Relevant bibliographies by topics / Next Generation Sequencin

Academic literature on the topic 'Next Generation Sequencin'

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Published: 11 March 2023

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Journal articles on the topic "Next Generation Sequencin"

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Barbosa, Cristina, Sofia Nogueira, Mário Gadanho, and Sandra Chaves. "Study on Commercial Spice and Herb Products Using Next-Generation Sequencing (NGS)." Journal of AOAC INTERNATIONAL 102, no. 2 (March 1, 2019): 369–75. http://dx.doi.org/10.5740/jaoacint.18-0407.

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Abstract Background: The use of deoxyribonucleic acid (DNA)-based testing methods is increasing in the food sector. DNA analyses can be a helpfultool for the analysis of many food products and can address some of the present concerns about adulteration and authenticity. Several analytical methods have been proposed to answer the specific topic of species composition in foods. Objective: The aim is to show that Next-generation sequencin(NGS) is a suitable tool for food analysis includingspices, herbs, seasoning, etc. Method: In the present study, we show how an internal NGSworkflow was setup and tested for species composition in real food seasoning samples. Results: Commercial samples of different spice and herb mixtures were analysed by our internal developed NGS workflow. The results obtained will be discussedbased on the labeling of the products relative tothetype of sample and species mixtures. Conclusions: Here we show that our internal NGS workflow can be successfully applied in complex commercial samples. Highlights: NGS can become a powerfull and reliable tool for authentication of spices and herbs products.
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C, Chinmayee, Amrita Nischal, and C. R. Manjunath Soumya K. N. "Next Generation Sequencing in Big Data." International Journal of Trend in Scientific Research and Development Volume-2, Issue-4 (June 30, 2018): 379–89. http://dx.doi.org/10.31142/ijtsrd12975.

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He, Jiahuan. "Next-Generation Sequencing on COVID-19 Pandemic." International Journal of Bioscience, Biochemistry and Bioinformatics 12, no. 2 (2022): 30–38. http://dx.doi.org/10.17706/ijbbb.2022.12.2.30-38.

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Vlk, D., and J. Řepková. "Application of next-generation sequencing in plant breeding." Czech Journal of Genetics and Plant Breeding 53, No. 3 (September 13, 2017): 89–96. http://dx.doi.org/10.17221/192/2016-cjgpb.

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In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilitated the development of methods to genotype very large numbers of single-nucleotide polymorphisms. Genotyping- by-sequencing and whole-genome resequencing can lead to the development of molecular markers suited to studies of genetic relationships among breeding materials, creation of detailed genetic mapping of targeted genes and genome-wide association studies. Plant genotyping can benefit plant breeding through selection of individuals resistant to climatic stress and to pathogens causing substantial losses in agriculture.
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Maver, Aleš, and Borut Peterlin. "Paediatria Croatica." Paediatria Croatica 57, no. 4 (December 20, 2013): 295–300. http://dx.doi.org/10.13112/pc.2013.1.

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Borodinov, A. G., V. V. Manoilov, I. V. Zarutsky, A. I. Petrov, and V. E. Kurochkin. "GENERATIONS OF DNA SEQUENCING METHODS (REVIEW)." NAUCHNOE PRIBOROSTROENIE 30, no. 4 (November 30, 2020): 3–20. http://dx.doi.org/10.18358/np-30-4-i320.

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Several decades have passed since the development of the revolutionary DNA sequencing method by Frederick Sanger and his colleagues. After the Human Genome Project, the time interval between sequencing technologies began to shrink, while the volume of scientific knowledge continued to grow exponentially. Following Sanger sequencing, considered as the first generation, new generations of DNA sequencing were consistently introduced into practice. Advances in next generation sequencing (NGS) technologies have contributed significantly to this trend by reducing costs and generating massive sequencing data. To date, there are three generations of sequencing technologies. Second generation se-quencing, which is currently the most commonly used NGS technology, consists of library preparation, amplification and sequencing steps, while in third generation sequencing, individual nucleic acids are sequenced directly to avoid bias and have higher throughput. The development of new generations of sequencing has made it possible to overcome the limitations of traditional DNA sequencing methods and has found application in a wide range of projects in molecular biology. On the other hand, with the development of next generation technologies, many technical problems arise that need to be deeply analyzed and solved. Each generation and sequencing platform, due to its methodological approach, has specific advantages and disadvantages that determine suitability for certain applications. Thus, the assessment of these characteristics, limitations and potential applications helps to shape the directions for further research on sequencing technologies.
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Mardis, Elaine, Timothy J. Ley, and Richard K. Wilson. "Sequencing Acute Myeloid Leukemia Genomes with “Next Generation” Technologies." Blood 112, no. 11 (November 16, 2008): sci—36—sci—36. http://dx.doi.org/10.1182/blood.v112.11.sci-36.sci-36.

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Abstract For most patients with a sporadic presentation of acute myeloid leukemia (AML), neither the initiating nor the progression mutations responsible for disease are known. Recent attempts to identify key mutations with directed sequencing approaches, or with array-based genomic studies, have had limited success, suggesting that unbiased whole genome sequencing approaches may be required to identify most of the mutations responsible for AML pathogenesis. Until recently, whole genome sequencing has been impractical due to the high cost of conventional capillary-based sequencing and the large numbers of enriched primary tumor cells required to yield the necessary genomic DNA for library preparation. “Next Generation” sequencing approaches have changed this landscape dramatically. Using the Solexa/Illumina platform, we have now sequenced the genomic DNA of highly enriched tumor cells and normal skin cells obtained from a carefully selected patient with a typical presentation of FAB M1 AML. We obtained 98.2 billion bases of sequences from the cytogenetically normal tumor cell genome (32.7 fold haploid coverage), and 41.8 billion bases of sequence from the normal skin genome (13.9 fold coverage). Using these data, we detected diploid sequence coverage of 91% of 46,320 heterozygous SNPs, defined in the tumor genome (by array-based genotyping), and 83% diploid coverage of the skin genome. Of 2,647,695 well-supported single nucleotide variants in the tumor genome, 2,588,486 (97.7%) were also detected in the patient’s skin genome, defining them as inherited. From the remaining variants, 8 have been fully validated as somatic mutations by conventional capillary sequencing using PCR-generated amplicons. We also detected somatic mutations in the FLT3 (ITD) and NPM1 genes (a classic NPMc mutation). Based on deep read-count data of the novel variants on a 454 sequencer, we hypothesize that all of the mutations are in virtually all of the tumor cells, and all were retained at relapse 11 months later, suggesting that a single dominant clone contained all of the mutations. None of the novel mutations has previously been detected in AML cases (and none were found in any of 187 additional AML cases studied here). A number of additional potential somatic mutations in regions lying near genes (but not altering coding sequences) are currently being validated and tested for recurrence in other AML samples. Whole genome sequencing of a second M1 AML genome is now underway. These results demonstrate the power of unbiased whole genome sequencing approaches to discover cancer-associated mutations in novel candidate genes.
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Kim, Minseok, Youlchang Baek, and Young Kyoon Oh. "Application of Next Generation Sequencing to Investigate Microbiome in the Livestock Sector." Journal of Animal Environmental Science 21, no. 3 (September 30, 2015): 93–98. http://dx.doi.org/10.11109/jaes.2015.21.3.93.

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Kim, Se Hee, Eun Young Nam, Kang-Hee Cho, Il Sheob Shin, Hyun Ran Kim, and Hae Seong Hwang. "Comparison of transcriptome analysis between red flash peach cultivar and white flash peach cultivar using next generation sequencing." Journal of Plant Biotechnology 39, no. 4 (December 31, 2012): 273–80. http://dx.doi.org/10.5010/jpb.2012.39.4.273.

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Zeeshan, Faiza, and Sadaf Razzak. "Next Generation Sequencing and its Role in Clinical Microbiology and Molecular Epidemiology." ANNALS of JINNAH SINDH MEDICAL UNIVERSITY 6, no. 1 (June 30, 2020): 31–32. http://dx.doi.org/10.46663/ajsmu.v6i1.31-32.

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Dissertations / Theses on the topic "Next Generation Sequencin"

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Espach, Yolandi. "The detection of mycoviral sequences in grapevine using next-generation sequencing." Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/80025.

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Thesis (MSc)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: Metagenomic studies that make use of next-generation sequencing (NGS) generate large amounts of sequence data, representing the genomes of multiple organisms of which no prior knowledge is necessarily available. In this study, a metagenomic NGS approach was used to detect multiple novel mycoviral sequences in grapevine phloem tissue. Individual sequencing libraries of doublestranded RNA (dsRNA) from two grapevine leafroll diseased (GLD) and three shiraz diseased (SD) vines were sequenced using an Illumina HiScanSQ instrument. Over 3.2 million reads were generated from each of the samples and these reads were trimmed and filtered for quality before being de novo assembled into longer contigs. The assembled contigs were subjected to BLAST (Basic Local Alignment Search Tool) analyses against the NCBI (National Centre for Biotechnology Information) database and classified according to database sequences with which they had the highest identity. Twenty-six putative mycovirus species were identified, belonging to the families Chrysoviridae, Endornaviridae, Narnaviridae, Partitiviridae and Totiviridae. Two of the identified mycoviruses, namely grapevine-associated chrysovirus (GaCV) and grapevine-associated mycovirus 1 (GaMV-1) have previously been identified in grapevine while the rest appeared to be novel mycoviruses not present in the NCBI database. Primers were designed from the de novo assembled mycoviral sequences and used to screen the grapevine dsRNA used for sequencing as well as endophytic fungi isolated from the five sample vines. Only two mycoviruses, related to sclerotinia sclerotiorum partitivirus S and chalara elegans endornavirus 1 (CeEV-1), could be detected in grapevine dsRNA and in fungus isolates. In order to validate the presence of mycoviruses in grapevine phloem tissue, two additional sequencing runs, using an Illumina HiScanSQ and an Applied Biosystems (ABI) SOLiD 5500xl instrument respectively, were performed. These runs generated more and higher quality sequence data than the first sequencing run. Twenty-two of the putative mycoviral sequences initially detected were detected in the subsequent sequence datasets, as well as an additional 29 species not identified in the first HiScanSQ sequence datasets. The samples harboured diverse mycovirus populations, with as many as 19 putative species identified in a single vine. This indicates that the complete virome of diseased grapevines will include a high number of mycoviruses. Additionally, the complete genome of a novel endornavirus, for which we propose the name grapevine endophyte endornavirus (GEEV), was assembled from one of the second HiScanSQ sequence datasets. This is the first complete genome of a mycovirus detected in grapevine. Grapevine endophyte endornavirus has the highest sequence similarity to CeEV-1 and is the same virus that was previously detected in fungus isolates using the mycovirus primers. The virus was detected in two fungus isolates, namely Stemphylium sp. and Aureobasidium pullulans, which is of interest since mycoviruses are not known to be naturally associated with two distinctly different fungus genera. Mycoviral sequence data generated in this study can be used to further investigate the diversity and the effect of mycoviruses in grapevine.
AFRIKAANSE OPSOMMING: Metagenomiese studies, wat gebruik maak van volgende-generasie volgordebepalingstegnologie, het die vermoë om die genetiese samestelling van veelvoudige onbekende organismes te bepaal deurdat dit groot hoeveelhede data genereer. Die bogenoemde tegniek was in hierdie studie aangewend om aantal nuwe mikovirusse in die floëem weefsel van wingerd te identifiseer. Dubbelstring-RNS was gesuiwer vanuit twee druiwestokke met rolbladsiekte en drie met shirazsiekte en Illumina HiScanSQ instrument is gebruik om meer as 3.2 miljoen volgorde fragmente te genereer van elk van die monsters. Lae-kwaliteit volgordes was verwyder en die oorblywende kort volgorde fragmente was saamgestel om langer konstrukte te vorm wat met behulp van BLAST soektogte teen die NCBI databasis geïdentifiseer kon word. Ses-en-twintig mikovirus spesies, wat aan die families Chrysoviridae, Endornaviridae, Narnaviridae, Partitiviridae en Totiviridae behoort, was geïdentifiseer. Twee van die geïdentifiseerde mikovirusse, naamlik grapevine-associated chrysovirus (GaCV) en grapevine-associated mycovirus 1 (GaMV-1), was voorheen al in wingerd gekry terwyl die res nuwe mikovirusse is wat tans nie in die NCBI databasis voorkom nie. Inleiers was ontwerp vanaf die saamgestelde mikovirus basisvolgordes en gebruik om wingerd dubbelstring-RNS sowel as swamme wat vanuit die wingerd geïsoleer is te toets vir die teenwoordigheid van hierdie mikovirusse. Slegs twee mikovirusse, wat onderskeidelik verwant is aan sclerotinia sclerotiorum partitivirus S en chalara elegans endornavirus 1 (CeEV-1), kon deur middel van die inleiers in wingerd en swam isolate geïdentifiseer word. Twee addisionele volgordebepalingsreaksies, wat gebruik gemaak het van die Illumina HiScanSQ en ABI SOLiD 5500xl volgordebepalingsplatforms, was gebruik om die teenwoordigheid van mikovirusse in wingerd te bevestig. Groter hoeveelheid volgorde fragmente was geprodusser wat ook van hoër gehalte was as dié van die eerste volgordebepalingsreaksie. Twee-en-twintig mikovirus spesies kon weer geïdentifiseer word, sowel as 29 spesies wat nie in die eerste HiScanSQ basisvolgorde datastelle gevind was nie. Die wingerdstokke wat in hierdie studie ondersoek was, het hoë diversiteit van mikovirusse bevat aangesien daar tot 19 mikovirus spesies in enkele wingerdstok geïdentifiseer was. Dit is aanduiding dat volledige virus profiele van siek wingerdstokke aantal mikovirusse sal insluit. Die vollengte genoomvolgorde van voorheen onbekende endornavirus was saamgestel vanuit een van die tweede HiScanSQ volgorde datastelle. Dit is die eerste mikovirus wat in wingerd gevind word waarvan die volledige genoomvolgorde bepaal is en ons stel die naam grapevine endophyte endornavirus (GEEV) voor vir hierdie virus. Grapevine endophyte endornavirus is die naaste verwant aan CeEV-1 en is dieselfde virus wat voorheen in wingerd dubbelstring-RNS en swam isolate gevind was deur middel van die mikovirus inleiers. Swam isolate waarin GEEV gevind is, was geïdentifiseer as Stemphylium sp. en Aureobasidium pullulans. Dit is van belang dat GEEV in twee swam isolate gevind is wat aan verskillende genusse behoort aangesien hierdie verskynsel nog nie voorheen in die natuur gevind is nie. Mikovirus nukleiensuurvolgordes wat in hierdie studie bepaal was kan gebruik word in toekomstige studies om die verskeidenheid en impak van mikovirusse in wingerd verder te ondersoek.
National Research Foundation (NRF)
Stellenbosch University
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TROVÃO, Nídia Isabel Sequeira. "Evaluation of next generation sequency protocols for VIH complete genome sequencing." Master's thesis, Instituto de Higiene e Medicina Tropical, 2011. http://hdl.handle.net/10362/51111.

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Vírus da imunodeficiência humana (VIH) é um retrovírus que deu origem a uma pandemia após transmissão zoonótica na primeira metade do século XX. A terapia actual, conhecida como terapia anti-retroviral altamente activa, pode retardar significativamente a progressão da doença. No entanto, apesar de mais de 25 anos de intensa investigação ainda não existe cura disponível. Todos os fármacos anti-retrovirais disponíveis são confrontados com o desafio colocado pelo alto potencial evolutivo do VIH. Isto implica que, independentemente do coquetel de fármacos administrados, resistência aos mesmos pode e vai desenvolver-se. Para gerir esses efeitos negativos, os pacientes devem ser vigiados regularmente, a fim de detectar o desenvolvimento de resistência a fármacos precocemente, de modo a que se possa ajustar oportunamente o regime terapêutico. É de notar que tanto as estirpes resistentes, que evoluíram de novo ou foram adquiridas por meio de transmissão, podem ter impacto negativo no resultado da terapia. Assim sendo, também os pacientes nunca sujeitos a terapia devem ser avaliados antes do início da mesma. Essa triagem geralmente envolve genotipagem da população viral através do sequenciamento directo dos produtos de RT-PCR. Infelizmente, essa abordagem não permite a detecção fiável de estirpes virais presentes em menos de 20% a 25% da população. A associação entre populações minoritárias codificantes de resistência a fármacos com a falha terapêutica, impulsionou as investigações para explorar a plataforma da Roche® 454, como tentativa de ganhar conhecimento mais preciso e em profundidade da população viral. Contudo, tais estudos estão limitados a determinadas regiões genómicas e por outro lado os procedimentos aplicados para fragmentação na plataforma da Roche® 454 requerem elevada quantidade de material primário. Esta tese impõe-se como parte de um projecto mais amplo, comparando os mais recentes protocolos de pré-processamento de amostras para sequenciação completa do genoma de VIH, proveniente de amostras clinicas de plasma e células mononucleares do sangue periférico, e identificação do reservatório mais adequado para detecção de resistência em pacientes recentemente infectados, como segundo objectivo. Assim sendo, este trabalho de investigação foca-se nos aspectos práticos correspondentes ao pré-processamento de amostras antes da geração de dados de sequência. Em detalhe, todos os procedimentos de laboratório, tanto para a estratégia de amplificação de sequência específica e de sequência aleatória foram realizadas. Para o primeiro, geramos 6 amplicões que se sobrepõem para cobrir o genoma inteiro do VIH-1. Depois de misturamos equimolarmente todos os amplicões para cada amostra, foram realizados dois métodos fragmentação enzimática. Estes serão comparados com o método convencional mecânico de fragmentação empregue pela Roche® 454. O sequenciamento com êxito de uma amostra e a conclusão de todos os procedimentos de pré-processamento são promissores para outras aplicações, mas uma avaliação abrangente dos dados de sequenciação a serem gerados é necessário fazer uma escolha informada entre as diferentes abordagens.
Human immunodeficiency virus (HIV) is a retrovirus that gave rise to a worldwide epidemic after its successful zoonotic transmission in the first half of the twentieth century. Current therapy, referred to as Highly Active AntiRetroviral Therapy (HAART), can significantly delay disease progression. However, despite more than 25 years of intensive research there is still no cure available. All available antiretroviral drugs are faced with the insurmountable challenge posed by the high evolutionary potential of HIV. This implies that regardless the administered drug cocktail, drug resistance can and will develop. To manage these negative effects, patients should be screened on a regular basis in order to detect the development of drug resistance in an early phase, so the therapy regimen can be timely adjusted. Importantly, both drug resistant variants that have evolved de novo or were acquired through transmission can negatively impact on therapy outcome. Thus, also therapy-naive patients should be screened before therapy onset. This screening usually involves genotyping of the viral population through the direct sequencing of the RT-PCR products. Unfortunately, this approach does not allow the reliable detection of viral variants present in less then at about 20%-25% of the population. The association of such minor variants harboring drug resistance mutations with therapy failure fueled investigations to exploit the recently developed Roche® 454 NGS platform in an attempt to gain a more accurate in-depth view of the viral population. These inquiries are characterized by two major drawbacks: their focus on limited genomic regions and the need for large amounts of input material characteristic for the proprietary Roche® 454 fragmentation approach. As part of a larger project on the comparison of currently available sample preprocessing protocols for complete genome sequencing of clinical HIV plasma and PBMC samples, and the identification of the most suitable viral reservoir for resistance testing in newly infected patients as a secondary objective, this thesis focuses on the corresponding practical aspects of pre-processing prior to sequence data generation. Specifically, all wet-lab procedures for both the sequence-specific and random priming amplification strategies were carried out. For the former, we generated 6 overlapping amplicons to cover the entire HIV-1 genome. After equimolar pooling of all amplicons for each sample, we performed two enzymatic fragmentation methods. These will be compared to conventional mechanical 454 shearing. The successful sequencing of one sample and the completion of all sample pre-processing procedures is promising for further applications but a comprehensive evaluation of the sequence data to be generated is necessary to make an informed choice among the different approaches.
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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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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
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. TopHat and Cufflinks were the software used to build the protocol that allowed for gene quantification. About 95% of the reads were mapped on the genome. 3693 genes were analyzed, of which 1338 had a non-standard start codon (TTG/CTG) and the percentage of expressed genes was 99.4%. Most genes have intermediate levels of expression, some have little or no expression and a minority is highly expressed. The distribution profile of the CUG between the three species is different, but it can be significantly associated to gene expression levels: genes with fewer CUGs are the most highly expressed. However, CUG content is not related to the conservation level: more and less conserved genes have, on average, an equal number of CUGs. The most conserved genes are the most expressed. The lipase genes corroborate the results obtained for most genes of C. cylindracea since they are very rich in CUGs and nothing conserved. The reduced amount of CUG codons that was observed in highly expressed genes may be due, possibly, to an insufficient number of tRNA genes to cope with more CUGs without compromising translational efficiency. From the enrichment analysis, it was confirmed that the most conserved genes are associated with basic functions such as translation, pathogenesis and metabolism. From this set, genes with more or less CUGs seem to have different functions. The key issues on the evolutionary phenomenon remain unclear. However, the results are consistent with previous observations and shows a variety of conclusions that in future analyzes should be taken into consideration, since it was the first time that such a study was conducted.
A descodificação não-standard do codão CUG na Candida cylindracea levanta uma série de questões sobre o processo evolutivo deste organismo e de outras espécies do subtipo Candida para as quais o codão é ambíguo. No sentido de encontrar algumas respostas procedeu-se ao estudo do transcriptoma de C. cylindracea, comparando o seu comportamento com o de Saccharomyces cerevisiae (descodificador standard) e de Candida albicans (descodificador ambíguo). A caracterização do transcriptoma foi realizada a partir de RNA-seq. Esta metodologia apresenta várias vantagens em relação aos microarrays e a sua aplicação encontra-se em franca expansão. TopHat e Cufflinks foram os softwares utilizados na construção do protocolo que permitiu efectuar a quantificação génica. Cerca de 95% das reads alinharam contra o genoma. Foram analisados 3693 genes, 1338 dos quais com codão start não-standard (TTG/CTG) e a percentagem de genoma expresso foi de 99,4%. Maioritarimente, os genes têm níveis de expressão intermédios, alguns apresentam pouca ou nenhuma expressão e uma minoria é altamente expressa. O perfil de distribuição do codão CUG entre as três espécies é muito diferente, mas pode associar-se significativamente aos níveis de expressão: os genes com menos CUGs são os mais altamente expressos. Porém, o conteúdo em CUG não se relaciona com o nível de conservação: genes mais e menos conservados têm, em média, igual número de CUGs. Os genes mais conservados são os mais expressos. Os genes de lipases corroboram os resultados obtidos para os genes de C. cylindracea em geral, sendo muito ricos em CUGs e nada conservados. A quantidade reduzida de codões CUG que se observa em genes altamente expressos pode dever-se, eventualmente, a um número insuficiente de genes de tRNA para fazer face a mais CUGs sem comprometer a eficiência da tradução. A partir da análise de enriquecimento foi possível confirmar que os genes mais conservados estão associados a funções básicas como tradução, patogénese e metabolismo. Dentro destes, os genes com mais e menos CUGs parecem ter funções diferentes. As questões-chave sobre o fenómeno evolutivo permanecem por esclarecer. No entanto, os resultados são compatíveis com as observações anteriores e são apresentadas várias conclusões que em futuras análises devem ser tidas em consideração, já que foi a primeira vez que um estudo deste tipo foi realizado.
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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 resources remains a challenge because of the short reads, the quality issues in these kinds of data, and the presence of contaminants and co-bionts in uncultured samples. In this thesis, I describe the process of creating high quality draft genomes and annotation resources for four nematode species representing three of the five major nematode clades: Caenorhabditis sp. 5, Meloidogyne floridensis, Dirofilaria immitis, and Litomosoides sigmodontis. I describe the new approaches I developed for visualising contamination and co-bionts, and I present the details of the robust workflow I devised to deal with the problems of generating low-cost genomic resources from Illumina short-read sequencing. Results: The draft genome assemblies created using the workflow described in this thesis are comparable to the draft nematode genomes created using Sanger sequencing. Armed with these genomes, I was able to answer two evolutionary genomics questions at very different scales. The first question was whether any non-coding elements were deeply conserved at the level of the whole phylum. Such elements had previously been hypothesised to be responsible for the phylum body plan in vertebrates, insects, and nematodes. I used twenty nematode genomes in several whole-genome alignments and concluded that no such elements were conserved across the whole phylum. The second question addressed the origins of the highly destructive plant-parasitic root-knot nematode Meloidogyne incognita. Comparisons with the newly sequenced Meloidogyne floridensis genome revealed the complex hybrid origins of both species, undermining previous assumptions about the rarity of hybrid speciation in animals. Conclusions: This thesis demonstrates the role of next-generation sequencing in democratising genome sequencing projects. Using the sequencing strategies, workflows, and tools described here, one can rapidly create genomic resources at a very low cost, even for unculturable metazoans. These genomes can be used to understand the evolutionary history of a genus or a phylum, as shown.
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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. However, new approaches for both the storage and analysis of sequencing data are in imminent needs. In this thesis, we introduce three methods that could be utilized in the management and analysis of sequencing data. In Chapter 1, we propose a novel and simple algorithm for compressing sequencing data that leverages on the scarcity of rare variant data, which enables the storage and analysis of sequencing data efficiently in current hardware environment. We also provide a C++ implementation that supports direct and parallel loading of the compressed format without requiring extra time for decompression. Chapter 2 and 3 focus on the association analysis of sequencing data in population-based design. In Chapter 2, we present a statistical methodology that allows the identification of genetic outliers to obtain a genetically homogeneous subpopulation, which reduces the false positives due to population substructure. Our approach is computationally efficient that can be applied to all the genetic loci in the data and does not require pruning of variants in linkage disequilibrium (LD). In Chapter 3, we propose a general analysis framework in which thousands of genetic loci can be tested simultaneously for association with complex phenotypes. The approach is built on spatial-clustering methodology, assuming that genetic loci that are associated with the target phenotype cluster in certain genomic regions. In contrast to standard methodology for multi-loci analysis, which has focused on the dimension reduction of data, the proposed approach profits from the availability of large numbers of genetic loci. Thus it will be especially relevant for whole-genome sequencing studies which commonly record several thousand loci per gene.
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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 bulking, and microbial source tracking of faecal contamination in bathing waters. Samples from 32 activated sludge plants (ASPs) were collected and analysed. Cell specific ammonia oxidation rates were calculated using the equation CSAOR =(A x M x 106) XrAOB x MLSS x V where A = grams of ammonia oxidised, M = the number of moles of ammonia in a gram, r = correction factor of 0.9 due to some ammonia removal by adsorption and assimilation (Daims, Ramsing, et al. 2001), MLSS = mixed liquor suspended solids in mg/L and V = the volume of the aeration basin in litres. The CSAOR in nitrifying plants ranged from one to ten mmol/cell/hour, in agreement with other CSAOR studies using alternative techniques. Biological foaming in ASPs occurs when the abundance of filamentous bacteria with hydrophobic surface membranes becomes excessive, though the exact abundance threshold above which foaming occurs has not yet been established. The relative abundance of bacteria associated with foaming was measured for all ASPs which were then categorised as non-foaming, occasionally-foaming or currently-foaming based on operator assessment. There was a significant difference in the abundance of foaming bacteria between non-foaming and occasionally foaming plants (ANOVA p < 0.001), with all non-foaming plants having less than 1% relative abundance of foaming bacteria. These results demonstrate that NGS could be a useful ASP process monitoring tool. A bathing water catchment was sampled throughout a bathing season, including a storm event. Partial least squares analysis showed there was a significant correlation between faecal indicator bacteria and the cumulative apportioned fraction of sources (using Bayesian statistics) in the bathing water community (p < 0.001, r2 = 87%). Faecal host marker analysis detected human contamination upstream of any wastewater network inputs, illustrating the impact of diffuse human pollution. Whole community analysis apportioned the bathing water microbial community to point and diffuse sources, and found that whilst human sources were dominant during storm conditions, in dry weather the primary source of faecal contamination was variable and in some cases could not be attributed to known faecal sources.
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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 and detail for clinical applications are sparse. Several softwares like Samtools, are able to calculate coverage values but does not further process this information in a useful way to produce a QC report of each base pair of interest. My master thesis has therefore been to create a new coverage analysis report tool, named CAR tool, that extract the coverage values from Samtools and further uses this data to produce a report consisting of tables, lists and figures. CAR tool is created to replace the currently used tool, ExCID, at the Clinical Genomics facility at SciLifeLab in Uppsala and was developed to meet the needs of the bioinformaticians and clinicians. CAR tool is written in python and launched from a terminal window. The main function of the tool is to display coverage breath values for each region of interest and to extract all sub regions below a chosen coverage depth threshold. The low coverage regions are then reported together with region name, start and stop positions, length and mean coverage value. To make the tool useful to as many as possible several settings are possible by entering different flags when calling the tool. Such settings can be to generate pie charts of each region’s coverage values, filtering of the read and bases by quality or write your own entry that will be used for the coverage calculation by Samtools. The tool has been proved to find these low coverage regions very well. Most low regions found are also found by ExCID, the currently used tool, some differences did however occur and every such region was verified by IGV. The coverage values shown in IGV coincided with those found by CAR tool. CAR tool is written to find all low coverage regions even if they are only one base pair long, while ExCID instead seem to generate larger low regions not taking very short low regions into account. To read more about the functions and how to use CAR tool I refer to User instructions in the appendix and on GitHub at the repository anod6351
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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 sequencing has allowed the development of an assortment of technologies for interrogating aspects of the genome, one of which is high-throughput RNA sequencing (RNA-Seq). This technology allows rapid, relatively cheap, and accurate quantification of transcripts at a genome-wide scale. By providing a greater number of advantages and fewer caveats than alternative methods of transcriptome quantification, RNA-Seq is a disruptive technology that is likely to supersede most others. Throughout this thesis, I have sought to demonstrate how these advantages assist in revealing significant and novel developmental, noncoding, coding, and alternative isoform information of relevance to disorders and diseases. I take advantage of methods that utilize the truly genome-wide coverage of RNA-Seq, that quantify large numbers of transcripts, and that interrogate novel splicing events. More specifically, I present (i) the identification of novel biomarkers of the various placode-derived vertebrate cranial nerves, (ii) differential gene networks which highlight the genetics of autism intellectual disability co-morbidity, and (iii) differential gene expression underlying a form of severe influenza susceptibility. In addition to these studies, this thesis presents an R package for RNA-Seq time-series experiments, including functionality for efficient model-based clustering, and the integration of gene ontology information for cluster number selection and for subsequent profiling. Overall, this thesis demonstrates how RNA-Seq is a powerful tool for understanding disease aetiology.
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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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Books on the topic "Next Generation Sequencin"

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Masoudi-Nejad, Ali, Zahra Narimani, and Nazanin Hosseinkhan. Next Generation Sequencing and Sequence Assembly. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7726-6.

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Wong, Lee-Jun C., ed. Next Generation Sequencing. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7001-4.

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Head, Steven R., Phillip Ordoukhanian, and Daniel R. Salomon, eds. Next Generation Sequencing. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7514-3.

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El-Metwally, Sara, Osama M. Ouda, and Mohamed Helmy. Next Generation Sequencing Technologies and Challenges in Sequence Assembly. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0715-1.

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Kwon, Young Min, and Steven C. Ricke, eds. High-Throughput Next Generation Sequencing. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-089-8.

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Harbers, Matthias, and Günter Kahl, eds. Tag-Based Next Generation Sequencing. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2011. http://dx.doi.org/10.1002/9783527644582.

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Kahl, Günter, and Matthias Harbers. Tag-based next generation sequencing. Weinheim: Wiley-Blackwell, 2012.

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Kappelmann-Fenzl, Melanie, ed. Next Generation Sequencing and Data Analysis. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-62490-3.

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Wu, Wei, and Hani Choudhry, eds. Next Generation Sequencing in Cancer Research. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7645-0.

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Elloumi, Mourad, ed. Algorithms for Next-Generation Sequencing Data. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-59826-0.

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Book chapters on the topic "Next Generation Sequencin"

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Masoudi-Nejad, Ali, Zahra Narimani, and Nazanin Hosseinkhan. "Next-Generation Sequencing Methodologies." In Next Generation Sequencing and Sequence Assembly, 1–9. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7726-6_1.

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Masoudi-Nejad, Ali, Zahra Narimani, and Nazanin Hosseinkhan. "Emergence of Next-Generation Sequencing." In Next Generation Sequencing and Sequence Assembly, 11–39. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7726-6_2.

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Masoudi-Nejad, Ali, Zahra Narimani, and Nazanin Hosseinkhan. "The Assembly of Sequencing Data." In Next Generation Sequencing and Sequence Assembly, 41–54. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7726-6_3.

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Masoudi-Nejad, Ali, Zahra Narimani, and Nazanin Hosseinkhan. "De Novo Assembly Algorithms." In Next Generation Sequencing and Sequence Assembly, 55–83. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7726-6_4.

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El-Metwally, Sara, Osama M. Ouda, and Mohamed Helmy. "Next-Generation Sequence Assemblers." In Next Generation Sequencing Technologies and Challenges in Sequence Assembly, 103–16. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0715-1_11.

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El-Metwally, Sara, Osama M. Ouda, and Mohamed Helmy. "Next-Generation Sequencing Platforms." In Next Generation Sequencing Technologies and Challenges in Sequence Assembly, 37–44. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0715-1_4.

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White, Lisa D. "History of DNA Sequencing Technologies." In Next Generation Sequencing, 3–17. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7001-4_1.

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Chen, Rui, and Feng Wang. "NGS Analysis of Heterogeneous Retinitis Pigmentosa." In Next Generation Sequencing, 187–202. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7001-4_10.

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Wong, Lee-Jun C. "Next-Generation Sequencing Analyses of the Whole Mitochondrial Genome." In Next Generation Sequencing, 203–19. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7001-4_11.

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Vasta, Valeria, and Si Houn Hahn. "Application of Next-Generation Sequencing of Nuclear Genes for Mitochondrial Disorders." In Next Generation Sequencing, 221–39. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7001-4_12.

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Conference papers on the topic "Next Generation Sequencin"

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COARFA, CRISTIAN, and ALEKSANDAR MILOSAVLJEVIC. "PASH 2.0: SCALEABLE SEQUENCE ANCHORING FOR NEXT-GENERATION SEQUENCING TECHNOLOGIES." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2007. http://dx.doi.org/10.1142/9789812776136_0012.

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"PROPOSAL FOR OPEN DISCUSSION - Informatics Challenges for Next Generation Sequencing Metagenomics Experiments." In Metagenomic Sequence Data Analysis. SciTePress - Science and and Technology Publications, 2011. http://dx.doi.org/10.5220/0003334203630366.

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Li, Jing, and Kun Huang. "Next generation sequencing data analysis." In the First ACM International Conference. New York, New York, USA: ACM Press, 2010. http://dx.doi.org/10.1145/1854776.1854781.

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Gupta, Ashutosh, Lala Bhaskar, Pradeep Kumar, and Jimmy Gautam. "Performance analysis of different PN sequence and Orthogonal Spreading sequences in DS-SS." In 2014 5th International Conference- Confluence The Next Generation Information Technology Summit. IEEE, 2014. http://dx.doi.org/10.1109/confluence.2014.6949258.

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Brenner, Jonathon, and Catherine Putonti. "HAsh-MaP-ERadicator: Filtering non-target sequences from next generation sequencing reads." In 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2015. http://dx.doi.org/10.1109/bibm.2015.7359835.

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Shen, Xiaohu, Manohar Shamaiah, and Haris Vikalo. "Message passing algorithm for inferring consensus sequence from next-generation sequencing data." In 2013 IEEE International Symposium on Information Theory (ISIT). IEEE, 2013. http://dx.doi.org/10.1109/isit.2013.6620503.

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Nalbantoglu, O. U., A. Riffle, and K. Sayood. "Compression of Next Generation Sequencing Data." In 2015 Data Compression Conference (DCC). IEEE, 2015. http://dx.doi.org/10.1109/dcc.2015.92.

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Misra, Sanchit, Ramanathan Narayanan, Wei-keng Liao, Alok Choudhary, and Simon Lin. "pFANGS: Parallel high speed sequence mapping for Next Generation 454-roche Sequencing reads." In Distributed Processing, Workshops and Phd Forum (IPDPSW 2010). IEEE, 2010. http://dx.doi.org/10.1109/ipdpsw.2010.5470894.

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Morente-Molinera, J. A., J. M. Martin, C. Cano, M. Cuadros, and A. Blanco. "SNP annotation from next generation sequencing data." In 2011 11th International Conference on Intelligent Systems Design and Applications (ISDA). IEEE, 2011. http://dx.doi.org/10.1109/isda.2011.6121821.

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Gao, Jingyang, Fei Qi, and Rui Guan. "Structural variation discovery with next-generation sequencing." In 2013 2nd International Symposium on Instrumentation & Measurement, Sensor Network and Automation (IMSNA). IEEE, 2013. http://dx.doi.org/10.1109/imsna.2013.6743374.

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Reports on the topic "Next Generation Sequencin"

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Chelsie, Geyer. Applications of Clinical Microbial Next-Generation Sequencing. American Society for Microbiology, April 2015. http://dx.doi.org/10.1128/aamcol.apr.2015.

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Vuyisich, Momchilo. Next generation sequencing (NGS)technologies and applications. Office of Scientific and Technical Information (OSTI), September 2012. http://dx.doi.org/10.2172/1050518.

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Lai, Qiang, Tao Cheng, Wentao Yang, Tianyong Han, and Shuyun Xu. The diagnostic value of metagenomic next-generation sequencing in sepsis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, June 2022. http://dx.doi.org/10.37766/inplasy2022.6.0008.

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Du, Zhi-Qiang, and Max F. Rothschild. Next Generation Sequencing to Discover Genetic Markers for Pacific White Shrimp. Ames (Iowa): Iowa State University, January 2011. http://dx.doi.org/10.31274/ans_air-180814-35.

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Olson, Nathanael D., Nancy J. Lin, and Scott A. Jackson. Standards for Pathogen Identification via Next-Generation Sequencing (SPIN) Workshop Summary Report. National Institute of Standards and Technology, July 2015. http://dx.doi.org/10.6028/nist.sp.1183.

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Koay, Chun Giok, Teng Fung Looi, and Rohit Kunnath Menon. Systematic review of studies evaluating the microbiome of periimplantitis using next generation sequencing techniques. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, December 2022. http://dx.doi.org/10.37766/inplasy2022.12.0111.

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Review question / Objective: This systematic review aims to summarize and critically analyse the methodology and findings of studies which have utilized sequencing techniques to elucidate the microbial profiles of peri-implantitis. Condition being studied: Peri-implantitis is defined as an infection of the peri-implant tissues accompanied by suppuration and clinically significant progressing crestal bone loss after the adaptive phase, leading to decreased osseointegration and pocket formation. Eligibility criteria: Original studies investigating the microbiome of peri-implant tissues through next-generation DNA sequencing methods will be included. Culture-based study, conference papers, review articles, studies regarding peri-implantitis associated with other systematic factors (smoking, diabetes mellitus, etc.), articles that examine only specific microorganisms will be excluded from this systematic review. Non-English language articles and research conducted on non-human specimens will be excluded.
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Yu, Guocan, Wuchen Zhao, Yanqin Shen, Pengfei Zhu, and Hong Zheng. Metatagenomic Next-Generation Sequencing for diagnosis of tuberculosis Meningitis: A protocol of systematic review and meta analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, July 2020. http://dx.doi.org/10.37766/inplasy2020.7.0100.

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Guo, Qiang, Xiulin Ye, Xiaoxing Ge, Xiaoji Su, and Shihai Zhang. Metagenomic Next Generation Sequencing for the Diagnosis pathogeny of Respiratory Infection : A Systematic Review and Meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, August 2021. http://dx.doi.org/10.37766/inplasy2021.8.0036.

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Qu, Chunrun, Yu Chen, Yuzhen Ouyang, Ruoyu Lu, Yu Zeng, and Zhixiong Liu. Metagenomics Next Generation Sequencing for the Diagnosis of Central Nervous System Infection: A Systematic Review and Meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, February 2021. http://dx.doi.org/10.37766/inplasy2021.2.0002.

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Carlson, Damian, Christian Cuevas, Jennifer De Lurio, Andrew Furman, Randy Hulshizer, and Marcus Lynch. PCORI COVID-19 Scan: Next-Generation Sequencing Assays, Point-of-Care Breath Test (August 6-August 19, 2020). Patient-Centered Outcomes Research Institute (PCORI), August 2020. http://dx.doi.org/10.25302/bcs7.2020.8.

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