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Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 42 for “"nanopore sequencing"”.
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Examining bacterial variation with genome graphs and Nanopore sequencing
… relating to a critical bacterial pathogen: can Nanopore sequencing of Mycobacterium tuberculosis provide high-quality public health information? We collect data from Madagascar, South Africa, and England to help answer this question. First, we assess outbreaks identified using single-reference …
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NANOPORE SEQUENCING AS A NEW TOOL TO EXPLORE COMPLEX TRANSCRIPTOMES
Long-read sequencing marked a revolution in the field of transcriptomics by helping to resolve isoform structure, unannotated splicing variants, complex loci and repetitive regions and proposing as a method for RNA modifications detection. This versatility permits its application to different …
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Protein characterization using a computational microscope: Nanopore sequencing and biological condensates
Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-08-01
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Mixed Strain Identification of Porcine Reproductive and Respiratory Syndrome Virus in Multiplexed Samples using Nanopore Sequencing
… turnaround time and long-read capacity of Oxford Nanopore Technology's MinION next-generation sequencer. We have developed a novel primer set designed to span Open Reading Frames 3 through 7 of the PRRSV genome, which has allowed for multiplexing of samples, thus reducing individual cost of …
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BIOINFORMATICS ANALYSIS OF FULL-LENGTH RNA NANOPORE SEQUENCING AT SINGLE CELL LEVEL TO STUDY TRANSCRIPTIONAL AND MUTATIONAL PATTERNS IN HUMAN LEUKEMIA
… multi-omics approach, Single Cell and Molecule sequencing (SCM-seq), was developed. This method integrates droplet-based single-cell RNA sequencing with Nanopore single-molecule sequencing, allowing comprehensive profiling of the tumor ecosystem in AML. SCM-seq was employed to analyze AML …
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Stability and bandwidth investigation of alternative structures for nanopore sensors
… cules may explain the drive and momentum for DNA sequencing research. The commonly used parallel sequencing methods require extensive sample preparation, long processing times and expensive chemical reagents. In or- der to realize the goal of $1000 genome sequencing, many alternative meth- ods are …
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Ion current modulation in bio-mimetic channel systems
… the modulation of ionic current is a signal for nanopore sensing. Here, several simulation studies focusing on ion channel conductance modulation and nanopore sensing are presented. Specifically, comprehensive research on a designed bio-mimetic channel can lead to the ionic current modulation by …
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Computational Tools for Improved Detection, Identification, and Classification of Plant Pathogens Using Genomics and Metagenomics
… the pathogen in question is unknown. Advances in sequencing technology have made it possible to sequence entire genomes and metagenomes in real-time and at a relatively low cost, opening an opportunity for the development of alternative methods for detection of novel and unknown plant pathogens. …
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Analysis of DNA methylation in canine osteosarcoma using next generation sequencing technology
… cell line (OSCA-29) was sequenced using Nanopore sequencing. Oxford Nanopore sequencing is a sequencing method that measures the variation in ionic current through a biological nanopore as a single-stranded nucleic acid is ratcheted through. These signals can then be used to determine DNA …
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Genomic Approaches for the Characterization of Shiga-toxigenic Escherichia coli (E. coli)
… method for the characterization of STEC using Nanopore sequencing. Finally, an STEC benchmark dataset was curated for use in the development of novel STEC methods.
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The Role of the Mismatch DNA Repair Protein MutL in Antigenic Variation of the Lyme Disease Spirochete
… complementation experiments. I have shown that nanopore sequencing can be used as an expedient method for measuring gene conversion at vlsE that surpasses previously described methods. Current results indicate that MutL from relapsing fever Borrelia species but not from Treponema pallidum or …
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A sequencing-based analyisis of epigenetic modifications of the mitochondrial genome
… has been studied using whole genome bisulfite sequencing (WGBS), but recent evidence has uncovered major technical issues, which introduce a potential bias during methylation quantification. In this study, we first validate the technical concerns with WGBS using publicly available datasets. …
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A streamlined Workflow for Transposon Mutagenesis in Corynebacterium glutamicum Based on Third-Generation Sequencing and its Application for Advanced Genetic Screens
… for transposon mutant library preparation and sequencing using Oxford Nanopore Technologies (ONT) nanopore Sequencing. Mobile genetic elements (MGEs) destabilize the genetic material of their hosts. While this can contribute to evolutionary plasticity in nature, it is often detrimental in a …
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Nanobiotechnology Enabled Environmental Sensing of Water and Wastewater
… isothermal amplification (LAMP) and nanopore sequencing were applied to develop assays for the detection of SARS-CoV-2, the causative agent of COVID-19, in wastewater samples. Second, surface-enhanced Raman spectroscopy (SERS) was applied for environmental detection of a range of …
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Integrated Analog Readout Array and Digital Backend for Mobile DNA Sequencing
… sequence of these nucleotides is known as DNA sequencing. An innovative approach to this is nanopore-based DNA sequencing. Unlike many other methods, nanopore sequencing detects DNA molecules directly, rather than relying on secondary phenomena, and can do so in real-time as the molecules pass …
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Engineered Replicases, Synthetic DNA, and Long-Read Sequencing Quality Control for Adeno-Associated Virus Production
… heterogeneity was lacking. In this work, rapid nanopore-sequencing, which is inexpensive and easy to access compared to other sequencing technologies, was established to sequence rAAV packaged DNA directly with high throughput. A prototypic rAAV used in research served as the model. Unlike …
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Characterizing the Microbiome of Scottish Freshwater Pearl Mussels (Margaritifera margaritifera): A Metabarcoding Analysis using Next-Generation Sequencing
… conducted via 16S rRNA gene metabarcoding. Two sequencing platforms were utilized: the MinION (Oxford Nanopore Technology) for full-length amplicons and MiSeq (Illumina) for short amplicons, enabling a comparative analysis of platform performance at the species level. Results revealed that the …
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Solid-state nanopore sensors for nucleic acid analysis
Nanopore DNA analysis is an emerging technique that involves electrophoretically driving DNA molecules through a nano-scale pore in solution and monitoring the corresponding change in ionic pore current. This versatile approach permits the label-free, amplification-free analysis of charged polymers …
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Equine Herpesvirus Type 1: Filling Gaps Toward Improved Outbreak Management
… by multiple detection methods. A new, efficient sequencing method, called nanopore sequencing, has been developed in a handheld device, called MinION, that provides thorough output in a timely manner. When combined with LAMP, it has been referred to as LAMPore. The first objective of our work was …
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Identifying individual ribosomal RNA gene repeats to investigate their behaviour
… both species. Therefore, I instead utilised deep sequencing to identify single nucleotide polymorphisms (SNPs) in the rDNA that enabled me to distinguish rDNA repeats in cultured human cells. I also used RNA-seq to identify expressed rRNA variants in the same cells. This enabled me to identify …
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