Characterization of Human Pseudogene-Derived Non-Coding RNAs for Functional Potential

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Beyond transposons: the epigenetic and somatic functions of the Piwi-piRNA mechanism

(2013) Jamy C Peng et al.   CURRENT OPINION IN CELL BIOLOGY

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells

(2013) Per Johnsson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma

(2013) Wen-Ling Chan et al.   NUCLEIC ACIDS RESEARCH

Axonal trafficking of an antisense RNA transcribed from a pseudogene is regulated by classical conditioning

(2013) Sergei A. Korneev et al.   Scientific Reports

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

(2012) Shanker Kalyana-Sundaram et al.   CELL

Small RNA in the nucleus: the RNA-chromatin ping-pong

(2012) Ivan Olovnikov et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Naturally occurring endo-siRNA silences LINE-1 retrotransposons in human cells through DNA methylation

(2012) Long Chen et al.   Epigenetics

Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome

(2012) A. T. Wierzbicki et al.   GENES & DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

(2012) Xuehua Zhong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pseudogenes: Newly Discovered Players in Human Cancer

(2012) L. Poliseno   Science Signaling

A Noncoding RNA Antisense to Moesin at 5p14.1 in Autism

(2012) T. Kerin et al.   Science Translational Medicine

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs

(2012) Ana C Marques et al.   GENOME BIOLOGY

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

Functional evidence of post-transcriptional regulation by pseudogenes

(2011) Enrique M. Muro et al.   BIOCHIMIE

RNA-dependent RNA polymerases in RNA silencing

(2011) Yoshiko Maida et al.   BIOLOGICAL CHEMISTRY

ceRNAs: miRNA Target Mimic Mimics

(2011) Ignacio Rubio-Somoza et al.   CELL

An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

(2011) Pavel Sumazin et al.   CELL

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

A transcribed pseudogene of MYLK promotes cell proliferation

(2011) Yoo Jeong Han et al.   FASEB JOURNAL

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

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

Transposase mediated construction of RNA-seq libraries

(2011) J. Gertz et al.   GENOME RESEARCH

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

Characterization of the Contradictory Chromatin Signatures at the 3′ Exons of Zinc Finger Genes

(2011) Kimberly R. Blahnik et al.   PLoS One

Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei

(2011) Y.-Z. Wen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pseudogenes: Pseudo-functional or key regulators in health and disease?

(2011) R. C. Pink et al.   RNA

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

(2011)   PLOS BIOLOGY

Pseudogenes as an alternative source of natural antisense transcripts

(2010) Enrique M Muro et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno 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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Assessing the genomic evidence for conserved transcribed pseudogenes under selection

(2009) Amit N Khachane et al.   BMC GENOMICS

Redefining MicroRNA Targets

(2009) Hervé Seitz   CURRENT BIOLOGY

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA

(2009) Yoshiko Maida et al.   NATURE

Small RNAs in transcriptional gene silencing and genome defence

(2009) Danesh Moazed   NATURE

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

Biogenesis of small RNAs in animals

(2009) V. Narry Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Small RNAs Originated from Pseudogenes: cis- or trans-Acting?

(2009) Xingyi Guo et al.   PLoS Computational Biology

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Genomics: Protein fossils live on as RNA

(2008) Rajkumar Sasidharan et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

Pseudofam: the pseudogene families database

(2008) Hugo Y. K. Lam et al.   NUCLEIC ACIDS RESEARCH