SurVirus: a repeat-aware virus integration caller

A virome-wide clonal integration analysis platform for discovering cancer viral etiology

(2019) Xun Chen et al.   GENOME RESEARCH

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer

(2018) Nam-phuong D Nguyen et al.   NUCLEIC ACIDS RESEARCH

Characterization of HPV integration, viral gene expression and E6E7 alternative transcripts by RNA-Seq: A descriptive study in invasive cervical cancer

(2018) Ayslan C. Brant et al.   GENOMICS

Identification of human papillomavirus (HPV) 16 DNA integration and the ensuing patterns of methylation in HPV-associated head and neck squamous cell carcinoma cell lines

(2017) Takashi Hatano et al.   INTERNATIONAL JOURNAL OF CANCER

Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma

(2016) Ling-Hao Zhao et al.   Nature Communications

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

Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability

(2015) Daniel WH Ho et al.   Oncotarget

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

(2015) Michael Forster et al.   Scientific Reports

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

(2015) Qingguo Wang et al.   Genome Medicine

SummonChimera infers integrated viral genomes with nucleotide precision from NGS data

(2014) Joshua P Katz et al.   BMC BIOINFORMATICS

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

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

pIRS: Profile-based Illumina pair-end reads simulator

(2012) Xuesong Hu 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

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

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

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Identifying viral integration sites using SeqMap 2.0

(2011) Troy B. Hawkins et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS