Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Comparison of Culture and Molecular Identification of Bacteria in Chronic Wounds

(2012) Daniel D. Rhoads et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform

(2012) Andrew S. Whiteley et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

A Format for Phylogenetic Placements

(2012) Frederick A. Matsen et al.   PLoS One

The Airway Microbiota in Cystic Fibrosis: A Complex Fungal and Bacterial Community—Implications for Therapeutic Management

(2012) Laurence Delhaes et al.   PLoS One

Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing

(2012) Sebastian Jünemann et al.   PLoS One

Decade-long bacterial community dynamics in cystic fibrosis airways

(2012) J. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiota, Disease, and Back to Health: A Metastable Journey

(2012) R. Blumberg et al.   Science Translational Medicine

Temporal Dynamics of the Human Vaginal Microbiota

(2012) P. Gajer et al.   Science Translational Medicine

Bacterial swimming, swarming and chemotactic response to heavy metal presence: which could be the influence on wastewater biotreatment efficiency?

(2012) Matías R. Barrionuevo et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Metagenomic Analysis of Brain Abscesses Identifies Specific Bacterial Associations

(2011) M. Al Masalma et al.   CLINICAL INFECTIOUS DISEASES

The airway microbiome in cystic fibrosis and implications for treatment

(2011) Edith T Zemanick et al.   CURRENT OPINION IN PEDIATRICS

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Culture Enriched Molecular Profiling of the Cystic Fibrosis Airway Microbiome

(2011) Christopher D. Sibley et al.   PLoS One

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prospects for the Future Using Genomics and Proteomics in Clinical Microbiology

(2010) Pierre-Edouard Fournier et al.   Annual Review of Microbiology

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis

(2010) Adam M Guss et al.   ISME Journal

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches

(2009) Ivan Nasidze et al.   ANALYTICAL BIOCHEMISTRY

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Studying bacterial infections through culture-independent approaches

(2009) G. B. Rogers et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria

(2009) Rudolph Spangler et al.   PLoS One

Detection of Anaerobic Bacteria in High Numbers in Sputum from Patients with Cystic Fibrosis

(2008) Michael M. Tunney et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes

(2008) J. A. Frank et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Coamplification of Eukaryotic DNA with 16S rRNA Gene-Based PCR Primers: Possible Consequences for Population Fingerprinting of Complex Microbial Communities

(2008) Geert Huys et al.   CURRENT MICROBIOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

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

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