Andrew E. Allen is a professor in the Microbial and Environmental Genomics Department. His research focus is related to genome biology, and comparative and functional genomics of eukaryotic marine phytoplankton. Other areas of interest include molecular microbial ecology and metagenomics of eukaryotic marine microbes and bacteria, molecular and genome evolution, chemical and biological oceanography, microbial metabolism, and bioinformatics. Primary areas of interest are based on understanding the molecular basis of carbon (C), nitrogen (N), and iron (Fe) assimilation and metabolism in marine phytoplankton populations as well as the evolution and ecological relevance of molecular and regulatory and signaling/sensing mechanisms that mediate acclimation responses to nutrient and abiotic stress and control biotic interactions. Various ongoing physiological and functional genomics based wet-lab, computational, metagenomic, and metatranscriptomic research projects are centered on addressing hypotheses related to controls on the diversity and activity of marine microorganisms.
Prior to joining JCVI, Dr. Allen was a postdoctoral fellow at the École Normale Supérieure in Paris, France and at Princeton University in the labs of Chris Bowler and Bess Ward where he worked on phytoplankton genomics. He received his PhD in Ecology from the University of Georgia under the direction of Marc Frischer and Peter Verity where he studied the molecular basis of nitrogen assimilation in marine bacteria. Dr. Allen earned his bachelor's degree in Biology and English from Vassar College.
Plant direct. 2022-12-26; 6.12: e472.
In vivo localization of iron starvation induced proteins under variable iron supplementation regimes in Phaeodactylum tricornutum
Environmental microbiology. 2022-11-01; 24.11: 5408-5424.
Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations
Nature communications. 2022-05-04; 13.1: 2448.
Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region
Nature communications. 2022-04-14; 13.1: 1995.
Adaptive responses of marine diatoms to zinc scarcity and ecological implications
Proceedings of the National Academy of Sciences of the United States of America. 2022-02-08; 119.6:
Domoic acid biosynthesis in the red alga Chondria armata suggests a complex evolutionary history for toxin production
The ISME journal. 2022-02-01; 16.2: 569-579.
Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom
The New phytologist. 2022-02-01; 233.4: 1797-1812.
Multiplexed CRISPR/Cas9 editing of the long-chain acyl-CoA synthetase family in the diatom Phaeodactylum tricornutum reveals that mitochondrial ptACSL3 is involved in the synthesis of storage lipids
Nature methods. 2022-02-01; 19.2: 134-136.
GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser
Journal of phycology. 2022-02-01; 58.1: 36-54.
Blowin' in the wind: Dispersal, structure, and metacommunity dynamics of aeolian diatoms in the McMurdo Sound region, Antarctica
Plant direct. 2022-01-20; 6.1: e376.
Proteomic analysis of metabolic pathways supports chloroplast-mitochondria cross-talk in a Cu-limited diatom
Environmental microbiology. 2021-11-01; 23.11: 6734-6748.
Relating sinking and suspended microbial communities in the California Current Ecosystem: digestion resistance and the contributions of phytoplankton taxa to export
mSystems. 2021-08-31; 6.4: e0057121.
Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
Science advances. 2021-08-06; 7.32:
Cellular costs underpin micronutrient limitation in phytoplankton
Scientific reports. 2021-08-02; 11.1: 15592.
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
Proceedings of the National Academy of Sciences of the United States of America. 2021-07-27; 118.30:
Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean
eLife. 2021-02-16; 10.
Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway
Nature microbiology. 2021-02-01; 6.2: 173-186.
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean
Science robotics. 2020-11-25; 5.48:
Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle
The New phytologist. 2020-11-01; 228.3: 946-958.
Mitochondrial fatty acid β-oxidation is required for storage-lipid catabolism in a marine diatom
Scientific reports. 2020-10-07; 10.1: 16687.
Common origin of ornithine-urea cycle in opisthokonts and stramenopiles
Biology. 2020-07-06; 9.7:
The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom
Molecular ecology. 2020-06-24; 29.11: 2080-2093.
Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location
Nature methods. 2020-05-01; 17.5: 551.
Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology
Nature methods. 2020-05-01; 17.5: 481-494.
Genetic tool development in marine protists: emerging model organisms for experimental cell biology
Harmful algae. 2020-03-10; 93.101777.
Comparative transcriptomics of toxin synthesis genes between the non-toxin producing dinoflagellate Cochlodinium polykrikoides and toxigenic Alexandrium pacificum
Proceedings of the National Academy of Sciences of the United States of America. 2019-11-19; 116.47: 23609-23617.
Reduction-dependent siderophore assimilation in a model pennate diatom
Nature communications. 2019-10-07; 10.1: 4552.
Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom
Nature communications. 2019-08-08; 10.1: 3582.
Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators
The New phytologist. 2019-05-01; 222.3: 1364-1379.
Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum
Science (New York, N.Y.). 2018-09-28; 361.6409: 1356-1358.
Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom
The Plant cell. 2017-08-01; 29.8: 2047-2070.
Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom
PLoS genetics. 2017-03-29; 13.3: e1006688.
Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
Nature reviews. Microbiology. 2017-01-01; 15.1: 6-20.
Probing the evolution, ecology and physiology of marine protists using transcriptomics
PLoS genetics. 2016-12-01; 12.12: e1006490.
Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
The New phytologist. 2016-05-01; 210.3: 890-904.
Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana
Biotechnology for biofuels. 2016-01-01; 9.258.
Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype
PloS one. 2016-01-01; 11.3: e0160929.
Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume
The ISME journal. 2015-05-01; 9.5: 1076-92.
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities
Nature communications. 2015-04-21; 6.6925.
Designer diatom episomes delivered by bacterial conjugation
Current biology : CB. 2015-02-02; 25.3: 364-71.
A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake
Molecular phylogenetics and evolution. 2014-02-01; 71.36-40.
Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae
Journal of biological engineering. 2013-12-10; 7.1: 30.
Assembly of eukaryotic algal chromosomes in yeast
Frontiers in chemistry. 2013-10-30; 1.25.
Dissolved and particulate trace metal micronutrients under the McMurdo Sound seasonal sea ice: basal sea ice communities as a capacitor for iron
Current opinion in microbiology. 2013-10-01; 16.5: 605-17.
Lineage specific gene family enrichment at the microscale in marine systems
Proceedings of the National Academy of Sciences of the United States of America. 2013-06-25; 110.26: E2390-9.
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
The New phytologist. 2013-04-01; 198.2: 398-407.
Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
Frontiers in microbiology. 2013-01-01; 4.120.
Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem
Nature communications. 2013-01-01; 4.2091.
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum
BMC genomics. 2012-09-20; 13.499.
Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana
Molecular systems biology. 2012-07-17; 8.595.
Global biogeography of SAR11 marine bacteria
The ISME journal. 2012-07-01; 6.7: 1403-14.
Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic
Trends in plant science. 2012-07-01; 17.7: 395-403.
Leveraging metabolomics for functional investigations in sequenced marine diatoms
Proceedings of the National Academy of Sciences of the United States of America. 2012-06-26; 109.26: E1762-71.
Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein
Proceedings of the National Academy of Sciences of the United States of America. 2012-02-07; 109.6: E317-25.
Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability
Molecular biology and evolution. 2012-01-01; 29.1: 367-79.
Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms
Frontiers in microbiology. 2012-01-01; 3.375.
Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton
Photosynthesis research. 2011-09-01; 109.1-3: 205-21.
Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana
Nature. 2011-05-12; 473.7346: 203-7.
Evolution and metabolic significance of the urea cycle in photosynthetic diatoms
Proceedings of the National Academy of Sciences of the United States of America. 2011-03-08; 108.10: 3830-7.
Efficiency of the CO2-concentrating mechanism of diatoms
PloS one. 2011-01-01; 6.12: e22870.
Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana
Nature. 2010-11-04; 468.7320: 60-6.
Genomic and functional adaptation in surface ocean planktonic prokaryotes
Current opinion in microbiology. 2010-10-01; 13.5: 652-60.
The voyage of the microbial eukaryote
Proceedings of the National Academy of Sciences of the United States of America. 2010-08-17; 107.33: 14679-84.
Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton
Nature. 2010-06-03; 465.7298: 617-21.
The Ectocarpus genome and the independent evolution of multicellularity in brown algae
Genome biology. 2010-01-01; 11.11: R85.
Digital expression profiling of novel diatom transcripts provides insight into their biological functions
Science (New York, N.Y.). 2009-04-10; 324.5924: 268-72.
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas
Current opinion in plant biology. 2006-06-01; 9.3: 264-73.
An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms
Science (New York, N.Y.). 2004-10-01; 306.5693: 79-86.
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism
Metagenomics Reports (METAREP) is an open source tool for high-performance comparative metagenomics.