Divergent gene expression among phytoplankton taxa in response to upwelling

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

(2017) Swaraj Basu et al.   NEW PHYTOLOGIST

Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum

(2016) Justin Ashworth et al.   Marine Genomics

Probing the evolution, ecology and physiology of marine protists using transcriptomics

(2016) David A. Caron et al.   NATURE REVIEWS MICROBIOLOGY

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A Diatom Ferritin Optimized for Iron Oxidation but Not Iron Storage

(2015) Stephanie Pfaffen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Subsurface seeding of surface harmful algal blooms observed through the integration of autonomous gliders, moored environmental sample processors, and satellite remote sensing in southern California

(2015) Bridget N. Seegers et al.   LIMNOLOGY AND OCEANOGRAPHY

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

Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean

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

Transcriptome sequencing of three Pseudo-nitzschia species reveals comparable gene sets and the presence of Nitric Oxide Synthase genes in diatoms

(2015) Valeria Di Dato et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

Coastal upwelling linked to toxic Pseudo-nitzschia australis blooms in Los Angeles coastal waters, 2005–2007

(2013) Astrid Schnetzer et al.   JOURNAL OF PLANKTON RESEARCH

Microbial biogeochemistry of coastal upwelling regimes in a changing ocean

(2013) Douglas G. Capone et al.   Nature Geoscience

Molecular and Photosynthetic Responses to Prolonged Darkness and Subsequent Acclimation to Re-Illumination in the Diatom Phaeodactylum tricornutum

(2013) Marianne Nymark et al.   PLoS One

Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana

(2013) J. Ashworth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic basis for coral resilience to climate change

(2013) Daniel J. Barshis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Response of biological production and air–sea CO2 fluxes to upwelling intensification in the California and Canary Current Systems

(2012) Zouhair Lachkar et al.   JOURNAL OF MARINE SYSTEMS

Interactions between Diatoms and Bacteria

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Pseudo-nitzschia (Bacillariophyceae) species, domoic acid and amnesic shellfish poisoning: revisiting previous paradigms

(2012) Aurélie Lelong et al.   PHYCOLOGIA

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

Phytoplankton succession and nitrogen utilization during the development of an upwelling bloom

(2011) SE Fawcett et al.   MARINE ECOLOGY PROGRESS SERIES

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

(2011) Andrew E. Allen et al.   NATURE

Blue and Red Light-Induced Germination of Resting Spores in the Red-Tide Diatom Leptocylindrus danicus†

(2011) Tomoyuki Shikata et al.   PHOTOCHEMISTRY AND PHOTOBIOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Biogeochemical responses to late-winter storms in the Sargasso Sea, II: Increased rates of biogenic silica production and export

(2009) Jeffrey W. Krause et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Arginine and nitrogen storage

(2008) José L Llácer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

THE ROLE OF NITRIC OXIDE IN DIATOM ADHESION IN RELATION TO SUBSTRATUM PROPERTIES1

(2008) Stephanie E. M. Thompson et al.   JOURNAL OF PHYCOLOGY

Stress-activated Genomic Expression Changes Serve a Preparative Role for Impending Stress in Yeast

(2008) David B. Berry et al.   MOLECULAR BIOLOGY OF THE CELL

Ferritin is used for iron storage in bloom-forming marine pennate diatoms

(2008) Adrian Marchetti et al.   NATURE

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

Fission Yeast Pot1-Tpp1 Protects Telomeres and Regulates Telomere Length

(2008) T. Miyoshi et al.   SCIENCE