Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Genetic and epigenetic variations contributed by Alu retrotransposition

(2011) Alexandre de Andrade et al.   BMC GENOMICS

From 'JUNK' to Just Unexplored Noncoding Knowledge: the case of transcribed Alus

(2011) R. Pandey et al.   Briefings in Functional Genomics

FLIP (Flice-like inhibitory protein) suppresses cytoplasmic double-stranded-RNA-induced apoptosis and NF-κB and IRF3-mediated signaling

(2011) Priya Handa et al.   Cell Communication and Signaling

Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal

(2011) Jianrong Wang et al.   CELL CYCLE

Regulation of CD95/Fas signaling at the DISC

(2011) I N Lavrik et al.   CELL DEATH AND DIFFERENTIATION

Tripartite Motif-Containing Protein 28 Is a Small Ubiquitin-Related Modifier E3 Ligase and Negative Regulator of IFN Regulatory Factor 7

(2011) Q. Liang et al.   JOURNAL OF IMMUNOLOGY

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

Competition between ADAR and RNAi pathways for an extensive class of RNA targets

(2011) Diane Wu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A Novel Human TPIP Splice-Variant (TPIP-C2) mRNA, Expressed in Human and Mouse Tissues, Strongly Inhibits Cell Growth in HeLa Cells

(2011) Rasmi Rekha Mishra et al.   PLoS One

Widespread establishment and regulatory impact of Alu exons in human genes

(2011) S. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Misfolded human tRNA isodecoder binds and neutralizes a 3' UTR-embedded Alu element

(2011) J. Rudinger-Thirion et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism

(2011) Rajesh Pandey et al.   GENOME BIOLOGY

DARNED: a DAtabase of RNa EDiting in humans

(2010) A. Kiran et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats

(2010) Ling-Ling Chen et al.   CELL CYCLE

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

Alu Sequences in Undifferentiated Human Embryonic Stem Cells Display High Levels of A-to-I RNA Editing

(2010) Sivan Osenberg et al.   PLoS One

Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates

(2010) N. Paz-Yaacov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Positive selection on apoptosis related genes

(2009) Rute R. da Fonseca et al.   FEBS LETTERS

InvAluable junk: The cellular impact and function of Alu and B2 RNAs

(2009) Ryan D. Walters et al.   IUBMB LIFE

Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA

(2009) Ling-Ling Chen et al.   MOLECULAR CELL

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Evidence for large diversity in the human transcriptome created by Alu RNA editing

(2009) Michal Barak et al.   NUCLEIC ACIDS RESEARCH

A Novel Protein Isoform of the Multicopy Human NAIP Gene Derives from Intragenic Alu SINE Promoters

(2009) Mark T. Romanish et al.   PLoS One

Widespread cleavage of A-to-I hyperediting substrates

(2009) S. Osenberg et al.   RNA

The Pivotal Roles of TIA Proteins in 5′ Splice-Site Selection of Alu Exons and Across Evolution

(2009) Nurit Gal-Mark et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Alu element-mediated gene silencing

(2008) Ling-Ling Chen et al.   EMBO JOURNAL

Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock

(2008) Peter D. Mariner et al.   MOLECULAR CELL

A-to-I RNA editing alters less-conserved residues of highly conserved coding regions: Implications for dual functions in evolution

(2008) Y. Yang et al.   RNA

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE

Human cis natural antisense transcripts initiated by transposable elements

(2008) Andrew B. Conley et al.   TRENDS IN GENETICS

Intronic Alus Influence Alternative Splicing

(2008) Galit Lev-Maor et al.   PLoS Genetics

Exon creation and establishment in human genes

(2008) André Corvelo et al.   GENOME BIOLOGY