Methods

Researchers from the Minerva Foundation Institute for Medical Research, Finland have developed the first strategy to use a competitive Extendable Blocking Probe (ExBP) for allele-specific priming with superior selectivity at the stage of reverse transcription. In order to analyze highly ...

Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. The MethylTranscriptome DataBase is the first comprehensive resource for N6-methyladenosine (m6A) in mammalian transcriptome. It includes a database that records publicaly available data sets ...

QuaCRS (Quality Control for RNA-Seq) is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses ...

Deep sequencing of small RNAs has become a routine process in recent years, but no dedicated viewer is as yet available to explore the sequence features simultaneously along with secondary structure and gene expression of microRNA (miRNA). A team led ...

As more small RNA sequencing libraries are becoming available, it clearly emerges that microRNAs (miRNAs) are highly heterogeneous both in length and sequence. In comparison to canonical miRNAs, miRNA isoforms (termed as “isomiRs”) might exhibit different biological properties, such as ...

High-throughput sequencing (HTS) methods for analyzing RNA populations (RNA-Seq) are gaining rapid application to many experimental situations. The steps in an RNA-Seq experiment require thought and planning, especially because the expense in time and materials is currently higher and the ...

RNA-seq allows for simultaneous transcript discovery and quantification, but reconstructing complete transcripts from such data remains difficult. Here, researchers from the University of Copenhagen introduce the Bayesembler, a novel probabilistic method for transcriptome assembly built on a Bayesian model of ...

Despite an enormous interest in the role of extracellular vesicles, including exosomes, in cancer and their use as biomarkers for diagnosis, prognosis, drug response and recurrence, there is no consensus on dependable isolation protocols. Now, researchers at Ghent University Hospital ...

Co-expression networks have proven effective at assigning putative functions to genes based on the functional annotation of their co-expressed partners, in candidate gene prioritization studies and in improving our understanding of regulatory networks. The growing number of genome resequencing efforts ...

A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. Researchers at the European Molecular Biology Laboratory present HTSeq, a ...