DUDes: a top-down taxonomic profiler for metagenomics

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS

(2015) Martin S. Lindner et al.   PLoS One

Microarrays for identifying binding sites and probing structure of RNAs

(2014) Ryszard Kierzek et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2014)   NUCLEIC ACIDS RESEARCH

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

(2014) M. J. PALLEN   PARASITOLOGY

Multiple hypothesis testing in genomics

(2014) Jelle J. Goeman et al.   STATISTICS IN MEDICINE

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

A Physicians' Wish List for the Clinical Application of Intestinal Metagenomics

(2014) Ingeborg Klymiuk et al.   PLOS MEDICINE

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

(2013) Migun Shakya et al.   ENVIRONMENTAL MICROBIOLOGY

Pathoscope: Species identification and strain attribution with unassembled sequencing data

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

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions

(2013) W. Florian Fricke et al.   NATURE REVIEWS GENETICS

Classification of metagenomic sequences: methods and challenges

(2012) S. S. Mande et al.   BRIEFINGS IN BIOINFORMATICS

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

(2012) Claudio U. Köser et al.   PLoS Pathogens

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Hierarchical testing of variable importance

(2008) N. Meinshausen   BIOMETRIKA