Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans

Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6.

(2020) Michael Heskett et al.   RNA

A CRISPR/Cas13-based approach demonstrates biological relevance of vlinc class of long non-coding RNAs in anticancer drug response

(2020) Dongyang Xu et al.   Scientific Reports

Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

(2020) Alexey A Gavrilov et al.   NUCLEIC ACIDS RESEARCH

Functional annotation of human long noncoding RNAs via molecular phenotyping

(2020) Jordan A. Ramilowski et al.   GENOME RESEARCH

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls

(2018) Huifen Cao et al.   TRENDS IN GENETICS

Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes

(2018) Maxime Caron et al.   PLoS One

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

(2017) Margarita Schlackow et al.   MOLECULAR CELL

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

GRID-seq reveals the global RNA–chromatin interactome

(2017) Xiao Li et al.   NATURE BIOTECHNOLOGY

The RNA Response to DNA Damage

(2016) Luciana E. Giono et al.   JOURNAL OF MOLECULAR BIOLOGY

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

(2016) Georges St. Laurent et al.   NUCLEIC ACIDS RESEARCH

The Landscape of long noncoding RNA classification

(2015) Georges St. Laurent et al.   TRENDS IN GENETICS

A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus

(2015) Sandra Lazorthes et al.   Nature Communications

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

(2014) Jason A. West et al.   MOLECULAR CELL

A promoter-level mammalian expression atlas

(2014)   NATURE

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies

(2014) Jingnan Sun et al.   NUCLEIC ACIDS RESEARCH

Long non-coding RNAs: modulators of nuclear structure and function

(2013) Jan H Bergmann et al.   CURRENT OPINION IN CELL BIOLOGY

The dark matter rises: the expanding world of regulatory RNAs

(2013) Michael B. Clark et al.   Essays in Biochemistry

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA Damage Response: Three Levels of DNA Repair Regulation

(2013) B. M. Sirbu et al.   Cold Spring Harbor Perspectives in Biology

VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer

(2013) Georges St Laurent et al.   GENOME BIOLOGY

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

(2012) T. Derrien et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape

(2012) Georges St. Laurent et al.   Frontiers in Genetics

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

(2011) Philipp Kapranov et al.   BMC BIOLOGY

Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice

(2011) Shinichi Nakagawa et al.   JOURNAL OF CELL BIOLOGY

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

A Comparison of Single Molecule and Amplification Based Sequencing of Cancer Transcriptomes

(2011) Lee T. Sam et al.   PLoS One

Protocol Dependence of Sequencing-Based Gene Expression Measurements

(2011) Tal Raz et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families

(2010) Eldar Giladi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

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

(2009) Mitchell Guttman et al.   NATURE

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS

Single-Molecule DNA Sequencing of a Viral Genome

(2008) T. D. Harris et al.   SCIENCE