NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome

Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism

(2015) Zheng Hu et al.   NATURE GENETICS

Development and Validation of a New HPV Genotyping Assay Based on Next-Generation Sequencing

(2014) Xin Yi et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

Variant detection sensitivity and biases in whole genome and exome sequencing

(2014) Alison M Meynert et al.   BMC BIOINFORMATICS

Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing

(2014) Adam Ameur et al.   Scientific Reports

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

(2013) Jing-Woei Li et al.   BIOINFORMATICS

HIVID: An efficient method to detect HBV integration using low coverage sequencing

(2013) Weiyang Li et al.   GENOMICS

Prevalence of high-risk human papillomavirus type 16 and 18 in oral and cervical cancers in population from Gujarat, West India

(2013) Kinjal R. Patel et al.   JOURNAL OF ORAL PATHOLOGY & MEDICINE

Multiplex Identification of Human Papillomavirus 16 DNA Integration Sites in Cervical Carcinomas

(2013) Bo Xu et al.   PLoS One

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

Metagenomic sequencing of “HPV-negative” condylomas detects novel putative HPV types

(2013) Hanna Johansson et al.   VIROLOGY

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

READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation

(2012) Raeece Naeem et al.   BIOINFORMATICS

The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis

(2012) Koenraad Van Doorslaer et al.   NUCLEIC ACIDS RESEARCH

Non-Random Integration of the HPV Genome in Cervical Cancer

(2012) Martina Schmitz et al.   PLoS One

HPV Genotyping and Site of Viral Integration in Cervical Cancers in Indian Women

(2012) Poulami Das et al.   PLoS One

A review of methods for detect human Papillomavirus infection

(2012) André L P Abreu et al.   Virology Journal

Human Papillomavirus Infection with Multiple Types: Pattern of Coinfection and Risk of Cervical Disease

(2011) Anil K. Chaturvedi et al.   JOURNAL OF INFECTIOUS DISEASES

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

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

The role of human papillomavirus in the pathogenesis of head & neck squamous cell carcinoma: an overview

(2011) Giuseppe Pannone et al.   Infectious Agents and Cancer

Concurrent Infection with Multiple Human Papillomavirus Types: Pooled Analysis of the IARC HPV Prevalence Surveys

(2010) S. Vaccarella et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Identification of human papillomavirus type 16 integration sites in high-grade precancerous cervical lesions

(2009) Mihaela Matovina et al.   GYNECOLOGIC ONCOLOGY

Role of human papillomavirus and its detection in potentially malignant and malignant head and neck lesions: updated review

(2009) Ajay Chaudhary et al.   Head and Neck Optical Diagnostics Society

Classification of weakly carcinogenic human papillomavirus types: addressing the limits of epidemiology at the borderline

(2009) Mark Schiffman et al.   Infectious Agents and Cancer