PGBD5 promotes site-specific oncogenic mutations in human tumors

Forward genetic screen of human transposase genomic rearrangements

(2016) Anton G. Henssen et al.   BMC GENOMICS

Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors

(2016) Jonathon Torchia et al.   CANCER CELL

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes

(2016) Pascal D. Johann et al.   CANCER CELL

Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways

(2016) Hye-Jung E. Chun et al.   CANCER CELL

Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma

(2015) Nemanja Rodić et al.   NATURE MEDICINE

Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes

(2015) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair

(2015) T. Ochi et al.   SCIENCE

Site- and allele-specific polycomb dysregulation in T-cell leukaemia

(2015) Jean-Marc Navarro et al.   Nature Communications

Machine-based method for multiplex in situ molecular characterization of tissues by immunofluorescence detection

(2015) Dmitry Yarilin et al.   Scientific Reports

Genomic DNA transposition induced by human PGBD5

(2015) Anton G Henssen et al.   eLife

Genome-wide approach to identify second gene targets for malignant rhabdoid tumors using high-density oligonucleotide microarrays

(2014) Junko Takita et al.   CANCER SCIENCE

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads

(2014) Valentí Moncunill et al.   NATURE BIOTECHNOLOGY

RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia

(2014) Elli Papaemmanuil et al.   NATURE GENETICS

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes

(2014) Robert Huether et al.   Nature Communications

The cancer gene WWOX behaves as an inhibitor of SMAD3 transcriptional activity via direct binding

(2013) Brent W Ferguson et al.   BMC CANCER

Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies

(2013) Eitan Halper-Stromberg et al.   BMC GENOMICS

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

piggyBac transposase tools for genome engineering

(2013) X. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Human THAP9 Gene Encodes an Active P-Element DNA Transposase

(2013) S. Majumdar et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

PGBD5: a neural-specific intron-containing piggyBac transposase domesticated over 500 million years ago and conserved from cephalochordates to humans

(2013) Thomas Pavelitz et al.   Mobile DNA

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS

(2012) Anne-Katrin Emde et al.   BIOINFORMATICS

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers

(2012) Ryan S. Lee et al.   JOURNAL OF CLINICAL INVESTIGATION

Dissecting the genomic complexity underlying medulloblastoma

(2012) David T. W. Jones et al.   NATURE

Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes

(2012) Jan J. Molenaar et al.   NATURE

Autocrine activation of the MET receptor tyrosine kinase in acute myeloid leukemia

(2012) Alex Kentsis et al.   NATURE MEDICINE

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

CREST maps somatic structural variation in cancer genomes with base-pair resolution

(2011) Jianmin Wang et al.   NATURE METHODS

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

(2011) R. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Metnase/SETMAR: a domesticated primate transposase that enhances DNA repair, replication, and decatenation

(2010) Montaser Shaheen et al.   GENETICA

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The CASPR2 cell adhesion molecule functions as a tumor suppressor gene in glioma

(2010) L B C Bralten et al.   ONCOGENE

Malignant rhabdoid tumours of the kidney (MRTKs), registered on recent SIOP protocols from 1993 to 2005: A report of the SIOP renal tumour study group

(2010) Marry M. van den Heuvel-Eibrink et al.   PEDIATRIC BLOOD & CANCER

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Simultaneous Inference in General Parametric Models

(2008) Torsten Hothorn et al.   BIOMETRICAL JOURNAL

H3K79 Methylation Profiles Define Murine and Human MLL-AF4 Leukemias

(2008) Andrei V. Krivtsov et al.   CANCER CELL

piggyBac can bypass DNA synthesis during cut and paste transposition

(2008) Rupak Mitra et al.   EMBO JOURNAL

Understanding how the V(D)J recombinase catalyzes transesterification: distinctions between DNA cleavage and transposition

(2008) Catherine P. Lu et al.   NUCLEIC ACIDS RESEARCH