RNA-Seq Blog
RNA-Seq Blog
RNA-Seq Blog

RNA-Seq Blog

Transcriptome Sequencing News & Information

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Co-LncRNA – investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data

DynaMIT – the dynamic motif integration toolkit - Researchers from the University of Trento have developed the Dynamic Motif Integration Toolkit (DynaMIT), a flexible platform designed to implement this vision: it provides the means to execute multiple motif search tools, integrate their output and display the obtained results in many different ways. It is customizable and extendible in all its aspects, allowing for a truly personalized and fine-tuned usage experience...

Introduction to RNA-Seq Analysis | RNA-Seq Blog

CADBURE – A generic tool to evaluate the performance of spliced aligners on RNA-Seq data - The fundamental task in RNA-Seq-based transcriptome analysis is alignment of millions of short reads to the reference genome or transcriptome. Choosing the right tool for the dataset in hand from many existent RNA-Seq alignment packages remains a critical challenge for downstream analysis. To facilitate this choice, researchers from Miami University designed a novel tool for comparing alignment…

Oscope – transcriptional dynamics of oscillating genes in single-cell RNA-Seq data - Oscillatory gene expression is fundamental to development, but technologies for monitoring expression oscillations are limited. Researchers at the University of Wisconsin-Madison have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population...

Defining cell lineages by single-cell RNA-Seq - Researchers at the Francis Crick Institute provide fundamental insights into early human development by single-cell RNA-sequencing of human and mouse preimplantation embryos. They elucidate conserved transcriptional programs along with those that are human-specific and validate their RNA-sequencing findings at the protein level. They identified several genes exclusively expressed in the human pluripotent epiblast including the transcription…

A new method for identifying rare cell types by single-cell mRNA sequencing - Scientists of Utrecht University and the Hubrecht Institute (Utrecht, the Netherlands) developed a new method for identifying rare cell types by single-cell mRNA sequencing. The newly developed algorithm, called RaceID, is very useful for identifying rare cell types in normal and diseased tissue. The research is published, ahead of print, on the website of Nature the 19th of August...

Proteomics Informed by Transcriptomics - With the recent advent of RNA-seq technology the proteomics community has begun to generate sample-specific protein databases for peptide and protein identification, an approach we call proteomics informed by transcriptomics (PIT). This approach has gained a lot of interest, particularly among researchers who work with non-model organisms or with particularly dynamic proteomes such as those observed in developmental biology and host-pathogen studies..

ROTS – reproducible RNA-Seq biomarker detector - Recent comprehensive assessments of RNA-seq technology support its utility in quantifying gene expression in various samples. The next step of rigorously quantifying differences between sample groups, however, still lacks well-defined best practices. Although a number of advanced statistical methods have been developed, several studies demonstrate that their performance depends strongly on the data under analysis, which compromises…