Monthly Archives: July 2014

JAGuaR: Junction Alignments to Genome for RNA-Seq Reads

rna-seq

JAGuaR is an alignment protocol for RNA-seq reads that uses an extended reference to increase alignment sensitivity. It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing for the possibility of ...

Read More »

A New Transcriptomes Dataset for C elegans

rna-seq

The nematode Caenorhabditis elegans is an important model for studies of germ cell biology, including the meiotic cell cycle, gamete specification as sperm or oocyte and gamete development. Fundamental to those studies is a genome-level knowledge of the germline transcriptome. ...

Read More »

Postdoc Positions Available – Johns Hopkins University

rna-seq

from NatureJobs Employer: Johns Hopkins University Location: Posted: June 28, 2014 Expires: August 22, 2014 The laboratory of Human Environmental Epigenomes of Dr. Zhibin Wang at Johns Hopkins University is looking for one or two postdoctoral fellow(s) to join a ...

Read More »

A Note To Our Readers

comments

Due to uncontrollable spam and attempts at hacking the site, we have been forced to close the comments on all posts.  Have no fear!  If you would like to make a comment on a particular post, please just send an ...

Read More »

An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

rna-seq

The preparation and high-throughput sequencing of cDNA libraries from samples of small RNA is a powerful tool to quantify known small RNAs (such as microRNAs) and to discover novel RNA species. Interest in identifying the small RNA repertoire present in ...

Read More »

Intracellular RNA-Seq

rna-seq

from Genetic Engineering News by Anton Simeonov, Ph.D. This literature review highlights a study led by George Church describing FISSEQ, or fluorescent in situ RNA sequencing. Methods such as fluorescence in situ hybridization (FISH) allow gene expression to be observed ...

Read More »

iRegulon: From a Gene List to a Gene Regulatory Network

rna-seq

Identifying master regulators of biological processes and mapping their downstream gene networks are key challenges in systems biology. Researchers at the KU Leuven Center for Human Genetics developed a computational method, called iRegulon, to reverse-engineer the transcriptional regulatory network underlying ...

Read More »

Single-cell RNA-seq: advances and future challenges

rna-seq

Phenotypically identical cells can dramatically vary with respect to behavior during their lifespan and this variation is reflected in their molecular composition such as the transcriptomic landscape. Single-cell transcriptomics using next-generation transcript sequencing (RNA-seq) is now emerging as a powerful ...

Read More »