Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination

lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs

(2014) Charny Park et al.   BIOINFORMATICS

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

(2014) Y. Zhang et al.   JOURNAL OF NEUROSCIENCE

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications

(2014) Aurélie Kapusta et al.   TRENDS IN GENETICS

Quantitative profiling of peptides from RNAs classified as noncoding

(2014) Sudhakaran Prabakaran et al.   Nature Communications

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

(2014) Alessandra M. Sullivan et al.   Cell Reports

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

(2013) Per Johnsson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Integration of Genome-wide Approaches Identifies lncRNAs of Adult Neural Stem Cells and Their Progeny In Vivo

(2013) Alexander D. Ramos et al.   Cell Stem Cell

Netrin 1 contributes to vascular remodeling in the subventricular zone and promotes progenitor emigration after demyelination

(2013) M. Cayre et al.   DEVELOPMENT

Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation

(2013) Olga A. Vakhrusheva et al.   Genome Biology and Evolution

Ascl1/Mash1 Promotes Brain Oligodendrogenesis during Myelination and Remyelination

(2013) H. Nakatani et al.   JOURNAL OF NEUROSCIENCE

Generation of oligodendroglial cells by direct lineage conversion

(2013) Nan Yang et al.   NATURE BIOTECHNOLOGY

Exploring long-range genome interactions using the WashU Epigenome Browser

(2013) Xin Zhou et al.   NATURE METHODS

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq Characterization of Spinal Cord Injury Transcriptome in Acute/Subacute Phases: A Resource for Understanding the Pathology at the Systems Level

(2013) Kenian Chen et al.   PLoS One

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Long Noncoding RNA MALAT1 Controls Cell Cycle Progression by Regulating the Expression of Oncogenic Transcription Factor B-MYB

(2013) Vidisha Tripathi et al.   PLoS Genetics

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

Mitochondrial dysfunction in Parkinson's disease: molecular mechanisms and pathophysiological consequences

(2012) Nicole Exner et al.   EMBO JOURNAL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Opposing Roles for Hoxa2 and Hoxb2 in Hindbrain Oligodendrocyte Patterning

(2012) A. Miguez et al.   JOURNAL OF NEUROSCIENCE

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

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

(2012) Cole Trapnell et al.   Nature Protocols

Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus

(2012) Michael Cowley et al.   NUCLEIC ACIDS RESEARCH

Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks

(2012) Xingli Guo et al.   NUCLEIC ACIDS RESEARCH

Involvement of long noncoding RNAs in diseases affecting the central nervous system

(2012) Chiara Pastori et al.   RNA Biology

Loss of the abundant nuclear non-coding RNAMALAT1is compatible with life and development

(2012) Moritz Eißmann et al.   RNA Biology

The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult

(2012) Bin Zhang et al.   Cell Reports

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

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

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

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation

(2010) Tim R Mercer et al.   BMC NEUROSCIENCE

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

Axonal Damage in Leukodystrophies

(2010) Soe Mar et al.   PEDIATRIC NEUROLOGY

Regulation of Oligodendrocyte Differentiation and Myelination

(2010) B. Emery   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Mitochondria in Huntington's disease

(2009) Maria Damiano et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Evolutionary Forces Act on Promoter Length: Identification of Enriched Cis-Regulatory Elements

(2009) E. Kristiansson et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2009) Mitchell Guttman et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of alternative polyadenylation by genomic imprinting

(2008) A. J. Wood et al.   GENES & DEVELOPMENT

Functional organization of the transcriptome in human brain

(2008) Michael C Oldham et al.   NATURE NEUROSCIENCE

Remyelination in the CNS: from biology to therapy

(2008) Robin J. M. Franklin et al.   NATURE REVIEWS NEUROSCIENCE

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY