Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

Integrase residues that determine nucleotide preferences at sites of HIV-1 integration: implications for the mechanism of target DNA binding

(2014) Erik Serrao et al.   NUCLEIC ACIDS RESEARCH

Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads

(2014) Laurent Gautier et al.   PLoS One

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

(2014) Wan-Ping Lee et al.   PLoS One

Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection

(2014) T. A. Wagner et al.   SCIENCE

Specific HIV integration sites are linked to clonal expansion and persistence of infected cells

(2014) F. Maldarelli et al.   SCIENCE

Vaccination with a piggyBac plasmid with transgene integration potential leads to sustained antigen expression and CD8+ T cell responses

(2014) Pietro Bertino et al.   VACCINE

ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution

(2013) Jing-Woei Li et al.   BIOINFORMATICS

Incidence of potentially human papillomavirus-related neoplasms in the United States, 1978 to 2007

(2013) George Kurdgelashvili et al.   CANCER

Fowlpox-based survivin vaccination for malignant mesothelioma therapy

(2013) Pietro Bertino et al.   INTERNATIONAL JOURNAL OF CANCER

VirusFinder: Software for Efficient and Accurate Detection of Viruses and Their Integration Sites in Host Genomes through Next Generation Sequencing Data

(2013) Qingguo Wang et al.   PLoS One

Human Papillomavirus-related Carcinomas of the Sinonasal Tract

(2012) Justin A. Bishop et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

Rapid identification of non-human sequences in high-throughput sequencing datasets

(2012) Aparna Bhaduri et al.   BIOINFORMATICS

VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

(2012) Yunxin Chen et al.   BIOINFORMATICS

HTLV-1-infected T cells contain a single integrated provirus in natural infection

(2012) L. B. Cook et al.   BLOOD

The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients

(2012) Z. Jiang et al.   GENOME RESEARCH

Retroviral Integrase Proteins and HIV-1 DNA Integration

(2012) Lavanya Krishnan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Radiation exposure from CT scans in childhood and subsequent risk of leukaemia and brain tumours: a retrospective cohort study

(2012) Mark S Pearce et al.   LANCET

Genomic landscape of liver cancer

(2012) Zemin Zhang   NATURE GENETICS

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

(2012) Wing-Kin Sung et al.   NATURE GENETICS

From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software

(2012) Michael Forster et al.   NUCLEIC ACIDS RESEARCH

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Current status of HTLV-1 infection

(2011) Toshiki Watanabe   INTERNATIONAL JOURNAL OF HEMATOLOGY

Biology, Risk Stratification, and Therapy of Pediatric Acute Leukemias: An Update

(2011) Ching-Hon Pui et al.   JOURNAL OF CLINICAL ONCOLOGY

Childhood leukemia – Risk factors and the need for an interdisciplinary research agenda

(2011) Gunde Ziegelberger et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Aetiology of childhood leukaemia

(2010) Tim Eden   CANCER TREATMENT REVIEWS

Herpesviruses and Chromosomal Integration

(2010) G. Morissette et al.   JOURNAL OF VIROLOGY

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

The latent human herpesvirus-6A genome specifically integrates in telomeres of human chromosomes in vivo and in vitro

(2010) J. H. Arbuckle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Hepatitis B virus–cell interactions and pathogenesis

(2008) David H. Nguyen et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Acute lymphoblastic leukaemia

(2008) Ching-Hon Pui et al.   LANCET