Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma

IRF5-mediated signaling and implications for SLE

(2014) Elisa Lazzari et al.   CLINICAL IMMUNOLOGY

The mutational landscape of Hodgkin lymphoma cell lines determined by whole-exome sequencing

(2014) Y Liu et al.   LEUKEMIA

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

Mapping of transcription factor motifs in active chromatin identifies IRF5 as key regulator in classical Hodgkin lymphoma

(2014) Stephan Kreher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hypomethylation of long interspersed nuclear element-1 (LINE-1) leads to activation of proto-oncogenes in human colorectal cancer metastasis

(2013) Keun Hur et al.   GUT

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

(2013) Mingchao Xie et al.   NATURE GENETICS

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

(2013) Aurélie Kapusta et al.   PLoS Genetics

VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer

(2013) Georges St Laurent et al.   GENOME BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

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

Gene expression profiling of microdissected Hodgkin Reed-Sternberg cells correlates with treatment outcome in classical Hodgkin lymphoma

(2012) C. Steidl et al.   BLOOD

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

C-GATE - catalogue of genes affected by transposable elements

(2012) Rita Rebollo et al.   Mobile DNA

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

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

(2011) Ryan D. Morin et al.   NATURE

Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms

(2011) Rita Rebollo et al.   PLoS Genetics

DNA hypomethylation in cancer: Epigenetic scars of a neoplastic journey

(2010) Charles De Smet et al.   Epigenetics

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma

(2010) Björn Lamprecht et al.   NATURE MEDICINE

Demethylation of a LINE-1 antisense promoter in the cMet locus impairs Met signalling through induction of illegitimate transcription

(2010) B Weber et al.   ONCOGENE

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Hypomethylation of a LINE-1 Promoter Activates an Alternate Transcript of the MET Oncogene in Bladders with Cancer

(2010) Erika M. Wolff et al.   PLoS Genetics

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

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

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