A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq

Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data

(2016) Shailesh Kumar et al.   Scientific Reports

Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution

(2015) Adam D. Ewing et al.   GENOME RESEARCH

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

Mobile DNA elements in the generation of diversity and complexity in the brain

(2014) Jennifer A. Erwin et al.   NATURE REVIEWS NEUROSCIENCE

Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma

(2014) F. E. Lock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Laminar and Temporal Expression Dynamics of Coding and Noncoding RNAs in the Mouse Neocortex

(2014) Sofia Fertuzinhos et al.   Cell Reports

Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

(2014) Jian Feng et al.   GENOME BIOLOGY

Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements

(2013) Marco De Cecco et al.   AGING CELL

Trim24-repressed VL30 retrotransposons regulate gene expression by producing noncoding RNA

(2013) Benjamin Herquel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Adaptive radiation-induced epigenetic alterations mitigated by antioxidants

(2012) Autumn J. Bernal et al.   FASEB JOURNAL

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

(2012) P. Batut et al.   GENOME RESEARCH

A greatly extended PPARGC1A genomic locus encodes several new brain-specific isoforms and influences Huntington disease age of onset†

(2012) Selma M. Soyal et al.   HUMAN MOLECULAR GENETICS

Nutrition and epigenetics: an interplay of dietary methyl donors, one-carbon metabolism and DNA methylation

(2012) Olivia S. Anderson et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

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

(2012) Cole Trapnell et al.   Nature Protocols

A “mille-feuille” of silencing: Epigenetic control of transposable elements

(2011) Mélanie Rigal et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

(2011) Mohammad M. Karimi et al.   Cell Stem Cell

Identification of a Negative Regulatory Region for the Exchange Activity and Characterization of T332I Mutant of Rho Guanine Nucleotide Exchange Factor 10 (ARHGEF10)

(2011) Taro Chaya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens

(2011) I. Maze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS