Rare biosphere exploration using high-throughput sequencing: research progress and perspectives

BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads

(2014) Yun Heo et al.   BIOINFORMATICS

The unseen world: environmental microbial sequencing and identification methods for ecologists

(2014) Naupaka Zimmerman et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Influence of Artifact Removal on Rare Species Recovery in Natural Complex Communities Using High-Throughput Sequencing

(2014) Aibin Zhan et al.   PLoS One

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

Reproducibility of pyrosequencing data for biodiversity assessment in complex communities

(2014) Aibin Zhan et al.   Methods in Ecology and Evolution

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

(2013) Matthieu Leray et al.   Frontiers in Zoology

Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi

(2013) Otso Ovaskainen et al.   ISME Journal

ITS1 versus ITS2 as DNA metabarcodes for fungi

(2013) R. Blaalid et al.   Molecular Ecology Resources

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

Evaluating Detection Limits of Next-Generation Sequencing for the Surveillance and Monitoring of International Marine Pests

(2013) Xavier Pochon et al.   PLoS One

SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons

(2013) Shanlin Liu et al.   Methods in Ecology and Evolution

High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities

(2013) Aibin Zhan et al.   Methods in Ecology and Evolution

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

A survey of error-correction methods for next-generation sequencing

(2012) X. Yang et al.   BRIEFINGS IN BIOINFORMATICS

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?

(2012) Tor Carlsen et al.   Fungal Ecology

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

DNA Barcoding of Recently Diverged Species: Relative Performance of Matching Methods

(2012) Robin van Velzen et al.   PLoS One

High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples

(2012) Hirokazu Toju et al.   PLoS One

PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences

(2012) Ryuji J. Machida et al.   PLoS One

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

(2012) C. Q. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The golden age of DNA metasystematics

(2012) Mehrdad Hajibabaei   TRENDS IN GENETICS

The Rare Bacterial Biosphere

(2011) Carlos Pedrós-Alió   Annual Review of Marine Science

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects

(2011) Harm-Jan Westra et al.   BIOINFORMATICS

Correcting errors in short reads by multiple alignments

(2011) L. Salmela et al.   BIOINFORMATICS

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

(2011) Surendra Kumar et al.   BMC BIOINFORMATICS

When should we save the most endangered species?

(2011) Howard B. Wilson et al.   ECOLOGY LETTERS

From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments

(2011) John A. Darling et al.   ENVIRONMENTAL RESEARCH

ECHO: A reference-free short-read error correction algorithm

(2011) W.-C. Kao et al.   GENOME RESEARCH

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

(2011) SANNE BOESSENKOOL et al.   MOLECULAR ECOLOGY

Monitoring endangered freshwater biodiversity using environmental DNA

(2011) PHILIP FRANCIS THOMSEN et al.   MOLECULAR ECOLOGY

Has the Earth’s sixth mass extinction already arrived?

(2011) Anthony D. Barnosky et al.   NATURE

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

HiTEC: accurate error correction in high-throughput sequencing data

(2010) L. Ilie et al.   BIOINFORMATICS

Correction of sequencing errors in a mixed set of reads

(2010) L. Salmela   BIOINFORMATICS

Reptile: representative tiling for short read error correction

(2010) X. Yang et al.   BIOINFORMATICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists

(2010) SIMON CREER   MOLECULAR ECOLOGY

Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome

(2010) Carlos W Nossa   WORLD JOURNAL OF GASTROENTEROLOGY

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

(2009) Julie A. Huber et al.   ENVIRONMENTAL MICROBIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

(2009) BRUCE E. DEAGLE et al.   MOLECULAR ECOLOGY

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS