Transcriptional landscape of repetitive elements in normal and cancer human cells

Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

(2013) Ruchi Shukla et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

Small MAFgenes variants and chronic myeloid leukemia

(2013) Angelica Martínez-Hernández et al.   EUROPEAN JOURNAL OF HAEMATOLOGY

Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles

(2013) Prabhat K. Mandal et al.   HUMAN MOLECULAR GENETICS

Differential L1 regulation in pluripotent stem cells of humans and apes

(2013) Maria C. N. Marchetto et al.   NATURE

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

(2013) Mingchao Xie et al.   NATURE GENETICS

(Some) Cellular Mechanisms Influencing the Transcription of Human Endogenous Retrovirus, HERV-Fc1

(2013) Magdalena Janina Laska et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings

(2012) Shancheng Ren et al.   CELL RESEARCH

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

(2012) D. Canella et al.   GENOME RESEARCH

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

Extensive somatic L1 retrotransposition in colorectal tumors

(2012) S. Solyom et al.   GENOME RESEARCH

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

(2012) T. Derrien et al.   GENOME RESEARCH

Expression of HERV-Fc1, a Human Endogenous Retrovirus, Is Increased in Patients with Active Multiple Sclerosis

(2012) M. J. Laska et al.   JOURNAL OF VIROLOGY

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

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Transposable Elements in TDP-43-Mediated Neurodegenerative Disorders

(2012) Wanhe Li et al.   PLoS One

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

Transcription by RNA polymerase III: more complex than we thought

(2011) Robert J. White   NATURE REVIEWS GENETICS

ENCODE whole-genome data in the UCSC Genome Browser: update 2012

(2011) K. R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags

(2010) Jianrong Wang et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells

(2010) D. Canella et al.   GENOME RESEARCH

L1 retrotransposition in neurons is modulated by MeCP2

(2010) Alysson R. Muotri et al.   NATURE

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

(2010) Andrew J Oler et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells

(2010) Zarmik Moqtaderi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Close association of RNA polymerase II and many transcription factors with Pol III genes

(2010) Debasish Raha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-range function of an intergenic retrotransposon

(2010) W. Pi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating enrichment of repetitive elements from high-throughput sequence data

(2010) Daniel S Day et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Comparative analysis of Alu repeats in primate genomes

(2009) G. E. Liu et al.   GENOME RESEARCH

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Trex1 Prevents Cell-Intrinsic Initiation of Autoimmunity

(2008) Daniel B. Stetson et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE

(2008) Geoffrey J. Faulkner et al.   GENOMICS

Modeling ChIP Sequencing In Silico with Applications

(2008) Zhengdong D. Zhang et al.   PLoS Computational Biology