Current methods for determining RNA structure with short-read sequencing cannot capture most differences between distinct transcript isoforms. Researchers at A*STAR, Singapore present RNA structure analysis using nanopore sequencing...
Read More »ScISOr-Seq – single-cell isoform RNA sequencing
Full-length isoform sequencing has advanced our knowledge of isoform biology. However, apart from applying full-length isoform sequencing to very few single cells, isoform sequencing has been limited...
Read More »Improved transcript discovery from partially observed short reads caused by missing information
The automated transcript discovery and quantification of high-throughput RNA sequencing (RNA-seq) data are important tasks of next-generation sequencing (NGS) research. However, these tasks are challenging due to the uncertainties that arise in the inference of complete splicing isoform variants from ...
Read More »SuperTranscripts – a substitute for a reference genome
Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here researchers from the Royal Children’s Hospital, Melbourne present superTranscripts, a substitute for ...
Read More »HapIso – Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads
Sequencing of RNA provides the possibility to study an individual’s transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental ...
Read More »Gene Expression’s Big Rethink
Genetic Engineering News by Richard Stein – Two technologies used to interrogate gene expression, RNA-Seq and microarray analysis, often return strongly correlated results. These technologies, however, have not been evaluated for their concordance at the isoform level. To understand the ...
Read More »Isolator – accurate and stable analysis of isoform-level expression in RNA-Seq experiments
While RNA-Seq has enabled great progress towards the goal of wide-scale isoform-level mRNA quantification, short reads have limitations when resolving complex or similar sets of isoforms. As a result, estimates of isoform abundance carry far more uncertainty than those made ...
Read More »Statistical modeling of isoform splicing dynamics from RNA-seq time series data
Isoform quantification is an important goal of RNA-seq experiments, yet it remains problematic for genes with low expression or several isoforms. These difficulties may in principle be ameliorated by exploiting correlated experimental designs, such as time series or dosage response ...
Read More »RNA-Seq methods for transcriptome analysis
Deep sequencing has been revolutionizing biology and medicine in recent years, providing single base-level precision for our understanding of nucleic acid sequences in high throughput fashion. Sequencing of RNA, or RNA-Seq, is now a common method to analyze gene expression ...
Read More »Expression data from RNA-sequencing can differentiate breast cancer histological grade
The histologic grade (HG) of breast cancer is an established prognostic factor. The grade is usually reported on a scale ranging from 1 to 3, where grade 3 tumours are the most aggressive. However, grade 2 is associated with an ...
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