Novel principles of gamma-retroviral insertional transcription activation in murine leukemia virus-induced end-stage tumors

Enhancers Are Major Targets for Murine Leukemia Virus Vector Integration

(2014) S. S. De Ravin et al.   JOURNAL OF VIROLOGY

MLV integration site selection is driven by strong enhancers and active promoters

(2014) Matthew C. LaFave et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNAs and the genetics of cancer

(2013) S W Cheetham et al.   BRITISH JOURNAL OF CANCER

Insertional Mutagenesis by Retroviral Vectors: Current Concepts and Methods of Analysis

(2013) Sean Knight et al.   CURRENT GENE THERAPY

A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity

(2013) B. Zhang et al.   GENOME RESEARCH

Mechanisms of Retroviral Integration and Mutagenesis

(2013) Alessia Cavazza et al.   HUMAN GENE THERAPY

Gene expression profiling of murine T-cell lymphoblastic lymphoma identifies deregulation of S-phase initiating genes

(2013) Magdalena Julia Dabrowska et al.   LEUKEMIA RESEARCH

Deletion of the LTR Enhancer/Promoter Has No Impact on the Integration Profile of MLV Vectors in Human Hematopoietic Progenitors

(2013) Arianna Moiani et al.   PLoS One

Genomic Interaction Profiles in Breast Cancer Reveal Altered Chromatin Architecture

(2013) Michael J. Zeitz et al.   PLoS One

BET proteins promote efficient murine leukemia virus integration at transcription start sites

(2013) A. Sharma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The BET Family of Proteins Targets Moloney Murine Leukemia Virus Integration near Transcription Start Sites

(2013) Jan De Rijck et al.   Cell Reports

Sequence signatures extracted from proximal promoters can be used to predict distal enhancers

(2013) Leila Taher et al.   GENOME BIOLOGY

The mutational landscape of chromatin regulatory factors across 4,623 tumor samples

(2013) Abel Gonzalez-Perez et al.   GENOME BIOLOGY

Kruppel-like factor 7 overexpression suppresses hematopoietic stem and progenitor cell function

(2012) L. G. Schuettpelz et al.   BLOOD

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

(2012) Shanker Kalyana-Sundaram et al.   CELL

Integration of retroviral vectors

(2012) Richard Gabriel et al.   CURRENT OPINION IN IMMUNOLOGY

A genome-wide analysis of lentivector integration sites using targeted sequence capture and next generation sequencing technology

(2012) Duran Ustek et al.   INFECTION GENETICS AND EVOLUTION

Whole transcriptome characterization of aberrant splicing events induced by lentiviral vector integrations

(2012) Daniela Cesana et al.   JOURNAL OF CLINICAL INVESTIGATION

Genetic Alterations Associated With Progression and Recurrence in Meningiomas

(2012) Elisa Pèrez-Magán et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY

Three Murine Leukemia Virus Integration Regions within 100 Kilobases Upstream of c-myb Are Proximal to the 5' Regulatory Region of the Gene through DNA Looping

(2012) J. Zhang et al.   JOURNAL OF VIROLOGY

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

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

(2012) Cole Trapnell et al.   Nature Protocols

Promoter cross-talk via a shared enhancer explains paternally biased expression of Nctc1 at the Igf2/H19/Nctc1 imprinted locus

(2012) Bokkee Eun et al.   NUCLEIC ACIDS RESEARCH

Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma

(2011) Hua Dong et al.   BMC Systems Biology

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors

(2011) M. J. Koudijs et al.   GENOME RESEARCH

Gammaretroviral Integration into Nucleosomal Target DNA In Vivo

(2011) S. L. Roth et al.   JOURNAL OF VIROLOGY

Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell

(2011) G. Lefebvre et al.   JOURNAL OF VIROLOGY

Deep sequencing of virus-infected cells reveals HIV-encoded small RNAs

(2011) N. C. T. Schopman et al.   NUCLEIC ACIDS RESEARCH

Dual-specificity phosphatase DUSP6 has tumor-promoting properties in human glioblastomas

(2011) S Messina et al.   ONCOGENE

Analyzing the Number of Common Integration Sites of Viral Vectors – New Methods and Computer Programs

(2011) Ulrich Abel et al.   PLoS One

Global Mapping of H3K4me1 and H3K4me3 Reveals the Chromatin State-Based Cell Type-Specific Gene Regulation in Human Treg Cells

(2011) Yi Tian et al.   PLoS One

Functional consequences of bidirectional promoters

(2011) Wu Wei et al.   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

High-definition mapping of retroviral integration sites identifies active regulatory elements in human multipotent hematopoietic progenitors

(2010) C. Cattoglio et al.   BLOOD

Integration profile of retroviral vector in gene therapy treated patients is cell-specific according to gene expression and chromatin conformation of target cell

(2010) Luca Biasco et al.   EMBO Molecular Medicine

Antisense Transcription in Gammaretroviruses as a Mechanism of Insertional Activation of Host Genes

(2010) M. H. Rasmussen et al.   JOURNAL OF VIROLOGY

Genome-wide analysis of epigenetic signatures for kidney-specific transporters

(2010) Ryota Kikuchi et al.   KIDNEY INTERNATIONAL

Identification of HIV integration sites in infected host genomic DNA

(2010) Angela Ciuffi et al.   METHODS

Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease

(2010) Stefan Stein et al.   NATURE MEDICINE

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

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering the Code for Retroviral Integration Target Site Selection

(2010) Federico Andrea Santoni et al.   PLoS Computational Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Identification of rare cancer driver mutations by network reconstruction

(2009) A. Torkamani et al.   GENOME RESEARCH

Predictive chromatin signatures in the mammalian genome

(2009) G. C. Hon et al.   HUMAN MOLECULAR GENETICS

Loss of MicroRNA Targets in the 3' Untranslated Region as a Mechanism of Retroviral Insertional Activation of Growth Factor Independence 1

(2009) M. J. Dabrowska et al.   JOURNAL OF VIROLOGY

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

A conditional transposon-based insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma

(2009) Vincent W Keng et al.   NATURE BIOTECHNOLOGY

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites

(2009) Anthony G Uren et al.   Nature Protocols

Murine Leukemias with Retroviral Insertions at Lmo2 Are Predictive of the Leukemias Induced in SCID-X1 Patients Following Retroviral Gene Therapy

(2009) Utpal P. Davé et al.   PLoS Genetics

The t(X;7)(q22;q34) in paediatric T-cell acute lymphoblastic leukaemia results in overexpression of the insulin receptor substrate 4 gene through illegitimate recombination with the T-cell receptor beta locus

(2008) Kristina Karrman et al.   BRITISH JOURNAL OF HAEMATOLOGY

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

(2008) A. G. Robertson et al.   GENOME RESEARCH

Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene therapy of SCID-X1 patients

(2008) Steven J. Howe et al.   JOURNAL OF CLINICAL INVESTIGATION

Pvt1-encoded microRNAs in oncogenesis

(2008) Gabriele B Beck-Engeser et al.   Retrovirology

Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia

(2008) C. G. Mullighan et al.   SCIENCE