebsiella spp. has been found to be one of the leading causes of sepsis, and the increasing occurrence of antibiotic resistance observed has become a major concern in clinical care. To study the genome and increase knowledge of the biodiversity of K. pneumoniae, K. variicola, and K. oxytoca, bacterial isolates were collected from blood, urine, nasopharynx, and wounds of patients with suspected sepsis. Next-generati

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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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19

Indap, Amit R. "Discovering rare variants from populations to families." Thesis, Boston College, 2013. http://hdl.handle.net/2345/3927.

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Thesis advisor: Gabor T. Marth<br>Partitioning an individual's phenotype into genetic and environmental components has been a major goal of genetics since the early 20th century. Formally, the proportion of phenotypic variance attributable to genetic variation in the population is known as heritability. Genome wide association studies have explained a modest percentage of variability of complex traits by genotyping common variants. Currently, there is great interest in what role rare variants play in explaining the missing heritability of complex traits. Advances of next generation sequencing

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Otto, Raik. "Distance-based methods for the analysis of Next-Generation sequencing data." Doctoral thesis, Humboldt-Universität zu Berlin, 2021. http://dx.doi.org/10.18452/23267.

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Die Analyse von NGS Daten ist ein zentraler Aspekt der modernen genomischen Forschung. Bei der Extraktion von Daten aus den beiden am häufigsten verwendeten Quellorganismen bestehen jedoch vielfältige Problemstellungen. Im ersten Kapitel wird ein neuartiger Ansatz vorgestellt welcher einen Abstand zwischen Krebszellinienkulturen auf Grundlage ihrer kleinen genomischen Varianten bestimmt um die Kulturen zu identifizieren. Eine Voll-Exom sequenzierte Kultur wird durch paarweise Vergleiche zu Referenzdatensätzen identifiziert so ein gemessener Abstand geringer ist als dies bei nicht verwandte

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Hu, Jinnan. "Exploring Genome Structure and Gene Regulation Related to Virulence in Fungal Phytopathogens Using Next Generation Sequencing Techniques." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1366213390.

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Moreno, Cabrera José Marcos. "A translational bioinformatics approach to improve genetic diagnostics of hereditary cancer using next-generation sequencing data." Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/672364.

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This PhD thesis has been carried out with the aim of improving, from a bioinformatic-based approach, the genetic diagnostics of hereditary cancer. More specifically, the aims were: 1. To perform a comprehensive evaluation of tools suitable for detecting CNVs from NGS panel data at single-exon resolution. 2. To select the best candidate tool to implement in the genetic diagnostics pipeline of the ICO-IGTP program on hereditary cancer. 3. After implementing it, to evaluate the impact of including the selected NGS CNV detection tool as a first-tier screening step prior to MLPA validation. 4.

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

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

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Williamson, Vernell. "Using Next Generation Sequencing (NGS) to identify and predict microRNAs (miRNAs) potentially affecting Schizophrenia and Bipolar Disorder." VCU Scholars Compass, 2012. http://scholarscompass.vcu.edu/etd/2880.

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The last decade has seen considerable research focusing on understanding the factors underlying schizophrenia and bipolar disorder. A major challenge encountered in studying these disorders, however, has been the contribution of genetic, or etiological, heterogeneity to the so-called “missing heritability” [1-6]. Further, recent successes of large-scale genome-wide association studies (GWAS) have nonetheless seen only limited advancements in the delineation of the specific roles of implicated genes in disease pathophysiology. The study of microRNAs (miRNAs), given their ability to alter the t

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Choudhry, Hani. "Genome-wide analysis of the hypoxic breast cancer transcriptome using next generation sequencing." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:9a66b553-a66c-4164-a854-5881be65ca45.

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Hypoxia pathways are associated with the pathogenesis of both ischaemic and neoplastic diseases. In response to hypoxia the transcription factor hypoxia‐inducible factor (HIF) induces the expression of hundreds of genes with diverse functions. These enable cells to adapt to low oxygen availability. To date, pan-genomic analyses of these transcriptional responses have focussed on protein-coding genes and microRNAs. However, the role of other classes of non-coding RNAs, in particular lncRNAs, in the hypoxia response is largely uncharacterised. My thesis aimed at improving understanding of the tr

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Pranckeviciene, Erinija. "Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation ChIP-Sequencing Data Analysis Pipeline." Thesis, Université d'Ottawa / University of Ottawa, 2015. http://hdl.handle.net/10393/31940.

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The rapidly advancing high-throughput and next generation sequencing technologies facilitate deeper insights into the molecular mechanisms underlying the expression of phenotypes in living organisms. Experimental data and scientific publications following this technological advancement have rapidly accumulated in public databases. Meaningful analysis of currently available data in genomic databases requires sophisticated computational tools and algorithms, and presents considerable challenges to molecular biologists without specialized training in bioinformatics. To study their phenotype of in

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

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Chauhan, Ritika. "Bioinformatics of next generation sequencing approaches : using 454 and Illumina data to look at insect genomes and transcriptomes." Thesis, University of Exeter, 2013. http://hdl.handle.net/10871/10123.

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By providing a rapid and cost effective means of generating sequencing resources for almost any organism, ‘Next generation sequencing technologies’ (NGS) have great potential to help address numerous gene and genome level questions in molecular biology. Progress in NGS is exponentially increasing sequence throughput and large scale studies in the genomics/transcriptomics of non-model organisms are becoming a reality. Therefore the main focus of the work presented in this thesis is on the analysis of the large scale non-model insect datasets generated by NGS technologies and their potential to

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Alnaji, Fadi. "Isolation and analysis of recombinants from mixed virus infections of poliovirus using next generation sequencing (NGS) and bioinformatics." Thesis, University of Warwick, 2016. http://wrap.warwick.ac.uk/98260/.

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RNA virus recombination is a key evolutionary mechanism and a driver of genetic diversity. In recent studies using an in vitro “CRE-REP” assay involving replication-compromised parental genomes, recombination was shown to be a biphasic process involving an initial imprecise crossover event which was followed by a resolution process that resulted in the formation of genome-length recombinants (Lowry K. et al 2014). We have extended this study to investigate recombination during dual infection by unmodified parental viruses in the absence of selection. Recombinants were generated by co-infecting

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

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

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Kalantar, Katrina. "Combined Host and Microbial Metagenomic Next-Generation Sequencing| Applying Integrated Analysis Approaches for a Comprehensive Evaluation of Infectious Disease Response to Inform Diagnosis, Surveillance, and Treatment." Thesis, University of California, San Francisco, 2019. http://pqdtopen.proquest.com/#viewpdf?dispub=13428465.

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<p> Infectious diseases are a leading cause of morbidity and mortality worldwide. Despite significant advancement in our understanding of infectious disease biology, existing microbiologic diagnostic tests often fail to identify etiologic pathogens in cases of suspected infection. Metagenomic next-generation sequencing (mNGS) offers the potential for a universal pathogen detection method, but analysis and interpretation of findings are challenging. This is especially true for lower respiratory tract infections (LRTIs) where mNGS data interpretation is complicated by the existence of a respirat

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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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Enroth, Stefan. "The Nucleosome as a Signal Carrying Unit : From Experimental Data to Combinatorial Models of Transcriptional Control." Doctoral thesis, Uppsala universitet, Centrum för bioinformatik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-129181.

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The human genome consists of over 3 billion nucleotides and would be around 2 meters long if uncoiled and laid out. Each human somatic cell contains all this in their nucleus which is only around 5 µm across. This extreme compaction is largely achieved by wrapping the DNA around a histone octamer, the nucleosome. Still, the DNA is accessible to the transcriptional machinery and this regulation is highly dynamic and change rapidly with, e.g. exposure to drugs. The individual histone proteins can carry specific modifications such as methylations and acetylations. These modifications are a major

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Kokkonen, Alexander. "Evaluation of next-generation sequencing as a tool for determining the presence of pathogens in clinical samples." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-17374.

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Metagenomic sequencing is an increasingly popular way of determining microbial diversity from environmental and clinical samples. By specifically targeting the 16S rRNA gene found in all bacteria, classifications of pathogens can be determined based on the variable and conserved regions found in the gene. Metagenomic sequencing can therefore highlight the vast difference in microbiological diversity between culture-dependent and culture-independent methods. Today, this has expanded into various next-generation sequencing platforms which can provide massively parallel sequencing of the target f

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Tausch, Simon H. [Verfasser]. "Development of bioinformatics tools for the rapid and sensitive detection of known and unknown pathogens from next generation sequencing data / Simon H. Tausch." Berlin : Freie Universität Berlin, 2019. http://d-nb.info/1177152568/34.

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Tausch, Simon [Verfasser]. "Development of bioinformatics tools for the rapid and sensitive detection of known and unknown pathogens from next generation sequencing data / Simon H. Tausch." Berlin : Freie Universität Berlin, 2019. http://d-nb.info/1177152568/34.

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Velmurugan, Karthik Raja. "Novel Microsatellite Detection, Microsatellite Based Biomarker Discovery In Lung Cancer And The Exome-Wide Effects Of A Dysfunctional DNA Repair Mechanism." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/85506.

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Since the dawn of the genomics era, the genetics of numerous human disorders has been understood which has led to improvements in targeted therapeutics. However, the focus of most research has been primarily on protein coding genes, which account for only 2% of the entire genome, leaving much of the remaining genome relatively unstudied. In particular, repetitive sequences, called microsatellites (MST), which are tandem repeats of 1 to 6 bases, are known to be mutational hotspots and have been linked to diseases, such as Huntington disease and Fragile X syndrome. This work represents a signifi

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

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

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

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

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

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

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

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

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

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

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

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Dumargne, Marie-Charlotte. "Genetic and epigenetic factors associated with human male infertility." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066068.

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La spermatogenèse est un processus complexe qui dépend de la coopération de nombreux gènes. Son produit final le spermatozoïde, est un sujet d’étude idéal car il renferme à la fois des indices d’événements passés ainsi que des informations qui seront transmises à l'ovocyte lors de la fécondation. L'identification de nouveaux acteurs de la spermatogenèse, des modifications spécifiques de l'ADN du sperme ou la présence de transcrits spécifiques pourraient servir comme biomarqueurs dans le diagnostic de l’infertilité. Cette thèse avait pour but d’analyser le génome, le transcriptome et l’épigénom

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Voegele, Catherine. "Development of an integrated Information Technology System for management of laboratory data and next-generation sequencing workflows within a cancer genomics research platform." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10095/document.

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L'objectif de mon travail de thèse était de développer des outils bio informatiques permettant d'améliorer la traditionnelle gestion de l'information scientifique au sein d'un grand centre de recherche et en particulier au sein d'une plateforme de génomique. Trois outils ont été développés: un cahier de laboratoire électronique, un système de gestion de l'information de laboratoire pour des applications de génomique dont le séquençage de nouvelle génération, ainsi qu'un système de gestion des échantillons pour de grandes bio-banques. Ce travail a été réalisé en étroite collaboration avec des b

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Andersson, Robin. "Decoding the Structural Layer of Transcriptional Regulation : Computational Analyses of Chromatin and Chromosomal Aberrations." Doctoral thesis, Uppsala universitet, Centrum för bioinformatik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-130999.

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Gene activity is regulated at two separate layers. Through structural and chemical properties of DNA – the primary layer of encoding – local signatures may enable, or disable, the binding of proteins or complexes of them with regulatory potential to the DNA. At a higher level – the structural layer of encoding – gene activity is regulated through the properties of higher order DNA structure, chromatin, and chromosome organization. Cells with abnormal chromosome compaction or organization, e.g. cancer cells, may thus have perturbed regulatory activities resulting in abnormal gene activity. Henc

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Savel, Daniel M. "Towards a Human Genomic Coevolution Network." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1524241451267546.

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Chakrabortty, Sharmistha. "SNPs and Indels Analysis in Human Genome using Computer Simulation and Sequencing Data." University of Toledo Health Science Campus / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=mco1501726874739045.

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Xu, Guorong. "Computational Pipeline for Human Transcriptome Quantification Using RNA-seq Data." ScholarWorks@UNO, 2011. http://scholarworks.uno.edu/td/343.

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The main theme of this thesis research is concerned with developing a computational pipeline for processing Next-generation RNA sequencing (RNA-seq) data. RNA-seq experiments generate tens of millions of short reads for each DNA/RNA sample. The alignment of a large volume of short reads to a reference genome is a key step in NGS data analysis. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing useful information. In order to assist biomedical researchers to conveniently ac

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