Relevant bibliographies by topics / ONT sequencing

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  2. Dissertations / Theses
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Academic literature on the topic 'ONT sequencing'

Author: Grafiati
Published: 30 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "ONT sequencing"

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Pradeep, Chaithra, Dharam Nandan, Arya A. Das, and Dinesh Velayutham. "Comparative Transcriptome Profiling of Disruptive Technology, Single- Molecule Direct RNA Sequencing." Current Bioinformatics 15, no. 2 (March 10, 2020): 165–72. http://dx.doi.org/10.2174/1574893614666191017154427.

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Background: The standard approach for transcriptomic profiling involves high throughput short-read sequencing technology, mainly dominated by Illumina. However, the short reads have limitations in transcriptome assembly and in obtaining full-length transcripts due to the complex nature of transcriptomes with variable length and multiple alternative spliced isoforms. Recent advances in long read sequencing by the Oxford Nanopore Technologies (ONT) offered both cDNA as well as direct RNA sequencing and has brought a paradigm change in the sequencing technology to greatly improve the assembly and expression estimates. ONT enables molecules to be sequenced without fragmentation resulting in ultra-long read length enabling the entire genes and transcripts to be fully characterized. The direct RNA sequencing method, in addition, circumvents the reverse transcription and amplification steps. Objective: In this study, RNA sequencing methods were assessed by comparing data from Illumina (ILM), ONT cDNA (OCD) and ONT direct RNA (ODR). Methods: The sensitivity & specificity of the isoform detection was determined from the data generated by Illumina, ONT cDNA and ONT direct RNA sequencing technologies using Saccharomyces cerevisiae as model. Comparative studies were conducted with two pipelines to detect the isoforms, novel genes and variable gene length. Results: Mapping metrics and qualitative profiles for different pipelines are presented to understand these disruptive technologies. The variability in sequencing technology and the analysis pipeline were studied.
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Weirather, Jason L., Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, and Kin Fai Au. "Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis." F1000Research 6 (February 3, 2017): 100. http://dx.doi.org/10.12688/f1000research.10571.1.

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Background: Given the demonstrated utility of Third Generation Sequencing [Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)] long reads in many studies, a comprehensive analysis and comparison of their data quality and applications is in high demand. Methods: Based on the transcriptome sequencing data from human embryonic stem cells, we analyzed multiple data features of PacBio and ONT, including error pattern, length, mappability and technical improvements over previous platforms. We also evaluated their application to transcriptome analyses, such as isoform identification and quantification and characterization of transcriptome complexity, by comparing the performance of PacBio, ONT and their corresponding Hybrid-Seq strategies (PacBio+Illumina and ONT+Illumina). Results: PacBio shows overall better data quality, while ONT provides a higher yield. As with data quality, PacBio performs marginally better than ONT in most aspects for both long reads only and Hybrid-Seq strategies in transcriptome analysis. In addition, Hybrid-Seq shows superior performance over long reads only in most transcriptome analyses. Conclusions: Both PacBio and ONT sequencing are suitable for full-length single-molecule transcriptome analysis. As this first use of ONT reads in a Hybrid-Seq analysis has shown, both PacBio and ONT can benefit from a combined Illumina strategy. The tools and analytical methods developed here provide a resource for future applications and evaluations of these rapidly-changing technologies.
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Weirather, Jason L., Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, and Kin Fai Au. "Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis." F1000Research 6 (June 19, 2017): 100. http://dx.doi.org/10.12688/f1000research.10571.2.

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Background: Given the demonstrated utility of Third Generation Sequencing [Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)] long reads in many studies, a comprehensive analysis and comparison of their data quality and applications is in high demand. Methods: Based on the transcriptome sequencing data from human embryonic stem cells, we analyzed multiple data features of PacBio and ONT, including error pattern, length, mappability and technical improvements over previous platforms. We also evaluated their application to transcriptome analyses, such as isoform identification and quantification and characterization of transcriptome complexity, by comparing the performance of size-selected PacBio, non-size-selected ONT and their corresponding Hybrid-Seq strategies (PacBio+Illumina and ONT+Illumina). Results: PacBio shows overall better data quality, while ONT provides a higher yield. As with data quality, PacBio performs marginally better than ONT in most aspects for both long reads only and Hybrid-Seq strategies in transcriptome analysis. In addition, Hybrid-Seq shows superior performance over long reads only in most transcriptome analyses. Conclusions: Both PacBio and ONT sequencing are suitable for full-length single-molecule transcriptome analysis. As this first use of ONT reads in a Hybrid-Seq analysis has shown, both PacBio and ONT can benefit from a combined Illumina strategy. The tools and analytical methods developed here provide a resource for future applications and evaluations of these rapidly-changing technologies.
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Fatima, Nazeefa, Anna Petri, Ulf Gyllensten, Lars Feuk, and Adam Ameur. "Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes." Genes 11, no. 12 (November 30, 2020): 1444. http://dx.doi.org/10.3390/genes11121444.

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Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× coverage). Our analysis inferred an average of 17k and 23k SVs from the ONT and PacBio data, respectively, with a majority of them overlapping with an available multi-platform SV dataset. When comparing the SV calls in the two Swedish individuals, we find a higher concordance between ONT and PacBio SVs detected in the same individual as compared to SVs detected by the same technology in different individuals. Downsampling of PacBio reads, performed to obtain similar coverage levels for all datasets, resulted in 17k SVs per individual and improved overlap with the ONT SVs. Our results suggest that ONT and PacBio have a similar performance for SV detection in human whole genome sequencing data, and that both technologies are feasible for population-scale studies.
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Zhang, Pengfei, Dike Jiang, Yin Wang, Xueping Yao, Yan Luo, and Zexiao Yang. "Comparison of De Novo Assembly Strategies for Bacterial Genomes." International Journal of Molecular Sciences 22, no. 14 (July 17, 2021): 7668. http://dx.doi.org/10.3390/ijms22147668.

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(1) Background: Short-read sequencing allows for the rapid and accurate analysis of the whole bacterial genome but does not usually enable complete genome assembly. Long-read sequencing greatly assists with the resolution of complex bacterial genomes, particularly when combined with short-read Illumina data. However, it is not clear how different assembly strategies affect genomic accuracy, completeness, and protein prediction. (2) Methods: we compare different assembly strategies for Haemophilus parasuis, which causes Glässer’s disease, characterized by fibrinous polyserositis and arthritis, in swine by using Illumina sequencing and long reads from the sequencing platforms of either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio). (3) Results: Assembly with either PacBio or ONT reads, followed by polishing with Illumina reads, facilitated high-quality genome reconstruction and was superior to the long-read-only assembly and hybrid-assembly strategies when evaluated in terms of accuracy and completeness. An equally excellent method was correction with Homopolish after the ONT-only assembly, which had the advantage of avoiding hybrid sequencing with Illumina. Furthermore, by aligning transcripts to assembled genomes and their predicted CDSs, the sequencing errors of the ONT assembly were mainly indels that were generated when homopolymer regions were sequenced, thus critically affecting protein prediction. Polishing can fill indels and correct mistakes. (4) Conclusions: The assembly of bacterial genomes can be directly achieved by using long-read sequencing techniques. To maximize assembly accuracy, it is essential to polish the assembly with homologous sequences of related genomes or sequencing data from short-read technology.
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Dumschott, Kathryn, Maximilian H.-W. Schmidt, Harmeet Singh Chawla, Rod Snowdon, and Björn Usadel. "Oxford Nanopore sequencing: new opportunities for plant genomics?" Journal of Experimental Botany 71, no. 18 (May 27, 2020): 5313–22. http://dx.doi.org/10.1093/jxb/eraa263.

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Abstract DNA sequencing was dominated by Sanger’s chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today’s long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.
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Maestri, Simone, Maria Giovanna Maturo, Emanuela Cosentino, Luca Marcolungo, Barbara Iadarola, Elisabetta Fortunati, Marzia Rossato, and Massimo Delledonne. "A Long-Read Sequencing Approach for Direct Haplotype Phasing in Clinical Settings." International Journal of Molecular Sciences 21, no. 23 (December 1, 2020): 9177. http://dx.doi.org/10.3390/ijms21239177.

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The reconstruction of individual haplotypes can facilitate the interpretation of disease risks; however, high costs and technical challenges still hinder their assessment in clinical settings. Second-generation sequencing is the gold standard for variant discovery but, due to the production of short reads covering small genomic regions, allows only indirect haplotyping based on statistical methods. In contrast, third-generation methods such as the nanopore sequencing platform developed by Oxford Nanopore Technologies (ONT) generate long reads that can be used for direct haplotyping, with fewer drawbacks. However, robust standards for variant phasing in ONT-based target resequencing efforts are not yet available. In this study, we presented a streamlined proof-of-concept workflow for variant calling and phasing based on ONT data in a clinically relevant 12-kb region of the APOE locus, a hotspot for variants and haplotypes associated with aging-related diseases and longevity. Starting with sequencing data from simple amplicons of the target locus, we demonstrated that ONT data allow for reliable single-nucleotide variant (SNV) calling and phasing from as little as 60 reads, although the recognition of indels is less efficient. Even so, we identified the best combination of ONT read sets (600) and software (BWA/Minimap2 and HapCUT2) that enables full haplotype reconstruction when both SNVs and indels have been identified previously using a highly-accurate sequencing platform. In conclusion, we established a rapid and inexpensive workflow for variant phasing based on ONT long reads. This allowed for the analysis of multiple samples in parallel and can easily be implemented in routine clinical practice, including diagnostic testing.
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Sutton, John M., Joshua D. Millwood, A. Case McCormack, and Janna L. Fierst. "Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies." Gigabyte 2021 (July 13, 2021): 1–26. http://dx.doi.org/10.46471/gigabyte.27.

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High quality reference genome sequences are the core of modern genomics. Oxford Nanopore Technologies (ONT) produces inexpensive DNA sequences, but has high error rates, which make sequence assembly and analysis difficult as genome size and complexity increases. Robust experimental design is necessary for ONT genome sequencing and assembly, but few studies have addressed eukaryotic organisms. Here, we present novel results using simulated and empirical ONT and DNA libraries to identify best practices for sequencing and assembly for several model species. We find that the unique error structure of ONT libraries causes errors to accumulate and assembly statistics plateau as sequence depth increases. High-quality assembled eukaryotic sequences require high-molecular-weight DNA extractions that increase sequence read length, and computational protocols that reduce error through pre-assembly correction and read selection. Our quantitative results will be helpful for researchers seeking guidance for de novo assembly projects.
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Volden, Roger, Theron Palmer, Ashley Byrne, Charles Cole, Robert J. Schmitz, Richard E. Green, and Christopher Vollmers. "Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA." Proceedings of the National Academy of Sciences 115, no. 39 (September 10, 2018): 9726–31. http://dx.doi.org/10.1073/pnas.1806447115.

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High-throughput short-read sequencing has revolutionized how transcriptomes are quantified and annotated. However, while Illumina short-read sequencers can be used to analyze entire transcriptomes down to the level of individual splicing events with great accuracy, they fall short of analyzing how these individual events are combined into complete RNA transcript isoforms. Because of this shortfall, long-distance information is required to complement short-read sequencing to analyze transcriptomes on the level of full-length RNA transcript isoforms. While long-read sequencing technology can provide this long-distance information, there are issues with both Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) long-read sequencing technologies that prevent their widespread adoption. Briefly, PacBio sequencers produce low numbers of reads with high accuracy, while ONT sequencers produce higher numbers of reads with lower accuracy. Here, we introduce and validate a long-read ONT-based sequencing method. At the same cost, our Rolling Circle Amplification to Concatemeric Consensus (R2C2) method generates more accurate reads of full-length RNA transcript isoforms than any other available long-read sequencing method. These reads can then be used to generate isoform-level transcriptomes for both genome annotation and differential expression analysis in bulk or single-cell samples.
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Abeynayake, Shamila Weerakoon, Sonia Fiorito, Adrian Dinsdale, Mark Whattam, Bill Crowe, Kate Sparks, Paul Richard Campbell, and Cherie Gambley. "A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes." Genes 12, no. 8 (July 27, 2021): 1138. http://dx.doi.org/10.3390/genes12081138.

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The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a rapid in-house workflow for DNA extraction, PCR amplification of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene and Oxford Nanopore Technologies (ONT) MinION sequencing of amplified products multiplexed after barcoding on ONT Flongle flow cells. A side-by-side comparison was conducted of DNA barcode sequencing-based identification and morphological identification of both large (>0.5 mm in length) and small (<0.5 mm in length) invertebrate specimens intercepted at the Australian border. DNA barcode sequencing results supported the morphological identification in most cases and enabled immature stages of invertebrates and their eggs to be identified more confidently. Results also showed that sequencing the COI barcode region using the ONT rapid sequencing principle is a cost-effective and field-adaptable approach for the rapid and accurate identification of invertebrate pests. Overall, the results suggest that MinION sequencing of DNA barcodes offers a complementary tool to the existing morphological diagnostic approaches and provides rapid, accurate, reliable and defendable evidence for identifying invertebrate pests at the border.
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Dissertations / Theses on the topic "ONT sequencing"

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Utterström, Johanna. "One Bead One Compound Screening for Cyclic Peptide Binding Partners." Thesis, Linköpings universitet, Molekylär fysik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-152282.

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In recent years a significant research focus has been on the development of biomimicking three-dimensional substrates for cell culturing. Hydrogels mimicking the extracellular matrix is a well-suited scaffold for this purpose and there are many different ways these can be cross-linked to retain their shape. The group of Molecular Materials at IFM, Linköping University, is focusing on the development of physical hydrogels hybridized through peptide-peptide interactions but all peptides used for this today are created using rational design and on top of this very large, making them time-consuming and expensive to fabricate. The aim of this project was to evaluate if One Bead One Compound (OBOC) libraries could be used as an alternative to rational design in the finding of cyclic peptide binding partners used in the hybridization of hydrogels. The results were not very promising though since only seven peptides passed all screening steps and of these only two could be sequenced. Of these two, only one was water soluble enough to enable binding interactions analysis but was then found to be a false hit. Nevertheless, it should be noticed that only a fraction of all possible combinations was screened and the results cannot exclude OBOC libraries as an approach in the quest of finding new cyclic peptide binding partners.
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Finsterbusch, Friederike. "Analysis of gene expression data from Massive Parallel Sequencing identifies so far uncharacterised regulators for meiosis with one candidate being fundamental for prophase I in male and female meiosis." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-202144.

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Meiosis is a specialized division of germ cells in sexually reproducing organisms, which is a fundamental process with key implications for evolution and biodiversity. In two consecutive rounds of cell division, meiosis I and meiosis II, a normal, diploid set of chromosome is halved. From diploid mother cells haploid gametes are generated to create genetic individual cells. This genetic uniqueness is obtained during prophase of meiosis I by essential meiotic processes in meiotic recombination, as double strand break (DSB) formation and repair, formation of crossovers (CO) and holiday junctions (HJs). Checkpoint mechanisms ensure a smooth progress of these events. Despite extensive research key mechanisms are still not understood. Based on an analysis of Massive Parallel Sequencing (MPS) data I could identify 2 genes, Mcmdc2 and Prr19, with high implication in meiotic recombination. In the absence of Mcmdc2 both sexes are infertile and meiocytes arrest at a stage equivalent to mid-­‐pachytene in wt. Investigations of the synaptonemal complex (SC) formation revealed severe defects suggesting a role for MCMDC2 in homology search. Moreover, MCMDC2 does not seem to be essential for DSB repair, as DSB markers of early and mid recombination nodules, like DMC1 and RPA, are decreased in oocytes. Nevertheless, late recombination nodules, which are positive for MutL homolog 1 (MLH1), do not form in both sexes. The absence of the asynapsis surveillance checkpoint mechanism in Hormad2 deficient ovaries with Mcmdc2 mutant background allowed survival of oocytes. This points into the direction that Mcmdc2 knock­out oocytes get eliminated after prophase I due to failed homologous synapsis. Interestingly, MCMDC2 contains a conserved helicase domain, like the MCM protein family members MCM8 and MCM9. I therefore hyphothesize that Mcmdc2 promotes homolgy search.
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Benazir, Katarina Marquez. "Molecular Marker Applications in Oat (Avena Sativa L.) Breeding and Germplasm Diagnostics." Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31148.

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The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.
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Renard, Émeline. "Folates et pathologies du neurodéveloppement : autisme et anomalies de fermeture du tube neural." Thesis, Université de Lorraine, 2018. http://www.theses.fr/2018LORR0279/document.

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Les folates sont des vitamines importantes dans le développement neurologique d’un enfant puisqu’elles sont impliquées dans deux pathologies : l’autisme et les anomalies de fermeture du tube neural (AFTN). Une carence en vitamine B9 et la présence de certains polymorphismes des gènes du métabolisme des monocarbones sont associées à un risque augmenté d’anomalies de fermeture du tube neural. A l’inverse, une supplémentation périconceptionnelle en vitamine B9 a permis de réduire l’incidence de ces malformations. Dans le cadre de l’autisme, la présence d’anticorps dirigés contre le récépteur aux folates FR aplha au niveau cérébral entraînant une carence en folate cérébral a été décrite avec une fréquence importante chez les enfants autistes. Un traitement par acide folinique permettrait une amélioration des symptômes en corrigeant la carence en folates grâce à un passage médié par le RFC (récépteur non bloqué par les anticorps). La première partie est une étude clinique randomisée versus placebo réalisée au CHU de Nancy dont le but est d’évaluer l’éfficacité d’un traitement par acide folinique pendant 12 semaines sur la réduction des troubles autistiques. 19 enfants ont été inclus dans l’étude.Une amélioration significative des symptômes autistiques est observée pour le score ADOS dans le groupe traité (p= 0,02), plus particulièrement pour les interactions sociales réciproques (p=0,019). La fréquence des Anticorps anti FR alpha au sein du groupe est de 58 %. Il n’y a pas de corrélation observée entre le taux d’anticorps et l’importance de la réponse au traitement. Aucun effet secondaire grave n’a été observé au cours de l’étude. La seconde partie est une étude par séquençage haut débit d’un large panel de gènes chez des patients présentant des anomalies de fermeture du tube neural (SureSelect Focused Exome Plus (Agilent®)). Le séquençage a été complété par une analyse de méthylation pan-génomique (Infinium HumanMethylation Beadchip (Illumina®)). 23 patients ont été inclus dans l’étude. Plusieurs variants rares ont été identifiés comme associés au risque de AFTN dont des variants de gènes du métabolisme des monocarbones : LRP2, rs137983840, p=0,005; MMAA, rs148142853, p= 0,005 ;TCN2, rs35838082, p=0,044, FPGS, rs41306702, p=0,0012, BHMT, rs763726268, p= 0,011 et de la voie Sonic Hedgehog (SHH) (GLI3, rs35364414, p=0,012). Une différence de méthylation significative a été mise en évidence au niveau du gène CFAP46 (hémiméthylation versus absence de méthylation chez les contrôles) chez un patient porteur des 4 variants à risque identifiés (LRP2, MMAA, BHMT et GLI3). Ces résultats renforcent l’implication des folates dans ces deux pathologies du neurodéveloppement que sont l’autisme et les anomalies de fermeture du tube neural. Une recherche des anticorps anti-FRalpha plus systématique chez les enfants autistes pourrait permettre de proposer un traitement par acide folinique ciblé. Dans le cadre des AFTN, notre étude a mis en évidence l’influence de gènes impliqués dans le métabolisme de la vitamine B12 et monocarbone sur le risque de AFTN. Un nouveau gène candidat (GLI3) est identifié ainsi qu’une signature de méthylation mettant en évidence l’influence de la voie SHH
Folates are essentials vitamins in children neurodevelopment with an implication in two pathologies : autism and neural tube defects (NTD). Folates deficiency and some polymorphisms of genes involved in one carbon metabolism (OCM) are associated with NTD. Contrary, periconceptional folate supplementation is associated with decreased NTD frequency.In autism, higher frequency of antibodies against Folate Receptor Alpha (FR alpha) is rapported and associated with folates cerebral deficiency. Folinic acid treatment could improve autistic symptoms by correcting cerebral folate deficiency (cerebral transport mediated by RFC, an other receptor which not blocked by antibodies anti-FR alpha). First part is a randomized controlled trial versus placebo realized in CHU of Nancy in order to evaluate efficiency of folinic acid treatment during 12 weeks on autistic symptoms. 19 children have been included in the study. A significative improvement of autistic symptoms is observed by ADOS score in folinic acid group (p= 0.02) and particularly for mutual social interactions (p=0.012). FRalpha antibodies are present in 58 % of the group. We didn’t observed correlation between antibodies titers and folinic acid response. No serious adverse effects have been observed during the study. Second part is hight throughput next generation sequencing of DNA from patients with NTD using SureSelect Focused Exome Plus (Agilent®). Sequencing has been completed with DNA methylation analysis (Infinium HumanMethylation Beadchip (Illumina®)). 23 patients were included in the study. Six variants have been associated with NTD: from genes of B12 metabolism LRP2, rs137983840, p=0.005; MMAA, rs148142853, p= 0.005 and TCN2, rs35838082, p=0.044), folate cellular metabolism (FPGS, rs41306702, p=0.0012; choline metabolism, BHMT, rs763726268, p= 0.011) and Sonic Hedgehog pathway(SHH) (GLI3, rs35364414, p=0.012). A significative difference of methylation is identified in the vicinity of CFAP46 gene (hemimethylation versus no methylation in pseudo-controls) in one patient exhibited variants of BHMT, LRP2etMMAA. These results highlight implication of folates in these two pathologies of neurodevelopment, wich are autism and NTD. Anti-FRalpha should be routinely evaluated in case of autism in order to propose folinic acid treatment if they are positives. In the NTD study, we identified new variants from gene from one carbon metabolism probably implicated. A new candidate gene is identified (GLI3) and a methylation signature in association with B12 metabolism and OCM gene variants
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Finsterbusch, Friederike [Verfasser], Attila [Akademischer Betreuer] Toth, Anthony [Gutachter] Hyman, and Attila [Gutachter] Toth. "Analysis of gene expression data from Massive Parallel Sequencing identifies so far uncharacterised regulators for meiosis with one candidate being fundamental for prophase I in male and female meiosis / Friederike Finsterbusch ; Gutachter: Anthony Hyman, Attila Toth ; Betreuer: Attila Toth." Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://d-nb.info/1160874816/34.

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David, Elena Izabela. "Applicazione di tecniche di sequenziamento per l'analisi microbiologica quantitativa degli alimenti: potenzialità e criticità." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2019.

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In questo lavoro di tesi è stata analizzata la capacità di quantificazione e identificazione di sequenze metagenomiche appartenenti a microrganismi inoculati sperimentalmente in due matrici alimentari sottoposte a metagenomica shotgun e target utilizzando quattro tools bioinformatici, valutando in modo indipendente le prestazioni in termini di assegnazione tassonomica dei microrganismi e la loro eventuale quantificazione. Le due matrici alimentari analizzate sono rappresentate da bocconcini di petto di pollo antibiotic free e filetti di salmone affumicato, inoculati con proporzioni conosciute di una mock community. I software bioinformatici valutati sono stati MG-RAST, MGmapper, CosmosID e One codex, tutti disponibili online ad eccezione di MGmapper. Complessivamente, i risultati delle analisi condotte su matrici alimentari inoculate sperimentalmente mostrano che tutti e quattro i tools bioinformatici utilizzati hanno ottenuto buoni risultati in termini di identificazione di batteri e parassiti, sebbene CosmosID e One codex siano stati in grado di identificare anche i virus. MG-RAST con il database RefSeq, seguito da MGmapper (database Silva), sono i software di analisi più affidabili nell'identificazione di specie batteriche. Al contrario, MG-RAST e MGmapper hanno mostrato una capacità molto limitata di identificare i virus, mentre CosmosID e One codex li hanno rilevati. Infine, MG-RAST e CosmosID sono stati in grado di identificare il protozoa Cryptosporidium parvum mentre il lievito Saccharomyces cerevisiae non ha superato il valore soglia di identificazione con nessuno dei software bioinformatici utilizzati. A livello quantitativo non è stato possibile identificare una correlazione diretta tra concentrazione di una specie inoculata e abundance delle reads per quella specie anche se in termini relativi la specie Propionibacterium freudenreichii inoculata alle concentrazioni più alte ha mostrato un’abundance delle read maggiore con tutti i software utilizzati.
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Mulero, Stephen. "Développement d’outils d’écologie moléculaire pour un suivi intégratif des maladies transmises par les mollusques d’eau douce dans un contexte d’émergences et de changements globaux A Multiplex Rapid Diagnostic PCR (RD-PCR) approach for xenomonitoring of human and animal schistosomiases in a One Health context Genetic diversity and relationships of the liver fluke Fasciola hepatica (Trematoda) with native and introduced definitive and intermediate hosts Simultaneous genotyping of gastropods and their trematode parasites using Amplicon Sequencing Pre-zygotic isolation mechanisms between Schistosoma haematobium and Schistosoma bovis parasites: from mating interactions to differential gene expression." Thesis, Perpignan, 2020. http://www.theses.fr/2020PERP0023.

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Les changements globaux, qu’ils soient d’origine climatique ou anthropique ont diverses conséquences en santé humaine et animale, mais aussi sur les écosystèmes mondiaux. L’une des plus importantes est la modification des aires de répartitions géographiques des espèces et de celle des pathogènes qui leurs sont associés. C’est dans ce contexte que nous assistons ces dernières années à une recrudescence des cas d’émergences et de réémergences de maladies infectieuses dans le monde. Alors que les efforts de recherche menés dans ce domaine se focalisent principalement sur les maladies virales, les maladies transmises par les mollusques d’eau douce, qui affectent plus d’un milliard d’individus dans le monde, sont également sujettes à ces évènements d’émergences devenus fréquents. Cependant, l’étude de la dynamique des parasites associés à ces maladies se focalisent essentiellement sur le diagnostic et le traitement des hôtes définitifs, en particulier l’Homme. Toutefois, une telle approche ne permet pas de prévenir de la transmission de ces parasites à l’Homme et encore moins de prévenir d’un évènement d’émergence, et les outils actuels utilisés pour le suivi de ces parasites dans l’environnement sont difficilement applicables à large échelle. Ce travail de thèse se propose donc d’apporter une vision plus environnementale de la dynamique de ces maladies. Avec l’exemple de l’émergence de bilharziose urogénitale en Corse, nous avons analysé cette émergence en intégrant l’étude des traits d’histoire de vie du parasite tropical en cause, notamment sa thermo tolérance, ainsi que le rôle des hôtes intermédiaires mollusques et des hôtes définitifs sauvages et domestiques dans le maintien local du cycle parasitaire. Dans un second temps nous avons développé des outils de diagnostic par ADN environnemental pour la détection de mollusques hôtes dans l’environnement afin d’identifier les zones à risque d’émergence, ainsi que des outils de détection intramolluscal de schistosomes pour identifier les sites de transmission actif, et donc permettre un suivi environnemental des acteurs de ces maladies. Pour compléter ces approches, nous avons développé un outil plus généraliste de metabarcoding environnemental pour caractériser les communautés de mollusques d’eau douce, et initié le développement d’un outil similaire pour la caractérisation des communautés de trématodes, ceci afin d’étudier les interactions entre ces organismes. Enfin nous discutons de l’intégrations de tous ces éléments dans de nouvelles stratégies de contrôle à l’encontre de maladies transmises par les mollusques d’eau douce
Global changes, whether climatic or anthropogenic, have various consequences in human and animal health, as well as for worldwide ecosystems. One of the most important is the modification of geographical ranges of species and those of their associated pathogens. It is in this context that in recent years we have witnessed a resurgence in the emergence and re-emergence of infectious diseases around the world. While research efforts in this field are mainly focused on viral diseases, freshwater snail-borne diseases, that affect more than 1 billion peoples around the world, are also subject to these outbreaks, which have become frequent. However, the study of the dynamics of parasites associated with these diseases focuses primarily on the diagnosis and treatment of the definitive hosts, particularly humans. Such an approach does not prevent the transmission of these parasites to humans and even less prevent an emergence event, and the existing tools used to monitor these parasites in the environment are difficult to apply at large scale. This thesis work, therefore aims to provide a more environmental vision of the dynamics of these diseases. With the example of the emergence of urogenital bilharziasis in Corsica, we analysed this emergence by integrating the study of the life history traits of the tropical parasite in question, particularly its thermo tolerance, as well as the role of mollusc intermediate hosts and wild and domestic definitive hosts in the local maintenance of the parasite lifecycle. In a second step, we have developed environmental DNA diagnostic tools for the detection of molluscs hosts in the environment in order to identify areas at risk of emergence, as well as tools for intramolluscal detection of schistosomes to identify active sites of transmission, and thus allow the environmental monitoring of the actors of these diseases. To complete these approaches, we have developed a more generalised environmental metabarcoding tool to characterise freshwater mollusc communities and initiated the development of a similar tool for the characterisation of trematode communities, in order to study the interactions between these organisms. Lastly, we discuss the integration of all these elements into new control strategies against snail-borne diseases
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Dippenaar, A., S. N. Goossens, M. Grobbelaar, S. Oostvogels, B. Cuypers, K. Laukens, Conor J. Meehan, R. M. Warren, and Rie A. van. "Nanopore sequencing for Mycobacterium tuberculosis: a critical review of the literature, new developments and future opportunities." 2021. http://hdl.handle.net/10454/18521.

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The next-generation short-read sequencing technologies that generate comprehensive, whole-genome data with single-nucleotide resolution have already advanced tuberculosis diagnosis, treatment, surveillance and source investigation. Their high costs, tedious and lengthy processes, and large equipment remain major hurdles for research use in high tuberculosis burden countries and implementation into routine care. The portable next-generation sequencing devices developed by Oxford Nanopore Technologies (ONT) are attractive alternatives due to their long-read sequence capability, compact low-cost hardware, and continued improvements in accuracy and throughput. A systematic review of the published literature demonstrated limited uptake of ONT sequencing in tuberculosis research and clinical care. Of the 12 eligible articles presenting ONT sequencing data on at least one Mycobacterium tuberculosis sample, four addressed software development for long read ONT sequencing data with potential applications for M. tuberculosis. Only eight studies presented results of ONT sequencing of M. tuberculosis, of which five performed whole-genome and three did targeted sequencing. Based on these findings, we summarize the standard processes, reflect on the current limitations of ONT sequencing technology, and the research needed to overcome the main hurdles. Summary: The low capital cost, portable nature and continued improvement in the performance of ONT sequencing make it an attractive option for sequencing for research and clinical care, but limited data is available on its application in the tuberculosis field. Important research investment is needed to unleash the full potential of ONT sequencing for tuberculosis research and care.
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Hsu, Sun-Ping, and 許尚評. "One Dimension Cutting Stock Problem - Decision Model of Cutting Sequencing." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/08268103212192115935.

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碩士
長庚大學
企業管理研究所
92
Abstract The purpose of this paper discusses the best way, under "one dimension cutting stock problem", to minimize the time of changing specifications by arranging the sequence of cutting. At first, we talk about the cut combinations (Pattern 1, Pattern 2,…….Pattern I) of completing orders, and the cut parameters (Cut 1, Cut 2, ….Cut i) corresponding with former combinations. Then, we debate the way to minimize the changed time by organizing the sequence of different cut combinations. By analyzing the transformation of different combinations pairly, we bring up “Cutting Point Move Distance Analysis Method, CPMD” which points out that the corresponding distance and the time period of cutting tools’ moving is linear correlation. Through the quantification of related variables, we can compare the time periods of change specification while transferring the different combinations. Our model could reduce the changed period of cutting-stock problem; also, it could be a reference tool to evaluate the advantages of other mathematical calculations.
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Huang, Chi-Ching, and 黃之敬. "On Analysis Of Two Teaching Sequencing Theories-illustrated By The Teaching Unit Of Equation With One Variable And One Degree." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/8xj4fj.

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碩士
國立臺中教育大學
數學教育學系
102
Textbook is not only important for primary and secondary students learning resources, but also the basis for teaching activities. However, even for the same unit, different versions of textbooks, teaching materials presented in the order in which content can be found have their differences, learning difficulties or misconceptions derived at this time, is likely to be organized as sequence from textbooks. In this research, the teaching hierarchy of the unit named equation with one variable and one degree was utilized to analyze STS and ISTS methods, respectively. We found that the objective function has the same value in some cases in terms of STS. However, this seldom occurred in ISTS. In addition, there is only one same result of the context strategy in the comparison between STS and ISTS. Finally, according to research findings on educational authorities and schools to make recommendations.
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Books on the topic "ONT sequencing"

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Straalen, Nico, and Dick Roelofs. Human Evolution and Development. NL Amsterdam: Amsterdam University Press, 2019. http://dx.doi.org/10.5117/9789463729208.

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Our understanding of human evolution is proceeding at an unprecedented rate over the last years due to spectacular fossil finds, reconstructions based on genome comparison, ancient DNA sequencing and new insights into developmental genetics. This book takes an integrative approach in which the development of the human embryo, the evolutionary history of our body, the structure of human populations, their dispersal over the world and their cultures are examined by integrating paleoanthropology, developmental biology, comparative zoology, population genetics and phylogenetic reconstruction. The authors discuss questions like: - What do we know about ancient humans? - What happens in the development of an embryo? - How did we manage to walk upright and why did we lose our hair? - What is the relationship between language, migration and evolution? - How does our body respond to the challenges of modern society? In addition to being a core text for the study of the life sciences, Human Evolution and Development is an easy-to-read overview for the interested layperson.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. DNA sequencing. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0007.

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The emergence of eDNA analysis is tightly linked to the development of next-generation sequencing. Chapter 7 “DNA sequencing” gives an overview of the characteristics and limitations of the main next-generation sequencing platforms. It focuses particularly on the Illumina platform, which is the only technology currently suitable for large-scale analysis with hundreds to thousands of samples. More specifically, Chapter 7 describes the Illumina library preparation process, the generation of sequencing clusters by bridge PCR on the flow cell, and the sequencing reaction itself, based on sequencing by synthesis. Finally, detailed information is provided on the meaning and coding of quality scores of the sequencing reads.
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Walker, Dan. Korg M-One Sequencing and Recording Handbook (Korg M-One Support Series). Alexander Pub, 1988.

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Newman, Abraham L. Sequencing, Layering, and Feedbacks in Global Regulation. Edited by Orfeo Fioretos, Tulia G. Falleti, and Adam Sheingate. Oxford University Press, 2016. http://dx.doi.org/10.1093/oxfordhb/9780199662814.013.38.

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From banking standards to data privacy, regulation has entered the lexicon of international affairs. Unlike trade or currencies, however, there are few formal treaty-based international organizations resolving disputes or setting the rules for the world. Instead, global regulation is frequently shaped by informal networks of regulators or at times by the extraterritorial extension of domestic law by large markets. Drawing on work from historical institutionalism, this chapter argues that the global politics of regulation is in important respects the product of domestic and international institutions interacting over time and across space. In developing three mechanisms—relative sequencing, cross-national layering, and transnational feedbacks —the chapter argues that historical institutionalism helps address lacunae in extant approaches to global regulation.
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Bantekas, Ilias. Sequencing Peace and Justice in Post-Conflict Africa. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198810568.003.0005.

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This chapter discusses the extent to which there is any conflict or harm in the ICC Prosecutor’s involvement in cases undergoing mediation by the international community, most of which are currently in Africa. The ICC Prosecutor’s discretion, as per the Court’s Statute, to hold a prosecution in abeyance in anticipation of the outcomes of mediating efforts which aim at ending a conflict is at best ambivalent. Recent practice suggests that stakeholders engaged in ending long-running African conflicts prefer the Prosecutor to decline to exercise jurisdiction in order to encourage the parties to reach some agreement. For obvious reasons, discussions on such matters are often held confidentially and not in the context of official debates. The African experience with the peace–justice nexus shows that the peace-versus-justice debate has not been resolved in favour of any camp.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. DNA metabarcoding data analysis. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0008.

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DNA metabarcoding generates huge amounts of data containing noise introduced by molecular methods. Chapter 8 “DNA metabarcoding data analysis” discusses the analytic steps and available software to curate and evaluate DNA metabarcoding data prior to final ecological analyses. It provides command lines to perform primary analyses of Illumina sequencing data with the OBITools, ranging from read assignment to samples to the formation of molecular operational taxonomic units (MOTUs) and their assignment to a taxon through comparison against reference databases. Chapter 8 also develops several methods to further curate sequencing data from contaminants or dysfunctional PCRs by using DNA extraction, PCR, and sequencing blank controls as well as PCR/biological replicates. It also presents several classical analyses to ensure that the diversity of the sample or the study site is appropriately covered. Finally, this chapter considers what conclusions on biodiversity and ecological processes can be really drawn from metabarcoding data.
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Sadleir, Lynette G., Jozef Gecz, and Ingrid E. Scheffer. Epilepsies That Occur Predominantly in Girls. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0041.

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Availability of DNA sequencing has led to an increase in the number of children being identified with mutations in specific genes in specific epilepsy phenotypes. The presence of mutations that cause epilepsy only in females is one of the discoveries revealed in the sequencing era. Mutations in PCDH19 and CDKL5 are distinctive and identifiable forms of female-only epilepsy, and clinicians should consider PCDH19 in normal girls presenting with clusters of afebrile or febrile seizures in the first 3 years of life, and CDKL5 in girls or boys presenting with severe developmental delay within the first 6 months of life followed by intractable seizures including spasms within the first 2 years.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. The future of eDNA metabarcoding. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0019.

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Environmental DNA-based research is undergoing rapid developments, but its democratization in basic and applied research remains hampered by the biases introduced by molecular approaches, the difficulties in estimating absolute organisms’ abundances, and a lack of general consensus in molecular protocols. Chapter 19 “The future of eDNA metabarcoding” provides an overview of these current challenges and discusses how shotgun sequencing, capture-based methods, inclusion of internal standards, and development of new data repositories could alleviate these limits and facilitate cross-experiments comparisons. This chapter finally turns to open questions on the potentiality of new sequencing methods and proposes directions to improve biodiversity estimates and ecological inferences and predictions from eDNA data, and ultimately stimulate further developments and integration of eDNA metabarcoding into academic and operational ecological research and monitoring.
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Maher, Christopher J., and Elaine R. Mardis. Genomic Landscape of Cancer. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0004.

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The study of cancer genomics has advanced rapidly during the last decade due to the development of next generation or massively parallel technology for DNA sequencing. The resulting knowledge is transforming the understanding of both inherited (germline) genetic susceptibility and the somatic changes in tumor tissue that drive abnormal growth and progression. The somatic alterations in tumor tissue vary depending on the type of cancer and its characteristic “genomic landscape.” New technologies have increased the speed and lowered the cost of DNA sequencing and have enabled high-volume characterization of RNA, DNA methylation, DNA-protein complexes, DNA conformation, and a host of other factors that, when altered, can contribute to the development and/or progression of the cancer. Technologic advances have greatly expanded research on somatic changes in tumor tissue, revealing both the singularity of individual cancer genomes and the commonality of genetic alterations that drive cancer in different tissues.
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Mammen, Andrew L., and Jessica R. Nance. Evaluation of hyperCKaemia. Edited by Hector Chinoy and Robert Cooper. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198754121.003.0007.

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Serum creatine kinase (CK) levels may be elevated in patients with muscle weakness or pain. In asymptomatic patients with CK elevations, the focus should be on identifying reversible causes, followed by investigation for inherited muscle diseases. In asymptomatic patients with an incidental finding of elevated CK, clinicians should look for reversible causes, then re-test the CK after 10 days of rest in the absence of potential triggers. If the CK remains markedly elevated and/or electromyography proves myopathic, a muscle biopsy should be considered. Women of childbearing age with elevation of serum CK should be evaluated for dystrophin mutation. Genetic causes of hyperCKaemia can be pursued with targeted gene sequencing, or whole exome or next generation sequencing. Patients with inherited skeletal muscle diseases may also have associated cardiac disease, so a cardiology evaluation should be considered in all patients with unexplained CK elevations.
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Book chapters on the topic "ONT sequencing"

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Mori, E., and R. Fani. "Sequencing of RAPD Markers." In Fingerprinting Methods Based on Arbitrarily Primed PCR, 171–76. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60441-6_20.

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Sterflinger, Katja, and Guadalupe Piñar. "Molecular-Based Techniques for the Study of Microbial Communities in Artworks." In Microorganisms in the Deterioration and Preservation of Cultural Heritage, 59–77. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-69411-1_3.

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AbstractThanks to the revolutionary invention of the polymerase chain reaction and the sequencing of DNA and RNA by means of “Sanger sequencing” in the 1970th and 1980th, it became possible to detect microorganisms in art and cultural assets that do not grow on culture media or that are non-viable. The following generation of sequencing systems (next generation sequencing, NGS) already allowed the detection of microbial communities on objects without the intermediate step of cloning, but still most of the NGS technologies used for the study of microbial communities in objects of art rely on “target sequencing” linked to the selectivity of the primers used for amplification. Today, with the third generation of sequencing technology, whole genome and metagenome sequencing is possible, allowing the detection of taxonomic units of all domains and kingdoms as well as functional genes in the produced metagenome. Currently, Nanopore sequencing technology is a good, affordable, and simple way to characterize microbial communities, especially in the field of Heritage Science. It also has the advantage that a bioinformatic analysis can be performed automatically. In addition to genomics and metagenomics, other “-omics” techniques such as transcriptomics, proteomics, and metabolomics have a great potential for the study of processes in art and cultural heritage, but are still in their infancy as far as their application in this field is concerned.
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Yang, Nianjun, and Xin Jiang. "DNA Sequencing Using Carbon Nanopores." In Springer Series on Chemical Sensors and Biosensors, 233–71. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/5346_2018_23.

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Murgai, Rajeev, Masahiro Fujita, and Sriram C. Krishnan. "Data Sequencing for Minimum-transition Transmission." In VLSI: Integrated Systems on Silicon, 365–76. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-0-387-35311-1_30.

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Lima-de-Faria, A. "From staining methods to DNA sequencing." In One Hundred Years of Chromosome Research and What Remains to be Learned, 47–56. Dordrecht: Springer Netherlands, 2003. http://dx.doi.org/10.1007/978-94-017-0167-9_11.

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Fu, Yong-Bi, and Mo-Hua Yang. "Genotyping-by-Sequencing and Its Application to Oat Genomic Research." In Methods in Molecular Biology, 169–87. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6682-0_13.

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Baroncelli, Riccardo, and Giovanni Cafà. "Genomic sequences for fungi." In Trends in the systematics of bacteria and fungi, 231–54. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0231.

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Abstract This chapter aims to give an overview of the basic knowledge, understanding and perspectives in fungal genomics. It is likely that fungal genome sequencing will soon become simpler and cheaper, and allow most research laboratories to undertake in-house, whole genome sequencing on a regular basis, as sequencers will be accessible to most laboratories. Nonetheless, most of the innovation in the next decade will be driven by theories in innovative perspectives and fields of investigation, rather than in novel technical approaches.
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Hansen, C., M. Jørgensen, M. Bévort, R. Hummel, M. Løfgreen, N. Pallisgaard, and H. Leffers. "Direct Automated Sequencing of DDRT-PCR Fragments." In Fingerprinting Methods Based on Arbitrarily Primed PCR, 345–51. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60441-6_35.

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Lécuyer, Flavien, Valérie Gouranton, Adrien Reuzeau, Ronan Gaugne, and Bruno Arnaldi. "Action Sequencing in VR, a No-Code Approach." In Transactions on Computational Science XXXVII, 57–76. Berlin, Heidelberg: Springer Berlin Heidelberg, 2020. http://dx.doi.org/10.1007/978-3-662-61983-4_4.

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Humphreys-Pereira, Danny A., Taeho Kim, and Joong-Ki Park. "Characterization of nematode mitochondrial genomes." In Techniques for work with plant and soil nematodes, 250–64. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0250.

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Abstract This chapter presents procedures on polymerase chain reaction (PCR) amplification, protocols for PCR, cloning and sequencing, and mitochondrial genome annotation and gene identification for the characterization of nematodes.
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Conference papers on the topic "ONT sequencing"

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Benslimane, Fatiha M., Hebah Al Khatib, Dana Albatesh, Ola Al-Jamal, Sonia Boughattas, Asmaa A. Althani, and Hadi M. Yassine. "Nanopore Sequencing SARS-CoV-2 Genome in Qatar." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0289.

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Background: The current pandemic, COVID-19, is cause by an RNA Coronavirus that was recently identified as SARS-CoV-2. RNA viruses tend to have a high mutation rate; the rate is around a million times greater than that of their hosts. The mutagenic potential of the virus depends on many factors, including the fidelity of nucleic acid-replicating viral enzymes, such as SARSCoV-2 RNA dependent RNA polymerase (RdRp). The rate of mutation drives viral evolution and genome variability, consequently allowing viruses to escape the immunity of the host and develop resistance to drugs. Therefore, the characterization of SARS-CoV-2 variants might lead to implement better therapeutics treatments, vaccines design and identify new diagnostics approaches. Aim: The aim of this study was to establish a fast sequencing method to identify SARS-CoV-2 mutations in Qatar. This will help to assess if there are new viral variants that are spreading in country. Methods: RNA was isolated from samples collected from Qatar COVID-19 positive patients. The Artic Network V3 primer scheme and Oxford Nanopore ligation sequencing kit were used to prepare the sequencing libraries. Libraries were loaded on to R9.4.1 flow cells and ran on a GridION. Bioinformatics analysis was done following the Artic Network SARA-CoV-2 bioinformatics tools. Results: Genome coverage of sequenced samples was >80% and the depth was average at 200x. The coverage was highly dependable on sample viral load; samples of CT value lower than 30 resulted in better sequence coverage. The sequenced genomes were deposited in GISAID and were mainly clustering with genomes deposited from the UK. Sequences were compared to Illumina and sanger sequences and they showed compatible results. Conclusion: The use of ONT to sequence SARA-CoV-2 is a quick, affordable, and reliable technique to determine viral mutation. Using this technique, the first sequences from Qatar were deposited in to GISAID. Up to date, 700 genomes have been sequenced from Qatari samples.
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Sormaz, Dusan N. "Agent-Based Process Sequencing Using Search Algorithms." In ASME 2006 International Manufacturing Science and Engineering Conference. ASMEDC, 2006. http://dx.doi.org/10.1115/msec2006-21071.

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Process sequencing represents one of very important tasks in the process planning. The order of tasks and the use of resources are determined by sequencing, and therefore the decision carries the burden of finally optimizing the whole process plan of the part. This paper proposes a flexible, agent-based framework for process sequencing which allows for realtime selection of the sequencing algorithm, dependent on the stage of the product development. The framework has been developed around a tool called space searcher which provides for application of space search algorithms in various domain. Space searcher receives a sequencing agent which provides the sequencing algorithm and executes a space search in order to generate context-specific optimal process sequence. Several process sequencing algorithms (and corresponding agents for space searcher) are described in detail. The application of those algorithms is illustrated on few examples.
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Hsuan-Pu Chang, Chun-Chia Wang, Kuen Han Jan, and T. K. Shih. "SCORM sequencing testing for sequencing control mode." In 20th International Conference on Advanced Information Networking and Applications - Volume 1 (AINA'06). IEEE, 2006. http://dx.doi.org/10.1109/aina.2006.295.

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Li, Hong, Si-Yang Liu, Yan-Wei Huang, Yong-Quan Chen, and Zhang-Hua Fu. "An Efficient 2-opt Operator for the Robotic Task Sequencing Problem." In 2019 IEEE International Conference on Real-time Computing and Robotics (RCAR). IEEE, 2019. http://dx.doi.org/10.1109/rcar47638.2019.9044008.

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Tauhid, Shafin, Hakan U. Artar, Saraj Gupta, and Gu¨l Okudan. "An Investigation of the Impact of Assembly Sequencing on the Product Family Design Outcomes." In ASME 2007 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/detc2007-35672.

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While many approaches have been proposed to optimize the product family design for measures of cost, revenue and performance, many of these approaches fail to incorporate the complexity of the manufacturing issues into family design decision-making. One of these issues is assembly sequencing. This paper presents a simulation study by which the impact of assembly sequencing on the product family design outcomes is investigated. Overall, the results indicate that when the product family design takes into account the assembly sequencing decisions, the outcomes at the shop floor level improve. The results have implications for companies that are looking into increasing their revenue without increasing their investment in the shop floor.
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Fazelpour, Mohammad, Apurva Patel, Prabhu Shankar, and Joshua D. Summers. "A User Study on Exploring the Sequencing of Unit Cell Design Guidelines." In ASME 2017 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/detc2017-67382.

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The objective of this user study is to evaluate the effect of sequencing of unit cell design guidelines. The unit cell design guidelines support engineers in intentionally redesigning the topology and shape of unit cells for a desired structural behavior. In this study, four different unit cell design guidelines are selected to enable designers in increasing the shear flexure in meso-scale periodic cellular materials. These guidelines are not necessarily objective and may result in different modified unit cells when applied by different designers. Therefore, this user study was designed to evaluate the effect of sequencing the guidelines on the subjectivity and the modified unit cells. Twelve different sequencing sets are tested and it is found that certain sequencing of guidelines resulted in more novel ideas than other cases with less subjective guidelines.
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Faheem, W., C. C. Hayes, D. M. Gaines, and J. F. Castaño. "Coordinator: A Robust Setup Planner That Does Early Detection of Fixture-Feature Interactions." In ASME 1998 Design Engineering Technical Conferences. American Society of Mechanical Engineers, 1998. http://dx.doi.org/10.1115/detc98/dfm-5741.

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Abstract This paper presents Coordinator, a process planner that uses a blend of geometric and manufacturing information to detect a broad variety of manufacturing interactions to sequence setups plans. This system is designed to be used by experts to reduce the time and effort required to produce good plans. Coordinator’s contributions is early detection of fixture-feature interactions (interferences between manufacturing operations in which one destroys clamping surfaces required by another). The ability to detect them early (i.e. prior to setup sequencing) eliminates the need for many re-planning cycles. These interactions are usually addressed only after set-up sequencing because sequencing determines part shape in each setup, which in turn affects clamping options. Coordinator addresses this problem through a representational which considers multiple possible workpiece shapes and clamping surfaces prior to setup sequencing. This representation enables Coordinator to consider fixture-feature interactions to sequence setups well in the first iteration, greatly reducing the need for iterative adjustment.
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Jiang, Zhaoliang, and Zhi Li. "Mixed-Model Assembly Line Sequencing Optimization Based on Workstation Overload Analysis." In ASME 2013 International Manufacturing Science and Engineering Conference collocated with the 41st North American Manufacturing Research Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/msec2013-1182.

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Reasonable task sequencing will be benefit for both productivity and industry energy saving. Mixed-model products assembly sequencing of mass customization manufacturing systems significantly affects material requirements, order delivery time, and manufacturing cost. A new approach for products sequencing of mixed model assembly line (MMAL) according to workstations overload analysis based on historical production data is proposed to obtain the optimized assembly sequence with the objectives of minimizing consumption waviness of each material, assembly line setup cost, and order delivery time. It will be efficient to cut down the assembly line blockage time, improve the assembly productivity, and save industry energy. A multi-objective optimization algorithm based on particle swarm is developed. An industrial case study has been performed in order to demonstrate the practicality and effectiveness of the proposed approach.
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Mastrangelo, Carlos H., S. Palaniappan, Piu Francis Man, Mark A. Burns, and David T. Burke. "Microchips for DNA sequencing." In Symposium on Micromachining and Microfabrication, edited by Chong H. Ahn and A. Bruno Frazier. SPIE, 1999. http://dx.doi.org/10.1117/12.359324.

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Gholami, Ali, Mohammad Ali Maddah-Ali, and Seyed Abolfazl Motahari. "Private Shotgun DNA Sequencing." In 2019 IEEE International Symposium on Information Theory (ISIT). IEEE, 2019. http://dx.doi.org/10.1109/isit.2019.8849382.

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Reports on the topic "ONT sequencing"

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Edwards, Sebastian. On the Sequencing of Structural Reforms. Cambridge, MA: National Bureau of Economic Research, October 1989. http://dx.doi.org/10.3386/w3138.

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Geringer, Nicholas. Sequencing the Regulations on Human Germline Editing Research. Journal of Young Investigators, August 2019. http://dx.doi.org/10.22186/jyi.37.2.22-23.

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Evans, G. A. DOE project on genome mapping and sequencing. Progress report, 1992. Office of Scientific and Technical Information (OSTI), December 1992. http://dx.doi.org/10.2172/639719.

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Shaw, B. R. [One-step PCR sequencing]. Final report, July 1, 1994--August 31, 1997. Office of Scientific and Technical Information (OSTI), December 1997. http://dx.doi.org/10.2172/353382.

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Libray, Spring. The Booming Field of Epitranscriptomics and its Role in Human Disease. Spring Library, April 2021. http://dx.doi.org/10.47496/sl.blog.26.

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Currently, the detection techniques used for transcriptome-wide identification of chemical modifications mainly depend on chemical and antibody-based detection methods followed by sequencing analysis.
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Edwards, Sebastian. Keynes on the Sequencing of Economic Policy: Recovery and Reform in 1933. Cambridge, MA: National Bureau of Economic Research, March 2018. http://dx.doi.org/10.3386/w24367.

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Davenport, Karen Walston. Short papers on current state of sequencing, metagenomics, and RNAseq for diagnostics. Office of Scientific and Technical Information (OSTI), March 2019. http://dx.doi.org/10.2172/1503174.

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Slezak, T., M. Borucki, E. Vitalis, M. Torres, and R. Lenhoff. LLNL Genomic Assessment: TMT Task 1.4 Final Report on Sequencing Knowledge Gaps. Office of Scientific and Technical Information (OSTI), January 2011. http://dx.doi.org/10.2172/1068287.

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Xie, Geoffrey G., Cynthia Irvine, and Tim Levin. Quantifying Effect of Network Latency and Clock Drift on Time-Driven Key Sequencing. Fort Belvoir, VA: Defense Technical Information Center, January 2002. http://dx.doi.org/10.21236/ada435468.

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Shaw, B. R. One-Step PCR Sequencing. Final Technical Progress Report for February 15, 1997 - November 30, 2001. Office of Scientific and Technical Information (OSTI), April 2004. http://dx.doi.org/10.2172/825879.

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