List of works by Andrew E. Allen

A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake

scientific article published on 31 December 2014

Adaptive responses of marine diatoms to zinc scarcity and ecological implications

scientific article published on 14 April 2022

An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms

scientific article

An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum.

scientific article published on 20 May 2015

Assembly of eukaryotic algal chromosomes in yeast

scientific article

Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom.

scientific article published in September 2018

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

scientific article

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

scientific article published on 14 March 2018

Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana

scientific article (publication date: 2011)

Colony formation in <i>Phaeocystis antarctica</i>: connecting molecular mechanisms with iron biogeochemistry

scientific article published in 2018

Common origin of ornithine-urea cycle in opisthokonts and stramenopiles

scientific article published on 07 October 2020

Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions

scientific article

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

scientific article published on 18 January 2012

Comparative transcriptomics of toxin synthesis genes between the non-toxin producing dinoflagellate Cochlodinium polykrikoides and toxigenic Alexandrium pacificum

scientific article published on 10 March 2020

Contrasting effects of copper limitation on the photosynthetic apparatus in two strains of the open ocean diatom Thalassiosira oceanica.

scientific article published on 24 August 2017

Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem

scientific article published on 30 May 2013

Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

scientific article published on 29 March 2017

Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum

scientific article published on 14 February 2019

Designer diatom episomes delivered by bacterial conjugation

scientific article

Diatom centromeres suggest a mechanism for nuclear DNA acquisition.

scientific article published on 3 July 2017

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

scientific article published on 18 July 2019

Digital expression profiling of novel diatom transcripts provides insight into their biological functions

scientific article

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

scientific article published on 04 January 2021

Dissolved and particulate trace metal micronutrients under the McMurdo Sound seasonal sea ice: basal sea ice communities as a capacitor for iron

scientific article

Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem

scientific article published on 06 July 2016

Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom

scientific article published on 22 November 2018

Efficiency of the CO2-concentrating mechanism of diatoms

scientific article

Erratum: Corrigendum: Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

scholarly article published in Nature Communications

Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms

scientific article published on 8 September 2011

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

scientific article

Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom

scientific article published on 07 October 2019

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

scientific article published on 16 January 2017

Functional tradeoffs underpin salinity-driven divergence in microbial community composition

scientific article

GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

scientific article published on 03 December 2021

Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms

scientific article published on 09 June 2016

Genetic tool development in marine protists: emerging model organisms for experimental cell biology

scientific article published on 06 April 2020

Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype

scientific article

Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom

scientific article

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

scientific article published on 21 October 2014

Genomes of uncultured eukaryotes: sorting FACS from fiction

scientific article

Genomic and functional adaptation in surface ocean planktonic prokaryotes

scientific article

Global biogeography of SAR11 marine bacteria

scientific article

Hydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific Ocean

scientific article published in 2021

IDENTIFICATION AND COMPARATIVE GENOMIC ANALYSIS OF SIGNALING AND REGULATORY COMPONENTS IN THE DIATOMTHALASSIOSIRA PSEUDONANA

article

Impact of meltwater flow intensity on the spatiotemporal heterogeneity of microbial mats in the McMurdo Dry Valleys, Antarctica

scientific article published in 2023

Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis

scientific article published on 10 October 2014

Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein

scientific article

Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region

scientific article published in 2022

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

scientific article published on 26 January 2012

Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton

scientific article published on 19 October 2012

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

scientific article published in January 2013

Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels

scientific article

Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms.

scientific article published on 19 March 2018

Leveraging metabolomics for functional investigations in sequenced marine diatoms

scientific article published on 30 March 2012

Lineage specific gene family enrichment at the microscale in marine systems

scientific article published on October 2013

Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana

scientific article published on 2 March 2011

Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators

scientific article published on 08 August 2019

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution

scientific article

Mitochondrial fatty acid β-oxidation is required for storage lipid catabolism in a marine diatom

scientific article published on 14 June 2020

Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum

article

Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean

scientific article published in 2021

Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9

scientific article published on 28 January 2020

Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom

scientific article

Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond

scientific article published on 30 May 2017

Oceanographic and biogeochemical insights from diatom genomes

scientific article

Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume

scientific article

Pervasive iron limitation at subsurface chlorophyll maxima of the California Current

article published in the 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

scientific article

Potential impact of stress activated retrotransposons on genome evolution in a marine diatom

scientific article

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

scientific article published on 21 November 2016

Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics

scientific article published in 2023

Prospects in diatom research

scientific article

Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology

scientific article published on 15 April 2020

Publisher Correction: Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region

scientific article published in 2022

Reduction-dependent siderophore assimilation in a model pennate diatom

scientific article published on 04 November 2019

Refinement of the Diatom Episome Maintenance Sequence and Improvement of Conjugation-Based DNA Delivery Methods

scientific article published on 08 August 2016

Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle

scientific article published on 01 November 2020

Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location

scientific article published on 24 June 2020

Silicon limitation facilitates virus infection and mortality of marine diatoms

scientific article published on 15 July 2019

Simultaneous quantum yield measurements of carbon uptake and oxygen evolution in microalgal cultures.

scientific article published on 19 June 2018

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

scientific article

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses

scientific article

The Ectocarpus Genome and Brown Algal Genomics

article published in 2012

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

scientific article

The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism

scientific article

The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom

scientific article published on 06 July 2020

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

scientific article

The voyage of the microbial eukaryote

scientific article

Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana

scientific article

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation.

scientific article

Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season

scientific article (publication date: April 2013)

Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana

scientific article

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

scholarly article

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