ConStrains identifies microbial strains in metagenomic datasets

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

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

(2014) Tae-Hyuk Ahn et al.   BIOINFORMATICS

Burkholderia pseudomalleisequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

(2014) Tannistha Nandi et al.   GENOME RESEARCH

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Recent advances in genomic DNA sequencing of microbial species from single cells

(2014) Roger S. Lasken et al.   NATURE REVIEWS GENETICS

Eight New Genomes and Synthetic Controls Increase the Accessibility of Rapid Melt-MAMA SNP Typing of Coxiella burnetii

(2014) Edvin Karlsson et al.   PLoS One

Insertions or Deletions (Indels) in the rrn 16S-23S rRNA Gene Internal Transcribed Spacer Region (ITS) Compromise the Typing and Identification of Strains within the Acinetobacter calcoaceticus-baumannii (Acb) Complex and Closely Related Members

(2014) Christopher Maslunka et al.   PLoS One

Population Structure of Clinical Vibrio parahaemolyticus from 17 Coastal Countries, Determined through Multilocus Sequence Analysis

(2014) Dongsheng Han et al.   PLoS One

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

(2014) Christopher W. Beitel et al.   PeerJ

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

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

(2014) Changjin Hong et al.   Microbiome

Bifidobacteria: their impact on gut microbiota composition and their applications as probiotics in infants

(2013) Diana Di Gioia et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold

(2013) J. F. Nijkamp et al.   BIOINFORMATICS

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman et al.   NATURE GENETICS

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Utilisation of Mucin Glycans by the Human Gut Symbiont Ruminococcus gnavus Is Strain-Dependent

(2013) Emmanuelle H. Crost et al.   PLoS One

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

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

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Individual genome assembly from complex community short-read metagenomic datasets

(2011) Chengwei Luo et al.   ISME Journal

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

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

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

(2008) D. A. Sela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA