Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf

Shape matters: the relationship between cell geometry and diversity in phytoplankton

(2021) Alexey Ryabov et al.   ECOLOGY LETTERS

A Review of Holography in the Aquatic Sciences: In situ Characterization of Particles, Plankton, and Small Scale Biophysical Interactions

(2021) Aditya R. Nayak et al.   Frontiers in Marine Science

Commentary: How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches

(2021) Ching Jian et al.   Frontiers in Cellular and Infection Microbiology

Seasonality of the Microbial Community Composition in the North Atlantic

(2021) Luis M. Bolaños et al.   Frontiers in Marine Science

The role of taxonomic expertise in interpretation of metabarcoding studies

(2021) Paula Pappalardo et al.   ICES JOURNAL OF MARINE SCIENCE

Marine snow morphology illuminates the evolution of phytoplankton blooms and determines their subsequent vertical export

(2021) Emilia Trudnowska et al.   Nature Communications

Machine Learning for the Study of Plankton and Marine Snow from Images

(2021) Jean-Olivier Irisson et al.   Annual Review of Marine Science

Small phytoplankton dominate western North Atlantic biomass

(2020) Luis M. Bolaños et al.   ISME Journal

Dynamics and functional diversity of the smallest phytoplankton on the Northeast US Shelf

(2020) Bethany L. Fowler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding

(2020) Luciana Santoferrara et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Paired high‐throughput, in situ imaging and high‐throughput sequencing illuminate acantharian abundance and vertical distribution

(2020) Margaret Mars Brisbin et al.   LIMNOLOGY AND OCEANOGRAPHY

Assessment of holographic microscopy for quantifying marine particle size and concentration

(2020) Noah L. Walcutt et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Fine-scale larval fish distributions and predator-prey dynamics in a coastal river-dominated ecosystem

(2020) KE Axler et al.   MARINE ECOLOGY PROGRESS SERIES

Phytoplankton Community Composition Determined From Co-variability Among Phytoplankton Pigments From the NAAMES Field Campaign

(2020) Sasha J. Kramer et al.   Frontiers in Marine Science

The Scripps Plankton Camera system: A framework and platform for in situ microscopy

(2020) Eric C. Orenstein et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Three-dimensional cross-shelf zooplankton distributions off the Central Oregon Coast during anomalous oceanographic conditions

(2020) Christian Briseño-Avena et al.   PROGRESS IN OCEANOGRAPHY

Automated plankton classification from holographic imagery with deep convolutional neural networks

(2020) Buyu Guo et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Mixotrophic protists display contrasted biogeographies in the global ocean

(2019) Emile Faure et al.   ISME Journal

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

(2019) Benjamin J Callahan et al.   NUCLEIC ACIDS RESEARCH

A field guide for the compositional analysis of any-omics data

(2019) Thomas P Quinn et al.   GigaScience

Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks

(2019) Attayeb Mohsen et al.   BMC BIOINFORMATICS

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

Rarefaction, Alpha Diversity, and Statistics

(2019) Amy D. Willis   Frontiers in Microbiology

Evaluation of marine zooplankton community structure through environmental DNA metabarcoding

(2018) Anni Djurhuus et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Lensless digital holographic microscopy and its applications in biomedicine and environmental monitoring

(2018) Yichen Wu et al.   METHODS

Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias

(2018) Søren M Karst et al.   NATURE BIOTECHNOLOGY

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Digital holography and its multidimensional imaging applications: a review

(2018) Tatsuki Tahara et al.   Microscopy

Multi-marker metabarcoding approach to study mesozooplankton at basin scale

(2018) Sergio Stefanni et al.   Scientific Reports

Towards quantitative microbiome community profiling using internal standards

(2018) Yajuan Lin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biogeography and diversity of Collodaria (Radiolaria) in the global ocean

(2017) Tristan Biard et al.   ISME Journal

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

(2017) Benjamin J Callahan et al.   ISME Journal

Influence of diatom diversity on the ocean biological carbon pump

(2017) Paul Tréguer et al.   Nature Geoscience

Abrupt cooling over the North Atlantic in modern climate models

(2017) Giovanni Sgubin et al.   Nature Communications

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes

(2017) Sebastien Colin et al.   eLife

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

(2017) André M. Comeau et al.   mSystems

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

The Impact of Submesoscale Physics on Primary Productivity of Plankton

(2016) Amala Mahadevan   Annual Review of Marine Science

Eukaryotic microbes, principally fungi and labyrinthulomycetes, dominate biomass on bathypelagic marine snow

(2016) Alexander B Bochdansky et al.   ISME Journal

Reference Tree and Environmental Sequence Diversity of Labyrinthulomycetes

(2016) Jingwen Pan et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

In situ imaging reveals the biomass of giant protists in the global ocean

(2016) Tristan Biard et al.   NATURE

Censusing marine eukaryotic diversity in the twenty-first century

(2016) Matthieu Leray et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Estimating diversity via frequency ratios

(2015) Amy Willis et al.   BIOMETRICS

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

Origin, dynamics, and implications of extracellular DNA pools in marine sediments

(2015) Andrea Torti et al.   Marine Genomics

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

(2015) Johan Decelle et al.   Molecular Ecology Resources

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

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities

(2015) Dominique A. Cowart et al.   PLoS One

High throughput holographic imaging-in-flow for the analysis of a wide plankton size range

(2014) Catherine Yourassowsky et al.   OPTICS EXPRESS

The others: our biased perspective of eukaryotic genomes

(2014) Javier del Campo et al.   TRENDS IN ECOLOGY & EVOLUTION

High throughput sequencing methods and analysis for microbiome research

(2013) Julia M. Di Bella et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Development and deployment of a point-source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m

(2013) Alexander B. Bochdansky et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R

(2013) Eric Pante et al.   PLoS One

Quantitative phase and refractive index measurements with point-source digital in-line holographic microscopy

(2012) M. H. Jericho et al.   APPLIED OPTICS

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

Basin-scale distribution patterns of photosynthetic picoeukaryotes along an Atlantic Meridional Transect

(2011) Amy R. Kirkham et al.   ENVIRONMENTAL MICROBIOLOGY

Arctic Ocean Microbial Community Structure before and after the 2007 Record Sea Ice Minimum

(2011) André M. Comeau et al.   PLoS One

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

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Principles and techniques of digital holographic microscopy

(2010) Myung K. Kim   Journal of Photonics for Energy

Freshwater export from the Labrador Current to the North Atlantic Current at the Tail of the Grand Banks of Newfoundland

(2009) Paula S. Fratantoni et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Decadal variability in North Atlantic phytoplankton blooms

(2009) Stephanie A. Henson et al.   JOURNAL OF GEOPHYSICAL RESEARCH

Reconstruction of high-resolution holographic microscopic images

(2009) M. Kanka et al.   OPTICS LETTERS

Seasonal variability of the Labrador Current and shelf circulation off Newfoundland

(2008) Guoqi Han et al.   JOURNAL OF GEOPHYSICAL RESEARCH

Underwater digital holography for studies of marine plankton

(2008) H Sun et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES