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

Viral-Human Chimeric Transcript Predisposes Risk to Liver Cancer Development and Progression

(2014) Chi-Chiu Lau et al.   CANCER CELL

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

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

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

(2014) Guorong Xu et al.   PLoS One

The Genomics of Emerging Pathogens

(2013) Cadhla Firth et al.   Annual Review of Genomics and Human Genetics

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

(2013) Jing-Woei Li et al.   BIOINFORMATICS

V-Phaser 2: variant inference for viral populations

(2013) Xiao Yang et al.   BMC GENOMICS

Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias

(2013) Kerensa McElroy et al.   BMC GENOMICS

Viral pathogen discovery

(2013) Charles Y Chiu   CURRENT OPINION IN MICROBIOLOGY

Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability

(2013) K. Akagi et al.   GENOME RESEARCH

Pathoscope: Species identification and strain attribution with unassembled sequencing data

(2013) O. E. Francis et al.   GENOME RESEARCH

Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data

(2013) Andrew Routh et al.   NUCLEIC ACIDS RESEARCH

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

Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline

(2013) Guoyan Zhao et al.   PLoS One

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes

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

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

(2012) Aparna Bhaduri et al.   BIOINFORMATICS

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

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

(2012) Raeece Naeem et al.   BIOINFORMATICS

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

(2012) Ivan Borozan et al.   BMC BIOINFORMATICS

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives

(2012) Q. Wang et al.   BRIEFINGS IN BIOINFORMATICS

Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory

(2012) W. M. Dunne et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

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

(2012) Z. Jiang et al.   GENOME RESEARCH

Global burden of cancers attributable to infections in 2008: a review and synthetic analysis

(2012) Catherine de Martel et al.   LANCET ONCOLOGY

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Sequence Analysis of the Human Virome in Febrile and Afebrile Children

(2012) Kristine M. Wylie et al.   PLoS One

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

(2012) Alexander R. Macalalad et al.   PLoS Computational Biology

Hybrid Capture and Next-Generation Sequencing Identify Viral Integration Sites from Formalin-Fixed, Paraffin-Embedded Tissue

(2011) Eric J. Duncavage et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

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

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

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

(2011) Jianmin Wang et al.   NATURE METHODS

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

(2010) Bruno Zeitouni et al.   BIOINFORMATICS

SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data

(2010) H. J. Abel et al.   BIOINFORMATICS

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

(2010) Thomas D. Otto et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS