High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

Improved definition of the mouse transcriptome via targeted RNA sequencing

(2016) Giovanni Bussotti et al.   GENOME RESEARCH

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

(2016) Marta Melé et al.   GENOME RESEARCH

Melanoma addiction to the long non-coding RNA SAMMSON

(2016) Eleonora Leucci et al.   NATURE

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)

(2016) Julien Lagarde et al.   Nature Communications

Identification of androgen-responsive lncRNAs as diagnostic and prognostic markers for prostate cancer

(2016) Xuechao Wan et al.   Oncotarget

Assessment of the latest NGS enrichment capture methods in clinical context

(2016) Gema García-García et al.   Scientific Reports

CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis

(2015) Samir Ounzain et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

(2015) Michael B Clark et al.   NATURE METHODS

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization

(2014) Dan E Arking et al.   NATURE GENETICS

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

(2014) Tim R Mercer et al.   Nature Protocols

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

(2014) Tanvir Alam et al.   PLoS One

Transcriptional diversity during lineage commitment of human blood progenitors

(2014) L. Chen et al.   SCIENCE

Magnon transistor for all-magnon data processing

(2014) Andrii V. Chumak et al.   Nature Communications

HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts

(2013) J Ferdin et al.   CELL DEATH AND DIFFERENTIATION

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

(2013) Martin Sauvageau et al.   eLife

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

(2013) Ana C Marques et al.   GENOME BIOLOGY

Characterization of in vitro transcription amplification linearity and variability in the low copy number regime using External RNA Control Consortium (ERCC) spike-ins

(2012) Jason G. Kralj et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks

(2012) Slavica Dimitrieva et al.   NUCLEIC ACIDS RESEARCH

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Colon cancer associated transcript-1: A novel RNA expressed in malignant and pre-malignant human tissues

(2011) Aviram Nissan et al.   INTERNATIONAL JOURNAL OF CANCER

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

BlastR—fast and accurate database searches for non-coding RNAs

(2011) Giovanni Bussotti et al.   NUCLEIC ACIDS RESEARCH

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Genome-wide computational identification and manual annotation of human long noncoding RNA genes

(2010) H. Jia et al.   RNA

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE