Global ETD Search
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 681 for “"RNA-seq"”.
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Automated, highly scalable RNA-seq analysis
RNA-sequencing is a sensitive method for inferring gene expression and provides additional information regarding splice variants, polymorphisms and novel genes and isoforms. Using this extra information greatly increases the complexity of an analysis and prevents novice investigators from analyzing …
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Performance comparison of five RNA-seq alignment tools
… genome is a critical task in high throughput sequencing. In recent years, a large number of mapping algorithms have been developed, all of which have in common that they align a vast number of reads to genomic or transcriptomic sequences. RNA-Seq data is discrete in nature, therefore with …
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Novel methods in transcriptome analysis using RNA-seq
RNA-seq has proven to be a powerful technique for transcriptome profiling based on next-generation sequencing (NGS) technologies. Using RNA-seq, we want to solve two critical challenges: identifying Splice Junctions (SJs) and annotating gene fusion transcripts. Due to the limited read length of NGS …
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Statistical methods for modeling RNA-Seq short-read data
… data generated using the next-generation sequencing technology, RNA-Seq. Two methods are developed which attempt to accurately calculate RNA expression, the first using a penalized regression approach to remove bias based on nucleotide composition, as well as a second which demonstrates …
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Computational Pipeline for Human Transcriptome Quantification Using RNA-seq Data
… pipeline for processing Next-generation RNA sequencing (RNA-seq) data. RNA-seq experiments generate tens of millions of short reads for each DNA/RNA sample. The alignment of a large volume of short reads to a reference genome is a key step in NGS data analysis. Although storing alignment …
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Identification of novel transcripts in hepatocellular carcinoma using RNA-seq
Recent advances in sequencing technologies have helped the finding of novel transcripts by deep RNA sequencing (RNA-Seq). The approach to identify novel transcripts using RNA-Seq has been studied, however, prediction of their functional roles in cancers are not studied thoroughly. Here, I …
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Statistical power for RNA-seq data to detect two epigenetic phenomena
… other than changing the underlying DNA sequence. Two epigenetic phenomena, genomic imprinting and Allelic Expression Imbalance (AEI), are discussed in this dissertation. RNA-seq is a powerful new technology for mapping and quantifying transcriptomes using ultra high throughput next …
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Comparison of different differential expression analysis tools for rna-seq data
In molecular biology research, RNA-seq is a relatively new method for transcriptome profiling. It utilizes the next generation sequencing technology to provide huge amount information about the variety and abundance of RNA present in an organism of interest at a specific state and a given time. One …
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Computational Modeling for Differential Analysis of RNA-seq and Methylation data
… approaches for differential analysis of RNA-seq and methylation data to detect aberrant events associated with cancers. We develop a novel Bayesian approach, BayesIso, to identify differentially expressed isoforms from RNA-seq data. BayesIso features a joint model of the variability of …
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Algorithms And Tools For Computational Analysis Of Human Transcriptome Using Rna-Seq
<p>Alternative splicing plays a key role in regulating gene expression, and more than 90% of human genes are alternatively spliced through different types of alternative splicing. Dysregulated alternative splicing events have been linked to a number of human diseases. Recently, high-throughput …
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Software for Estimation of Human Transcriptome Isoform Expression Using RNA-Seq Data
… research was to develop software to be used with RNA-Seq data for transcriptome quantification that was capable of handling multireads and quantifying isoforms on a more global level. Current software available for these purposes uses various forms of parameter alteration in order to work with …
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Polyaseeker: a computational framework for identifying polyadenylation cleavage site from RNA-seq
Alternative polyadenylation (APA) of mRNA plays a crucial role for post-transcriptional gene regulation. Recently, advances in next generation sequencing technology have made it possible to efficiently characterize the transcriptome and identify the 3'end of polyadenylated RNAs. However, no …
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RNA-SEQ driven analysis of seasonal gene expression variation in miscanthus �� giganteus
… In this study, two separate M. × giganteus RNA-Seq datasets were generated to help explore the characteristics of M. × giganteus at the level of gene expression: a ten-tissue dataset suitable for examining genes with tissue-preferred expression, and a twenty-four sample dataset for examining …
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Understanding Osmoregulation and Immunity in Heteromyid Rodents Through Insights Gained from RNA-Seq
… transcriptomes of related taxa we can identify sequence and regulatory differences that represent molecular signatures of these different selection regimes. When we study these differences between taxa that have evolved under opposing selective forces we can identify the genetic underpinnings of …
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Statistical Models for Gene and Transcripts Quantification and Identification Using RNA-Seq Technology
<p>RNA-Seq has emerged as a powerful technique for transcriptome study. As much as the improved sensitivity and coverage, RNA-Seq also brings challenges for data analysis. The massive amount of sequence reads data, excessive variability, uncertainties, and bias and noises stemming from multiple …
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RNA-Seq Reveals Transcriptomic Program Associated with Stemness in Taxane Resistant Prostate Cancer
… cells to maintain therapy-resistance. Using RNAsequencing—an innovative approach for quantifying gene expression changes—this dissertation sought to elucidate chemoresistance-associated molecular pathways as a catalyst to develop new therapeutic targets. Results revealed a differential …
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Annotating and characterizing orphan gene in Zea mays via diverse RNA-Seq data
… the recently emerged young genes, which share no sequence similarity with proteins in any other species. In the last 20 years, thousands of orphan genes have been experimentally shown to play important roles in diverse species. However, there remain significant limitation in our knowledge about …
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Análise de dados de RNA-Seq com diferentes números de fatores e repetições
A tecnologia RNA-Seq mostrou-se ser revolucionária para o estudo de expressão gênica. Porém, mais estudos na literatura sobre a análise de dados de RNA-Seq são necessários, até mesmo porque se trata de um método de elevado custo. Devido a este alto custo, é importante o aproveitamento das amostras …
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Single cell RNA-seq analysis uncovers transcription regulation mechanisms in mouse germline cells
Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-08-01
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