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

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

(2012) Yunxin Chen et al.   BIOINFORMATICS

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

(2012) Z. Jiang et al.   GENOME RESEARCH

Non-Random Integration of the HPV Genome in Cervical Cancer

(2012) Martina Schmitz et al.   PLoS One

Identifying viral integration sites using SeqMap 2.0

(2011) Troy B. Hawkins et al.   BIOINFORMATICS

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

(2011) Shin Suzuki et al.   BMC BIOINFORMATICS

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

(2011) Jianmin Wang et al.   NATURE METHODS

Dr.VIS: a database of human disease-related viral integration sites

(2011) X. Zhao et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Heng Li et al.   BIOINFORMATICS

Herpesviruses and Chromosomal Integration

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

A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq

(2010) Liguo Wang et al.   PLoS One

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 induced hepatocellular carcinoma

(2009) I. Chemin et al.   CANCER LETTERS

The Majority of Viral-Cellular Fusion Transcripts in Cervical Carcinomas Cotranscribe Cellular Sequences of Known or Predicted Genes

(2008) I. Kraus et al.   CANCER RESEARCH