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RNA Sequencing: From Sample Preparation to Analysis
2014The introduction of RNA sequencing (RNA-seq), as a direct result of rapid progression of next-generation sequencing technologies, has revolutionized the world of transcriptomics. It enables quantification of the complete set of RNA with all its isoforms in a given cell, in far greater accuracy than before.
Sho, Maekawa +3 more
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Bioinformatic Analysis of Small RNA Sequencing Libraries
2019Bioinformatic analysis of small RNA sequencing libraries consists of transforming a series of small RNA sequencing experiment fastq files into a table containing small RNA sequences and their abundance. This is achieved by cleaning the reads, aligning the cleaned reads to a reference, and parsing the alignment results.
Ricardo A, Chávez Montes +2 more
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Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing
Plant Molecular Biology, 1991A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup ...
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Sequence and Structure Analysis of Noncoding RNAs
2009Noncoding RNAs (ncRNAs) are increasingly recognized as important functional molecules in the cell. Here we give a short overview of fundamental computational techniques to analyze ncRNAs that can help us better understand their function. Topics covered include prediction of secondary structure from the primary sequence, prediction of consensus ...
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RNA 5-Methylcytosine Analysis by Bisulfite Sequencing
2015Cells have developed molecular machineries, which can chemically modify DNA and RNA nucleosides. One particular and chemically simple modification, (cytosine-5) methylation (m(5)C), has been detected both in RNA and DNA suggesting universal use of m(5)C for the function of these nucleotide polymers.
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Cluster Analysis of RNA-Sequencing Data
2014RNA-seq technology has been widely adopted to study global gene expression. By grouping genes with similar expression profiles across treatments, cluster analysis enables us to organize and visualize results from RNA-seq experiments. Such analysis often provides insights into gene functions and gene networks, and hence it is a useful technique that has
Peng Liu, Yaqing Si
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Comparative Sequence Analysis of Structural RNA
1991Abstract : This report summarizes the results of a graduate student fellowship award which resulted in the awarding of a Ph.D. in the emerging research area of theoretical molecular biology. The report includes a description of the student's research work on the comparative sequence analysis of structural RNA.
Timmothy Haselman, George E. Fox
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Deep Sequencing Analysis of Nucleolar Small RNAs: Bioinformatics
2016Small RNAs (size 20-30 nt) of various types have been actively investigated in recent years, and their subcellular compartmentalization and relative concentrations are likely to be of importance to their cellular and physiological functions. Comprehensive data on this subset of the transcriptome can only be obtained by application of high-throughput ...
Baoyan, Bai, Marikki, Laiho
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Cancer epigenetics in clinical practice
Ca-A Cancer Journal for Clinicians, 2023Veronica Davalos, Manel Esteller
exaly