Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean

Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate

(2020) Ramon Massana et al.   ISME Journal

Community-Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems

(2019) Luigi Caputi et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Metatranscriptomic Signatures Associated With Phytoplankton Regime Shift From Diatom Dominance to a Dinoflagellate Bloom

(2019) Yaqun Zhang et al.   Frontiers in Microbiology

Mixotroph ecology: More than the sum of its parts

(2019) Ben A. Ward   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mixotrophy in nanoflagellates across environmental gradients in the ocean

(2019) Kyle F. Edwards   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A guide to methods for estimating phago-mixotrophy in nanophytoplankton

(2019) Beatrix E Beisner et al.   JOURNAL OF PLANKTON RESEARCH

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection

(2019) B. C. Kolody et al.   ISME Journal

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Expression of genes involved in phagocytosis in uncultured heterotrophic flagellates

(2019) Aurelie Labarre et al.   LIMNOLOGY AND OCEANOGRAPHY

The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments

(2019) Susanne Wilken et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparative metatranscriptomic profiling and microRNA sequencing to reveal active metabolic pathways associated with a dinoflagellate bloom

(2019) Liying Yu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Shifting metabolic priorities among key protistan taxa within and below the euphotic zone

(2018) Sarah K. Hu et al.   ENVIRONMENTAL MICROBIOLOGY

Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre

(2018) Daniel K. Olson et al.   ISME Journal

dinoref : A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene

(2018) Solenn Mordret et al.   Molecular Ecology Resources

A global ocean atlas of eukaryotic genes

(2018) Quentin Carradec et al.   Nature Communications

Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic

(2018) John A. Burns et al.   Nature Ecology & Evolution

Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms

(2018) Jeffrey B. McQuaid et al.   NATURE

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Quantifying post-transcriptional regulation in the development of Drosophila melanogaster

(2018) Kolja Becker et al.   Nature Communications

Global evaluation of particulate organic carbon flux parameterizations and implications for atmospheric pCO2

(2017) Lucas Gloege et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Development of a molecular-based index for assessing iron status in bloom-forming pennate diatoms

(2017) Adrian Marchetti et al.   JOURNAL OF PHYCOLOGY

Differential effects of nitrate, ammonium, and urea as N sources for microbial communities in the North Pacific Ocean

(2017) I. N. Shilova et al.   LIMNOLOGY AND OCEANOGRAPHY

Utilization of urea and expression profiles of related genes in the dinoflagellate Prorocentrum donghaiense

(2017) Xiaoli Jing et al.   PLoS One

Assessing species biomass contributions in microbial communities via metaproteomics

(2017) Manuel Kleiner et al.   Nature Communications

Marine protist associations and environmental impacts across trophic levels in the twilight zone and below

(2016) VP Edgcomb   CURRENT OPINION IN MICROBIOLOGY

Mixotrophy in the phototrophic dinoflagellate Takayama helix (family Kareniaceae): Predator of diverse toxic and harmful dinoflagellates

(2016) Hae Jin Jeong et al.   HARMFUL ALGAE

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

Insights into global diatom distribution and diversity in the world’s ocean

(2016) Shruti Malviya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Marine mixotrophy increases trophic transfer efficiency, mean organism size, and vertical carbon flux

(2016) Ben A. Ward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake

(2015) Joe Morrissey et al.   CURRENT BIOLOGY

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

(2015) Noan Le Bescot et al.   ENVIRONMENTAL MICROBIOLOGY

Mercury species concentrations and fluxes in the Central Tropical Pacific Ocean

(2015) Kathleen M. Munson et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Metatranscriptome profiling reveals versatile N-nutrient utilization, CO2 limitation, oxidative stress, and active toxin production in an Alexandrium fundyense bloom

(2015) Yunyun Zhuang et al.   HARMFUL ALGAE

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

(2015) Massimo C Pernice et al.   ISME Journal

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

(2015) Johan Decelle et al.   Molecular Ecology Resources

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

(2015) Harriet Alexander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge

(2015) Erin M. Bertrand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Needles in the blue sea: Sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome

(2015) Mak A. Saito et al.   PROTEOMICS

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Diversity and Evolutionary History of Iron Metabolism Genes in Diatoms

(2015) Ryan D. Groussman et al.   PLoS One

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genetic indicators of iron limitation in wild populations of Thalassiosira oceanica from the northeast Pacific Ocean

(2014) P Dreux Chappell et al.   ISME Journal

Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

(2014) Chris L Dupont et al.   ISME Journal

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

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

De Novo Transcriptomes of a Mixotrophic and a Heterotrophic Ciliate from Marine Plankton

(2014) Luciana F. Santoferrara et al.   PLoS One

Light-Promoted Rhodopsin Expression and Starvation Survival in the Marine Dinoflagellate Oxyrrhis marina

(2014) Zhiling Guo et al.   PLoS One

Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers

(2014) M. A. Saito et al.   SCIENCE

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

(2013) Henrik Nordberg et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Cold-Induced Cysts of the Photosynthetic Dinoflagellate Lingulodinium polyedrum Have an Arrested Circadian Bioluminescence Rhythm and Lower Levels of Protein Phosphorylation

(2013) S. Roy et al.   PLANT PHYSIOLOGY

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

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

Misuse of the phytoplankton–zooplankton dichotomy: the need to assign organisms as mixotrophs within plankton functional types

(2012) Kevin J. Flynn et al.   JOURNAL OF PLANKTON RESEARCH

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

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

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability

(2012) A. Marchetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Biophysical Aspects of Resource Acquisition and Competition in Algal Mixotrophs

(2011) Ben A. Ward et al.   AMERICAN NATURALIST

Marine Protistan Diversity

(2011) David A. Caron et al.   Annual Review of Marine Science

Identification and removal of ribosomal RNA sequences from metatranscriptomes

(2011) Robert Schmieder et al.   BIOINFORMATICS

Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition

(2011) Jeanine S Morey et al.   BMC GENOMICS

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

(2011) Daniel PR Herlemann et al.   ISME Journal

The Role of Photosynthesis and Food Uptake for the Growth of Marine Mixotrophic Dinoflagellates1

(2011) PER JUEL HANSEN   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Coupled Effects of Light and Nitrogen Source on the Urea Cycle and Nitrogen Metabolism over a Diel Cycle in the Marine Diatom Thalassiosira pseudonana

(2011) Sara J. Bender et al.   PROTIST

Genomic understanding of dinoflagellates

(2011) Senjie Lin   RESEARCH IN MICROBIOLOGY

A bacterial proteorhodopsin proton pump in marine eukaryotes

(2011) Claudio H. Slamovits et al.   Nature Communications

Refinements to Label Free Proteome Quantitation: How to Deal with Peptides Shared by Multiple Proteins

(2010) Ying Zhang et al.   ANALYTICAL CHEMISTRY

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Mesopelagic zone ecology and biogeochemistry – a synthesis

(2010) Carol Robinson et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Biomass, size structure and depth distributions of the microbial community in the eastern equatorial Pacific

(2010) Andrew G. Taylor et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

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

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Adaptations and selection of harmful and other dinoflagellate species in upwelling systems. 2. Motility and migratory behaviour

(2010) T.J. Smayda   PROGRESS IN OCEANOGRAPHY

Growth, feeding and ecological roles of the mixotrophic and heterotrophic dinoflagellates in marine planktonic food webs

(2010) Hae Jin Jeong et al.   Ocean Science Journal

Grazing by Karenia brevis on Synechococcus enhances its growth rate and may help to sustain blooms

(2009) PM Glibert et al.   AQUATIC MICROBIAL ECOLOGY

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

The origins of phagocytosis and eukaryogenesis

(2009) Natalya Yutin et al.   Biology Direct

Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes

(2009) Yubo Hou et al.   PLoS One

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Expression and regulation of carbonic anhydrases in the marine diatom Thalassiosira pseudonana and in natural phytoplankton assemblages from Great Bay, New Jersey

(2008) Patrick J. McGinn et al.   PHYSIOLOGIA PLANTARUM

Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation

(2008) A. E. Allen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA