The Landscape of long noncoding RNA classification

GS Laurent, C Wahlestedt, P Kapranov - Trends in genetics, 2015 - cell.com
Advances in the depth and quality of transcriptome sequencing have revealed many new
classes of long noncoding RNAs (lncRNAs). lncRNA classification has mushroomed to …

[HTML][HTML] lincRNAs: genomics, evolution, and mechanisms

I Ulitsky, DP Bartel - Cell, 2013 - cell.com
Long intervening noncoding RNAs (lincRNAs) are transcribed from thousands of loci in
mammalian genomes and might play widespread roles in gene regulation and other cellular …

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

NA O'Leary, MW Wright, JR Brister, S Ciufo… - Nucleic acids …, 2016 - academic.oup.com
The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains
and curates a publicly available database of annotated genomic, transcript, and protein …

An atlas of active enhancers across human cell types and tissues

R Andersson, C Gebhard, I Miguel-Escalada, I Hoof… - Nature, 2014 - nature.com
Enhancers control the correct temporal and cell-type-specific activation of gene expression
in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial …

Analysis of RNA-Seq data using TopHat and Cufflinks

S Ghosh, CKK Chan - Plant Bioinformatics: Methods and Protocols, 2016 - Springer
The recent advances in high throughput RNA sequencing (RNA-Seq) have generated huge
amounts of data in a very short span of time for a single sample. These data have required …

[HTML][HTML] Choosing the right tool for the job: RNAi, TALEN, or CRISPR

M Boettcher, MT McManus - Molecular cell, 2015 - cell.com
The most widely used approach for defining gene function is to reduce or completely disrupt
its normal expression. For over a decade, RNAi has ruled the lab, offering a magic bullet to …

Landscape of transcription in human cells

S Djebali, CA Davis, A Merkel, A Dobin, T Lassmann… - Nature, 2012 - nature.com
Eukaryotic cells make many types of primary and processed RNAs that are found either in
specific subcellular compartments or throughout the cells. A complete catalogue of these …

Chemical ecology of endophytic fungi: origins of secondary metabolites

S Kusari, C Hertweck, M Spiteller - Chemistry & biology, 2012 - cell.com
Endophytes constitute a remarkably multifarious group of microorganisms ubiquitous in
plants and maintain an imperceptible association with their hosts for at least a part of their …

Dual RNA-seq of pathogen and host

AJ Westermann, SA Gorski, J Vogel - Nature Reviews Microbiology, 2012 - nature.com
A comprehensive understanding of host–pathogen interactions requires a knowledge of the
associated gene expression changes in both the pathogen and the host. Traditional, probe …

RNA-Seq: a revolutionary tool for transcriptomics

Z Wang, M Gerstein, M Snyder - Nature reviews genetics, 2009 - nature.com
RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-
sequencing technologies. Studies using this method have already altered our view of the …