Finding and identifying the viral needle in the metagenomic haystack: trends and challenges

Rapidly expanding knowledge on the role of the gut microbiome in health and disease

(2014) M.C. Cénit et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

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

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome

(2014) Ohad Manor et al.   Cell Metabolism

Bacterial Vesicles in Marine Ecosystems

(2014) S. J. Biller et al.   SCIENCE

Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics

(2014) Muriel Vayssier-Taussat et al.   Frontiers in Cellular and Infection Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

Lignocellulose-degrading enzymes from termites and their symbiotic microbiota

(2013) Jinfeng Ni et al.   BIOTECHNOLOGY ADVANCES

Human intestinal metagenomics: state of the art and future

(2013) Hervé M Blottière et al.   CURRENT OPINION IN MICROBIOLOGY

Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery

(2013) Richard J. Hall et al.   JOURNAL OF VIROLOGICAL METHODS

An instance level analysis of data complexity

(2013) Michael R. Smith et al.   MACHINE LEARNING

The human virome: new tools and concepts

(2013) Marc Lecuit et al.   TRENDS IN MICROBIOLOGY

Plant Virus Metagenomics: Biodiversity and Ecology

(2012) Marilyn J. Roossinck   Annual Review of Genetics

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

(2012) H. Teeling et al.   BRIEFINGS IN BIOINFORMATICS

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

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

Hypervariable loci in the human gut virome

(2012) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational tools for viral metagenomics and their application in clinical research

(2012) L. Fancello et al.   VIROLOGY

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

(2011) Ozkan U Nalbantoglu et al.   BMC BIOINFORMATICS

Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems

(2011) Simon Roux et al.   FEMS MICROBIOLOGY ECOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Exploring the viral world through metagenomics

(2011) Karyna Rosario et al.   Current Opinion in Virology

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

Metagenomics: Facts and Artifacts, and Computational Challenges

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

Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard

(2010) Beatrix Coetzee et al.   VIROLOGY

Frequency Analysis Techniques for Identification of Viral Genetic Data

(2010) V. Trifonov et al.   mBio

Metagenomic Pyrosequencing and Microbial Identification

(2009) J. F. Petrosino et al.   CLINICAL CHEMISTRY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH