imGLAD: accurate detection and quantification of target organisms in metagenomes

How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?

(2018) Luis M. Rodriguez-R et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods

(2016) Andrew D. Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ultrasensitive electrochemical immunoassay for surface array protein, a Bacillus anthracis biomarker using Au–Pd nanocrystals loaded on boron-nitride nanosheets as catalytic labels

(2016) Mukesh Kumar Sharma et al.   BIOSENSORS & BIOELECTRONICS

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

(2016) Moreno Zolfo et al.   NUCLEIC ACIDS RESEARCH

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

(2015) Tracey Allen K. Freitas et al.   NUCLEIC ACIDS RESEARCH

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

(2014) Tae-Hyuk Ahn et al.   BIOINFORMATICS

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples

(2014) Changjin Hong et al.   Microbiome

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

(2013) Chengwei Luo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Detection of Bacillus anthracis DNA in Complex Soil and Air Samples Using Next-Generation Sequencing

(2013) Nicholas A. Be et al.   PLoS One

Metagenomics for pathogen detection in public health

(2013) Ruth R Miller et al.   Genome Medicine

Classification of metagenomic sequences: methods and challenges

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

Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens’ theorem

(2012) Michael C. Wendl et al.   JOURNAL OF MATHEMATICAL BIOLOGY

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

Distinct Acid Resistance and Survival Fitness Displayed by Curli Variants of Enterohemorrhagic Escherichia coli O157:H7

(2011) Michelle Q. Carter et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Bacterial species may exist, metagenomics reveal

(2011) Alejandro Caro-Quintero et al.   ENVIRONMENTAL MICROBIOLOGY