Enteric Virome and Carcinogenesis in the Gut

Bacterial community structure and effects of picornavirus infection on the anterior nares microbiome in early childhood

(2019) Mahrrouz Caputo et al.   BMC MICROBIOLOGY

Going Viral: a Novel Role for Bacteriophage in Colorectal Cancer

(2019) Scott A. Handley et al.   mBio

Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses

(2019) Claude Kwe Yinda et al.   mSphere

Phages trump bacteria in immune interactions

(2019) Louis J. Cohen   Science Translational Medicine

Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis

(2019) Lasha Gogokhia et al.   Cell Host & Microbe

Global Increasing Incidence of Young-Onset Colorectal Cancer Across 5 Continents: A Joinpoint Regression Analysis of 1,922,167 Cases

(2019) Rashid N Lui et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Mining, analyzing, and integrating viral signals from metagenomic data

(2019) Tingting Zheng et al.   Microbiome

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach

(2019) Sarah Mollerup et al.   JOURNAL OF INFECTIOUS DISEASES

Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut

(2019) Tasha M. Santiago-Rodriguez et al.   Viruses-Basel

The Intestinal Microbiota in Colorectal Cancer

(2018) Herbert Tilg et al.   CANCER CELL

Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes

(2018) Geicho Nakatsu et al.   GASTROENTEROLOGY

Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy

(2018) Pakorn Aiewsakun et al.   JOURNAL OF GENERAL VIROLOGY

Overview of Virus Metagenomic Classification Methods and Their Biological Applications

(2018) Sam Nooij et al.   Frontiers in Microbiology

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

(2018) Pakorn Aiewsakun et al.   Microbiome

The human papillomavirus (HPV)-related cancer biology: An overview

(2018) Rodrigo Pinheiro Araldi et al.   BIOMEDICINE & PHARMACOTHERAPY

Enteric Virome and Bacterial Microbiota in Children with Ulcerative Colitis and Crohnʼs Disease

(2018) Melissa A. Fernandes et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Ancient hepatitis B viruses from the Bronze Age to the Medieval period

(2018) Barbara Mühlemann et al.   NATURE

Human polyomaviruses and cancer: an overview

(2018) JC Prado et al.   Clinics

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

(2018) Geoffrey D. Hannigan et al.   mBio

NOD2 Genetic Variants Predispose One of Two Familial Adenomatous Polyposis Siblings to Pouchitis Through Microbiome Dysbiosis

(2017) Kathleen M Schieffer et al.   Journal of Crohns & Colitis

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

(2017) Elliot J Lefkowitz et al.   NUCLEIC ACIDS RESEARCH

Recent advances in inferring viral diversity from high-throughput sequencing data

(2017) Susana Posada-Cespedes et al.   VIRUS RESEARCH

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers

(2017) Sophie Nguyen et al.   mBio

Association between human papillomavirus and prostate cancer: A meta-analysis

(2017) Binbin Yin et al.   Oncology Letters

Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells

(2017) Timo A. Lehti et al.   Nature Communications

The blood DNA virome in 8,000 humans

(2017) Ahmed Moustafa et al.   PLoS Pathogens

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases

(2017) David F. Nieuwenhuijse et al.   Frontiers in Microbiology

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

(2017) Donald Pan et al.   Frontiers in Microbiology

Normalization of the microbiota in patients after treatment for colonic lesions

(2017) Marc A. Sze et al.   Microbiome

The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction

(2016) A. A. Abbas et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome

(2016) Cynthia L. Monaco et al.   Cell Host & Microbe

Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice

(2016) Min-Soo Kim et al.   ENVIRONMENTAL MICROBIOLOGY

Simian virus 40 is not likely involved in the development of colorectal adenocarcinoma

(2016) Mohamad Nidal Khabaz et al.   Future Virology

BK polyomavirus association with colorectal cancer development

(2016) M.N. Khabaz et al.   GENETICS AND MOLECULAR RESEARCH

The Expanding Family of Virophages

(2016) Meriem Bekliz et al.   Viruses-Basel

Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions

(2016) Nielson T. Baxter et al.   Genome Medicine

Global burden of cancers attributable to infections in 2012: a synthetic analysis

(2016) Martyn Plummer et al.   Lancet Global Health

DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model

(2016) Nielson T. Baxter et al.   Microbiome

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies

(2016) Martin Norling et al.   PLoS One

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

(2015) Matthias Scheuch et al.   BMC BIOINFORMATICS

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

Filamentous Bacteriophage Promote Biofilm Assembly and Function

(2015) Patrick R. Secor et al.   Cell Host & Microbe

Metabolism Links Bacterial Biofilms and Colon Carcinogenesis

(2015) Caroline H. Johnson et al.   Cell Metabolism

Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains

(2015) Dagmara W. Lewandowska et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Enhanced virome sequencing using targeted sequence capture

(2015) Todd N. Wylie et al.   GENOME RESEARCH

Benefits and drawbacks of molecular techniques for diagnosis of viral respiratory infections. Experience with two multiplex PCR assays

(2015) Laura García-Arroyo et al.   JOURNAL OF MEDICAL VIROLOGY

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data

(2015) Xutao Deng et al.   NUCLEIC ACIDS RESEARCH

Human papillomavirus molecular biology and disease association

(2015) John Doorbar et al.   REVIEWS IN MEDICAL VIROLOGY

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

(2015) Lasse Vinner et al.   Scientific Reports

The human gut virome: a multifaceted majority

(2015) Lesley A. Ogilvie et al.   Frontiers in Microbiology

Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes

(2015) Shira R. Abeles 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

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut

(2014) Jorge F Vázquez-Castellanos et al.   BMC GENOMICS

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer

(2014) J. P. Zackular et al.   Cancer Prevention Research

Human Viral Oncogenesis: A Cancer Hallmarks Analysis

(2014) Enrique A. Mesri et al.   Cell Host & Microbe

The Bacteroides fragilis Toxin Gene Is Prevalent in the Colon Mucosa of Colorectal Cancer Patients

(2014) Annemarie Boleij et al.   CLINICAL INFECTIOUS DISEASES

Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections

(2014) M. J. PALLEN   PARASITOLOGY

Four Escherichia coli O157:H7 Phages: A New Bacteriophage Genus and Taxonomic Classification of T1-Like Phages

(2014) Yan D. Niu et al.   PLoS One

Microbiota organization is a distinct feature of proximal colorectal cancers

(2014) Christine M. Dejea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Altered Oral Viral Ecology in Association with Periodontal Disease

(2014) M. Ly et al.   mBio

OMICtools: an informative directory for multi-omic data analysis

(2014) V. J. Henry et al.   Database-The Journal of Biological Databases and Curation

Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs

(2014) Matthew Scholz et al.   Scientific Reports

Assembly of viral genomes from metagenomes

(2014) Saskia L. Smits et al.   Frontiers in Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

The saga of XMRV: a virus that infects human cells but is not a human virus

(2014) Maribel Arias et al.   Emerging Microbes & Infections

Detection of HBV Resistance to Lamivudine in Patients with Chronic Hepatitis B Using Zip Nucleic Acid Probes in Kerman, Southeast of Iran

(2013) Reza Malekpour Afshar et al.   Asian Pacific Journal of Cancer Prevention

Human Polyomavirus Reactivation: Disease Pathogenesis and Treatment Approaches

(2013) Cillian F. De Gascun et al.   Clinical & Developmental Immunology

Human papillomavirus infection and colorectal cancer risk: a meta-analysis

(2013) D. C. Damin et al.   Colorectal Disease

Higher Specificity of Nucleic Acid Sequence-Based Amplification Isothermal Technology than of Real-Time PCR for Quantification of HIV-1 RNA on Dried Blood Spots

(2013) S. Mercier-Delarue et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

Rapid evolution of the human gut virome

(2013) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A systematic review of the prevalence of mucosal and cutaneous human papillomavirus types

(2013) Davit Bzhalava et al.   VIROLOGY

Human polyomaviruses in disease and cancer

(2013) Tina Dalianis et al.   VIROLOGY

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

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

(2012) Aparna Bhaduri et al.   BIOINFORMATICS

Going viral: next-generation sequencing applied to phage populations in the human gut

(2012) Alejandro Reyes et al.   NATURE REVIEWS MICROBIOLOGY

Prevalence of JC Virus in Chinese Patients with Colorectal Cancer

(2012) Xiaozhou Mou et al.   PLoS One

Computational tools for viral metagenomics and their application in clinical research

(2012) L. Fancello et al.   VIROLOGY

A Multicenter Blinded Analysis Indicates No Association between Chronic Fatigue Syndrome/Myalgic Encephalomyelitis and either Xenotropic Murine Leukemia Virus-Related Virus or Polytropic Murine Leukemia Virus

(2012) H. J. Alter et al.   mBio

VIROME: a standard operating procedure for analysis of viral metagenome sequences

(2012) K. Eric Wommack et al.   Standards in Genomic Sciences

Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

(2011) Min-Soo Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Presence of JC Virus DNA in the Tumor Tissue and Normal Mucosa of Patients with Sporadic Colorectal Cancer (CRC) or with Positive Family History and Bethesda Criteria

(2011) Alex Vilkin et al.   DIGESTIVE DISEASES AND SCIENCES

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

(2011) M. Castellarin et al.   GENOME RESEARCH

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Red meat consumption and cancer: Reasons to suspect involvement of bovine infectious factors in colorectal cancer

(2011) Harald zur Hausen   INTERNATIONAL JOURNAL OF CANCER

Microbial Dysbiosis in Colorectal Cancer (CRC) Patients

(2011) Iradj Sobhani et al.   PLoS One

DNA Extraction Columns Contaminated with Murine Sequences

(2011) Otto Erlwein et al.   PLoS One

Detection of viral DNA sequences in sporadic colorectal cancers in relation to CpG island methylation and methylator phenotype

(2011) Pawel Karpinski et al.   TUMOR BIOLOGY

Metagenomics for the discovery of novel human viruses

(2010) Patrick Tang et al.   Future Microbiology

JC Virus Infection

(2010) Dana E. Rollison   JOURNAL OF CLINICAL GASTROENTEROLOGY

Metagenomics: Facts and Artifacts, and Computational Challenges

(2010) John C. Wooley et al.   JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY

Endogenous non-retroviral RNA virus elements in mammalian genomes

(2010) Masayuki Horie et al.   NATURE

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells

(2010) G. Cuevas-Ramos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

Roles of viruses in the environment

(2009) Forest Rohwer et al.   ENVIRONMENTAL MICROBIOLOGY

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Recombination of Retrotransposon and Exogenous RNA Virus Results in Nonretroviral cDNA Integration

(2009) M. B. Geuking et al.   SCIENCE

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil

(2008) K.-H. Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RespiFinder: a New Multiparameter Test To Differentially Identify Fifteen Respiratory Viruses

(2008) M. Reijans et al.   JOURNAL OF CLINICAL MICROBIOLOGY