Evaluation of accuracy and precision in an amplicon sequencing workflow for marine protist communities

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

(2019) Jeremiah J. Minich et al.   mSystems

Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton

(2018) Emma K. Wear et al.   ENVIRONMENTAL MICROBIOLOGY

Linking patterns of net community production and marine microbial community structure in the western North Atlantic

(2018) Seaver Wang et al.   ISME Journal

Short-term dynamics and interactions of marine protist communities during the spring–summer transition

(2018) Lyria Berdjeb et al.   ISME Journal

Phytoplankton Pigment Communities Can be Modeled Using Unique Relationships With Spectral Absorption Signatures in a Dynamic Coastal Environment

(2018) D. Catlett et al.   JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS

Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run

(2018) Yi-Chun Yeh et al.   mSystems

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Genomic GC-Content Affects the Accuracy of 16S rRNA Gene Sequencing Based Microbial Profiling due to PCR Bias

(2017) Martin F. Laursen et al.   Frontiers in Microbiology

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

(2017) Luisa W. Hugerth et al.   Frontiers in Microbiology

Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities

(2016) Ian M. Bradley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

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

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

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

Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom

(2016) David M. Needham et al.   Nature Microbiology

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Estimating Protistan Diversity Using High-Throughput Sequencing

(2015) Sarah K. Hu et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

An Improved DNA Extraction Method for Efficient and Quantitative Recovery of Phytoplankton Diversity in Natural Assemblages

(2015) Jian Yuan et al.   PLoS One

Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes

(2015) A. Z. Worden et al.   SCIENCE

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia

(2014) Luisa W. Hugerth et al.   PLoS One

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Revised Classification of Eukaryotes

(2012) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Quantification of Diatom and Dinoflagellate Biomasses in Coastal Marine Seawater Samples by Real-Time PCR

(2008) A. Godhe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs

(2008) Hege Vestheim et al.   Frontiers in Zoology