Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

A guide to phylogenetic metrics for conservation, community ecology and macroecology

(2016) Caroline M. Tucker et al.   BIOLOGICAL REVIEWS

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

(2016) Fiona Fouhy et al.   BMC MICROBIOLOGY

Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability

(2016) Andreas Hiergeist et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Improving the microbial community reconstruction at the genus level by multiple 16S rRNA regions

(2016) Shengqin Wang et al.   JOURNAL OF THEORETICAL BIOLOGY

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples

(2016) Jennifer J. Barb et al.   PLoS One

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

(2016) James L. O’Donnell et al.   PLoS One

Primer and platform effects on 16S rRNA tag sequencing

(2015) Julien Tremblay et al.   Frontiers in Microbiology

SEK: sparsity exploiting k-mer-based estimation of bacterial community composition

(2014) S. Chatterjee et al.   BIOINFORMATICS

Artificial sweeteners induce glucose intolerance by altering the gut microbiota

(2014) Jotham Suez et al.   NATURE

Delayed development induced by toxicity to the host can be inherited by a bacterial-dependent, transgenerational effect

(2014) Yael Fridmann-Sirkis et al.   Frontiers in Genetics

Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing

(2013) David Koslicki et al.   BIOINFORMATICS

High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions

(2013) Amnon Amir et al.   NUCLEIC ACIDS RESEARCH

Microbiomic Signatures of Psoriasis: Feasibility and Methodology Comparison

(2013) Alexander Statnikov et al.   Scientific Reports

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Coverage evaluation of universal bacterial primers using the metagenomic datasets

(2012) Dan-Ping Mao et al.   BMC MICROBIOLOGY

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

(2012)   PLoS One

A Statistical Framework for Accurate Taxonomic Assignment of Metagenomic Sequencing Reads

(2012) Hongmei Jiang et al.   PLoS One

Epigenetically Heritable Alteration of Fly Development in Response to Toxic Challenge

(2012) Shay Stern et al.   Cell Reports

Analyzing and minimizing bias in Illumina sequencing libraries

(2012) Daniel Aird et al.   GENOME BIOLOGY

Comparison of bacterial microbiota in skin biopsies from normal and psoriatic skin

(2011) Annika Fahlén et al.   ARCHIVES OF DERMATOLOGICAL RESEARCH

Mixture models for analysis of the taxonomic composition of metagenomes

(2011) Peter Meinicke et al.   BIOINFORMATICS

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

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

454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants

(2011) Tong Zhang et al.   ISME Journal

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY