Tumour virology in the era of high-throughput genomics

The blood DNA virome in 8,000 humans

(2017) Ahmed Moustafa et al.   PLoS Pathogens

Epigenetics and Genetics of Viral Latency

(2016) Paul M. Lieberman   Cell Host & Microbe

Genomic characterization of viral integration sites in HPV-related cancers

(2016) Clara Bodelon et al.   INTERNATIONAL JOURNAL OF CANCER

A new protoparvovirus in human fecal samples and cutaneous T cell lymphomas (mycosis fungoides)

(2016) Tung G. Phan et al.   VIROLOGY

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

(2016) Jens Friis-Nielsen et al.   Viruses-Basel

Detection of DNA viruses in prostate cancer

(2016) Vitaly Smelov et al.   Scientific Reports

A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association

(2016) Michael J. Strong et al.   Acta Neuropathologica Communications

Application of targeted enrichment to next-generation sequencing of retroviruses integrated into the host human genome

(2016) Paola Miyazato et al.   Scientific Reports

The tumor virus landscape of AIDS-related lymphomas

(2015) A. Arvey et al.   BLOOD

No significant viral transcription detected in whole breast cancer transcriptomes

(2015) Danai Fimereli et al.   BMC CANCER

HeLa Nucleic Acid Contamination in The Cancer Genome Atlas Leads to the Misidentification of Human Papillomavirus 18

(2015) Paul G. Cantalupo et al.   JOURNAL OF VIROLOGY

Possible Human Papillomavirus 38 Contamination of Endometrial Cancer RNA Sequencing Samples in The Cancer Genome Atlas Database

(2015) Majid Kazemian et al.   JOURNAL OF VIROLOGY

Correction for Strong et al., Epstein-Barr Virus and Human Herpesvirus 6 Detection in a Non-Hodgkin's Diffuse Large B-Cell Lymphoma Cohort by Using RNA Sequencing

(2015) Michael J. Strong et al.   JOURNAL OF VIROLOGY

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

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

(2015) Michael Forster et al.   Scientific Reports

Large T and small T antigens of Merkel cell polyomavirus

(2015) Justin A Wendzicki et al.   Current Opinion in Virology

VERSE: a novel approach to detect virus integration in host genomes through reference genome customization

(2015) Qingguo Wang et al.   Genome Medicine

Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells

(2015) Liang Wu et al.   GigaScience

Identification of Pathogen Signatures in Prostate Cancer Using RNA-seq

(2015) Yunqin Chen et al.   PLoS One

The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemia/lymphoma

(2014) L. B. Cook et al.   BLOOD

Prevalence of Human Papillomavirus in endometrial cancer: A systematic review and meta-analysis

(2014) Tina Bech Olesen et al.   GYNECOLOGIC ONCOLOGY

Absence of cytomegalovirus in high-coverage DNA sequencing of human glioblastoma multiforme

(2014) Ka-Wei Tang et al.   INTERNATIONAL JOURNAL OF CANCER

Human papillomavirus type 197 is commonly present in skin tumors

(2014) L. Sara Arroyo Mühr et al.   INTERNATIONAL JOURNAL OF CANCER

Endogenous Retroviruses and the Development of Cancer

(2014) G. Kassiotis   JOURNAL OF IMMUNOLOGY

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Comprehensive molecular characterization of urothelial bladder carcinoma

(2014)   NATURE

Human cytomegalovirus infection in tumor cells of the nervous system is not detectable with standardized pathologico-virological diagnostics

(2014) P. Baumgarten et al.   NEURO-ONCOLOGY

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets

(2014) Guorong Xu et al.   PLoS One

Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data

(2014) Richard W. Lusk   PLoS One

Characterization of HPV and host genome interactions in primary head and neck cancers

(2014) M. Parfenov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis

(2014) S. N. Naccache et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

(2014) Michael J. Strong et al.   PLoS Pathogens

Revisiting a role for a mammary tumor retrovirus in human breast cancer

(2013) Brian Salmons et al.   INTERNATIONAL JOURNAL OF CANCER

Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response

(2013) Érika Cosset et al.   INTERNATIONAL JOURNAL OF CANCER

Epstein-Barr Virus and Human Herpesvirus 6 Detection in a Non-Hodgkin's Diffuse Large B-Cell Lymphoma Cohort by Using RNA Sequencing

(2013) Michael J. Strong et al.   JOURNAL OF VIROLOGY

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

(2013) J. D. Khoury et al.   JOURNAL OF VIROLOGY

Landscape of genomic alterations in cervical carcinomas

(2013) Akinyemi I. Ojesina et al.   NATURE

Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing

(2013) B. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The conundrum of causality in tumor virology: The cases of KSHV and MCV

(2013) Patrick S. Moore et al.   SEMINARS IN CANCER BIOLOGY

The landscape of viral expression and host gene fusion and adaptation in human cancer

(2013) Ka-Wei Tang et al.   Nature Communications

Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes

(2013) Sven-Eric Schelhorn et al.   PLoS Computational Biology

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

(2012) Yunxin Chen et al.   BIOINFORMATICS

CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes

(2012) Ivan Borozan et al.   BMC BIOINFORMATICS

Human papilloma virus genome is rare in North American non-small cell lung carcinoma patients

(2012) Naoki Yanagawa et al.   LUNG CANCER

Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators

(2012) Akihiro Fujimoto et al.   NATURE GENETICS

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

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

In-Depth Investigation of Archival and Prospectively Collected Samples Reveals No Evidence for XMRV Infection in Prostate Cancer

(2012) Deanna Lee et al.   PLoS One

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Recurrent Targeted Genes of Hepatitis B Virus in the Liver Cancer Genomes Identified by a Next-Generation Sequencing–Based Approach

(2012) Dong Ding et al.   PLoS Genetics

The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones

(2011) N. A. Gillet et al.   BLOOD

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

Disease-associated XMRV sequences are consistent with laboratory contamination

(2011) Stephane Hue et al.   Retrovirology

Recombinant Origin of the Retrovirus XMRV

(2011) T. Paprotka et al.   SCIENCE

Genomes in Conflict: Maintaining Genome Integrity During Virus Infection

(2010) Matthew D. Weitzman et al.   Annual Review of Microbiology

Etiologic role of human papillomavirus infection in bladder carcinoma

(2010) Kazuyoshi Shigehara et al.   CANCER

Prevalence of Polyomavirus BK and JC Infection and Replication in 400 Healthy Blood Donors

(2009) Adrian Egli et al.   JOURNAL OF INFECTIOUS DISEASES

Mechanism of Genomic Instability in Cells Infected with the High-Risk Human Papillomaviruses

(2009) Meelis Kadaja et al.   PLoS Pathogens

Polyoma virus infection and urothelial carcinoma of the bladder following renal transplantation

(2008) I S D Roberts et al.   BRITISH JOURNAL OF CANCER

A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases

(2008) Gustavo Palacios et al.   NEW ENGLAND JOURNAL OF MEDICINE

Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma

(2008) H. Feng et al.   SCIENCE