Co-occurrence of Bacillariophyceae-based- and Cryptophyceae-based planktonic food webs in a temperate estuarine ecosystem revealed via eDNA

Microbial dynamics of elevated carbon flux in the open ocean’s abyss

(2021) Kirsten E. Poff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula

(2021) Yajuan Lin et al.   Nature Communications

Morphological Redescriptions and Molecular Phylogeny of Three Stentor Species (Ciliophora: Heterotrichea: Stentoridae) from Korea

(2020) MD ABU TAHER et al.   ZOOTAXA

Environmental DNA reveals seasonal shifts and potential interactions in a marine community

(2020) Anni Djurhuus et al.   Nature Communications

Co‐occurrence is not evidence of ecological interactions

(2020) F. Guillaume Blanchet et al.   ECOLOGY LETTERS

A Review and Perspective of eDNA Application to Eutrophication and HAB Control in Freshwater and Marine Ecosystems

(2020) Qi Liu et al.   Microorganisms

Reconstructing marine plankton food web interactions using DNA metabarcoding

(2020) Sara Zamora‐Terol et al.   MOLECULAR ECOLOGY

Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area

(2020) Natalia Fraija‐Fernández et al.   Ecology and Evolution

Variation of Amoebophrya community during bloom of Prorocentrum donghaiense Lu in coastal waters of the East China Sea

(2020) Tiantian Chen et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Identifying patterns in the multitrophic community and food-web structure of a low-turbidity temperate estuarine bay

(2020) Hee Yoon Kang et al.   Scientific Reports

Marine Microbial Food Web Networks During Phytoplankton Bloom and Non-bloom Periods: Warming Favors Smaller Organism Interactions and Intensifies Trophic Cascade

(2020) Thomas Trombetta et al.   Frontiers in Microbiology

Dominance of Autochthonous Phytoplankton-Derived Particulate Organic Matter in a Low-Turbidity Temperate Estuarine Embayment, Gwangyang Bay, Korea

(2020) Riaz Bibi et al.   Frontiers in Marine Science

Year-to-year variation in phytoplankton biomass in an anthropogenically polluted and complex estuary: A novel paradigm for river discharge influence

(2020) Yoonja Kang et al.   MARINE POLLUTION BULLETIN

“Candidatus Hafkinia simulans” gen. nov., sp. nov., a Novel Holospora-Like Bacterium from the Macronucleus of the Rare Brackish Water Ciliate Frontonia salmastra (Oligohymenophorea, Ciliophora): Multidisciplinary Characterization of the New Endosymbiont and Its Host

(2019) Sergei I. Fokin et al.   MICROBIAL ECOLOGY

Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding

(2019) Natalie A. Sawaya et al.   Ecology and Evolution

Using environmental DNA to estimate the seasonal distribution and habitat preferences of a Japanese basket clam in Lake Shinji, Japan

(2019) Teruhiko Takahara et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Difficulty in inferring microbial community structure based on co-occurrence network approaches

(2019) Hokuto Hirano et al.   BMC BIOINFORMATICS

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Modelling approaches for studying the microbiome

(2019) Manish Kumar et al.   Nature Microbiology

Comparison of Water Sampling between Environmental DNA Metabarcoding and Conventional Microscopic Identification: A Case Study in Gwangyang Bay, South Korea

(2019) Kim et al.   Applied Sciences-Basel

Discrimination of Spatial Distribution of Aquatic Organisms in a Coastal Ecosystem Using eDNA

(2019) Hyunbin Jo et al.   Applied Sciences-Basel

Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies

(2019) Ryan P. Kelly et al.   Scientific Reports

OUP accepted manuscript

(2018)   BIOINFORMATICS

Eukaryotic phytoplankton community spatiotemporal dynamics as identified through gene expression within a eutrophic estuary

(2018) Weida Gong et al.   ENVIRONMENTAL MICROBIOLOGY

Tidal Influences on Biotic and Abiotic Factors in the Seomjin River Estuary and Gwangyang Bay, Korea

(2018) Minji Lee et al.   Estuaries and Coasts

Cryptophyta as major bacterivores in freshwater summer plankton

(2018) Vesna Grujcic et al.   ISME Journal

Evaluation of marine zooplankton community structure through environmental DNA metabarcoding

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

Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: A network analysis

(2018) Xinyi Cao et al.   Scientific Reports

Assessing the fate of brown trout (Salmo trutta) environmental DNA in a natural stream using a sensitive and specific dual-labelled probe

(2018) Björn Deutschmann et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta

(2017) Margot Tragin et al.   ENVIRONMENTAL MICROBIOLOGY

Mixotrophy in the marine red-tide cryptophyte Teleaulax amphioxeia and ingestion and grazing impact of cryptophytes on natural populations of bacteria in Korean coastal waters

(2017) Yeong Du Yoo et al.   HARMFUL ALGAE

Persistence of marine fish environmental DNA and the influence of sunlight

(2017) Elizabeth A. Andruszkiewicz et al.   PLoS One

A framework for inferring biological communities from environmental DNA

(2016) Andrew Olaf Shelton et al.   ECOLOGICAL APPLICATIONS

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

(2016) Tomas Roslin et al.   GENOME

Cryptophyte gene regulation in the kleptoplastidic, karyokleptic ciliate Mesodinium rubrum

(2016) Gwang Hoon Kim et al.   HARMFUL ALGAE

Morphology and phylogeny of three trachelocercids (Protozoa, Ciliophora, Karyorelictea), with description of two new species and insight into the evolution of the family Trachelocercidae

(2016) Ying Yan et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

The interactive roles of nutrient loading and zooplankton grazing in facilitating the expansion of harmful algal blooms caused by the pelagophyte, Aureoumbra lagunensis, to the Indian River Lagoon, FL, USA

(2015) Yoonja Kang et al.   HARMFUL ALGAE

A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes

(2015) Kimiko Uchii et al.   Molecular Ecology Resources

Network of Interactions Between Ciliates and Phytoplankton During Spring

(2015) Thomas Posch et al.   Frontiers in Microbiology

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

(2014) Linda A. Amaral-Zettler et al.   PLoS One

A molecular gut content study ofThemisto abyssorum(Amphipoda) from Arctic hydrothermal vent and cold seep systems

(2013) Bernt Rydland Olsen et al.   MOLECULAR ECOLOGY

Further insights into the phylogeny of two ciliate classes Nassophorea and Prostomatea (Protista, Ciliophora)

(2013) Qianqian Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Global-scale carbon and energy flows through the marine planktonic food web: An analysis with a coupled physical–biological model

(2013) Charles A. Stock et al.   PROGRESS IN OCEANOGRAPHY

Virus-driven nitrogen cycling enhances phytoplankton growth

(2012) EJ Shelford et al.   AQUATIC MICROBIAL ECOLOGY

Ultrafast clustering algorithms for metagenomic sequence analysis

(2012) W. Li et al.   BRIEFINGS IN BIOINFORMATICS

Interactions between Diatoms and Bacteria

(2012) S. A. Amin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Applying stable isotopes to examine food-web structure: an overview of analytical tools

(2011) Craig A. Layman et al.   BIOLOGICAL REVIEWS

Morphological and molecular phylogeny of dileptid and tracheliid ciliates: Resolution at the base of the class Litostomatea (Ciliophora, Rhynchostomatia)

(2011) Peter Vďačný et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Correlation Network Analysis Applied to Complex Biofilm Communities

(2011) Ana E. Duran-Pinedo et al.   PLoS One

Biogenic carbon flows through the planktonic food web of the Amundsen Gulf (Arctic Ocean): A synthesis of field measurements and inverse modeling analyses

(2011) Alexandre Forest et al.   PROGRESS IN OCEANOGRAPHY

Global patterns and predictors of marine biodiversity across taxa

(2010) Derek P. Tittensor et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

“CandidatusCryptoprodotis polytropus,” A NovelRickettsia-Like Organism in the Ciliated ProtistPseudomicrothorax dubius(Ciliophora, Nassophorea)

(2009) FILIPPO FERRANTINI et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Phylogeny of Six Genera of the Subclass Haptoria (Ciliophora, Litostomatea) Inferred from Sequences of the Gene Coding for Small Subunit Ribosomal RNA

(2008) SHAN GAO et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY