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

What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

(2015) Lynsey K. Whitacre et al.   BMC GENOMICS

Traces of ATCV-1 associated with laboratory component contamination

(2015) Kristín Rós Kjartansdóttir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing

(2015) Lasse Vinner et al.   Scientific Reports

Target-Dependent Enrichment of Virions Determines the Reduction of High-Throughput Sequencing in Virus Discovery

(2015) Randi Holm Jensen et al.   PLoS One

New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics

(2015) Thomas Arn Hansen et al.   PLoS One

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

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

Comprehensive Human Virus Screening Using High-Throughput Sequencing with a User-Friendly Representation of Bioinformatics Analysis: a Pilot Study

(2014) Tom J. Petty et al.   JOURNAL OF CLINICAL MICROBIOLOGY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Full Genome Virus Detection in Fecal Samples Using Sensitive Nucleic Acid Preparation, Deep Sequencing, and a Novel Iterative Sequence Classification Algorithm

(2014) Matthew Cotten et al.   PLoS One

False-Positive Results in Metagenomic Virus Discovery: A Strong Case for Follow-Up Diagnosis

(2014) T. Rosseel et al.   Transboundary and Emerging Diseases

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

(2013) S. N. Naccache et al.   JOURNAL OF VIROLOGY

Novel Hybrid Parvovirus-Like Virus, NIH-CQV/PHV, Contaminants in Silica Column-Based Nucleic Acid Extraction Kits

(2013) H. Smuts et al.   JOURNAL OF VIROLOGY

A cornucopia of human polyomaviruses

(2013) James A. DeCaprio et al.   NATURE REVIEWS MICROBIOLOGY

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

(2013) Guoyan Zhao et al.   PLoS One

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

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

(2012) Aparna Bhaduri et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

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

(2012) Ivan Borozan et al.   BMC BIOINFORMATICS

A framework for human microbiome research

(2012)   NATURE

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

(2012) Christine M. Malboeuf et al.   NUCLEIC ACIDS RESEARCH

Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing

(2012) Fredrik Lysholm et al.   PLoS One

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

Artificial Neural Networks Trained to Detect Viral and Phage Structural Proteins

(2012) Victor Seguritan et al.   PLoS Computational Biology

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

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

Failure to Confirm XMRV/MLVs in the Blood of Patients with Chronic Fatigue Syndrome: A Multi-Laboratory Study

(2011) G. Simmons et al.   SCIENCE

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

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

(2010) Bruno Zeitouni et al.   BIOINFORMATICS

In Silico Prediction of Human Pathogenicity in the γ-Proteobacteria

(2010) Massimo Andreatta et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A review of human carcinogens—Part B: biological agents

(2009) Véronique Bouvard et al.   LANCET ONCOLOGY

How does multiple testing correction work?

(2009) William S Noble   NATURE BIOTECHNOLOGY

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

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

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

Avian myeoloblastosis virus (AMV): only one side of the coin

(2008) Bernard Perbal   Retrovirology

Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma

(2008) H. Feng et al.   SCIENCE