Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals

A Long ncRNA Links Copy Number Variation to a Polycomb/Trithorax Epigenetic Switch in FSHD Muscular Dystrophy

(2012) Daphne S. Cabianca et al.   CELL

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

(2012) T. Derrien et al.   GENOME RESEARCH

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Single-stranded Noncoding RNAs Mediate Local Epigenetic Alterations at Gene Promoters in Rat Cell Lines

(2011) Junko Tomikawa et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Regulation of Emx2 Expression by Antisense Transcripts in Murine Cortico-Cerebral Precursors

(2010) Giulia Spigoni et al.   PLoS One

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery

(2009) Leping Li   JOURNAL OF COMPUTATIONAL BIOLOGY

On the road to reading the RNA-interference code

(2009) Haruhiko Siomi et al.   NATURE

Small RNAs in transcriptional gene silencing and genome defence

(2009) Danesh Moazed   NATURE

PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element

(2008) A. K. Ebralidze et al.   GENES & DEVELOPMENT

A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition

(2008) M. Beltran et al.   GENES & DEVELOPMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY