Phage-bacteria interaction network in human oral microbiome

Human oral viruses are personal, persistent and gender-consistent

(2014) Shira R Abeles et al.   ISME Journal

Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients

(2014) Yan Li et al.   ISME Journal

Viromes, Not Gene Markers, for Studying Double-Stranded DNA Virus Communities

(2014) Matthew B. Sullivan   JOURNAL OF VIROLOGY

The Placenta Harbors a Unique Microbiome

(2014) K. Aagaard et al.   Science Translational Medicine

Altered Oral Viral Ecology in Association with Periodontal Disease

(2014) M. Ly et al.   mBio

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

Sequencing platform and library preparation choices impact viral metagenomes

(2013) Sergei A Solonenko et al.   BMC GENOMICS

Phage-Mediated Selection on Microbiota of a Long-Lived Host

(2013) Britt Koskella   CURRENT BIOLOGY

Association between living environment and human oral viral ecology

(2013) Refugio Robles-Sikisaka et al.   ISME Journal

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease

(2013) Jinfeng Wang et al.   Scientific Reports

Study of the Viral and Microbial Communities Associated With Crohn’s Disease: A Metagenomic Approach

(2013) Vicente Pérez-Brocal et al.   Clinical and Translational Gastroenterology

Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses

(2012) David T. Pride et al.   ENVIRONMENTAL MICROBIOLOGY

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

(2012) Bonnie L. Hurwitz et al.   ENVIRONMENTAL MICROBIOLOGY

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

(2012) Melissa B. Duhaime et al.   ENVIRONMENTAL MICROBIOLOGY

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages

(2012) Cesar O Flores et al.   ISME Journal

A framework for human microbiome research

(2012)   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

(2012) Alejandro Reyes et al.   NATURE REVIEWS MICROBIOLOGY

Knocking Out ACR2 Does Not Affect Arsenic Redox Status in Arabidopsis thaliana: Implications for As Detoxification and Accumulation in Plants

(2012) Wenju Liu et al.   PLoS One

Phage–bacteria infection networks

(2012) Joshua S. Weitz et al.   TRENDS IN MICROBIOLOGY

Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline

(2012) Melissa B. Duhaime et al.   VIROLOGY

Local Biotic Environment Shapes the Spatial Scale of Bacteriophage Adaptation to Bacteria

(2011) Britt Koskella et al.   AMERICAN NATURALIST

Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses

(2011) Kyoung-Ho Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Relationship of the Oral Microbiotia to Periodontal Health and Disease

(2011) Michael A. Curtis et al.   Cell Host & Microbe

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing

(2011) Ann L Griffen et al.   ISME Journal

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

(2011) David T Pride et al.   ISME Journal

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical structure of host-phage interactions

(2011) C. O. Flores et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic Analysis of Fever, Thrombocytopenia and Leukopenia Syndrome (FTLS) in Henan Province, China: Discovery of a New Bunyavirus

(2011) Bianli Xu et al.   PLoS Pathogens

Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time

(2010) D. T. Pride et al.   GENOME RESEARCH

Multiple displacement amplification compromises quantitative analysis of metagenomes

(2010) Suzan Yilmaz et al.   NATURE METHODS

Reducing the risk of CVD in patients with periodontitis

(2010) Robert J. Genco et al.   Nature Reviews Cardiology

Periodontitis: a polymicrobial disruption of host homeostasis

(2010) Richard P. Darveau   NATURE REVIEWS MICROBIOLOGY

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity

(2010) D. Willner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human oral, gut, and plaque microbiota in patients with atherosclerosis

(2010) O. Koren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE

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

Local Adaptation of Bacteriophages to Their Bacterial Hosts in Soil

(2009) M. Vos et al.   SCIENCE

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Preventing biofilms of clinically relevant organisms using bacteriophage

(2009) Rodney M. Donlan   TRENDS IN MICROBIOLOGY

A bacterial metapopulation adapts locally to phage predation despite global dispersal

(2007) V. Kunin et al.   GENOME RESEARCH