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.


Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations.
Environmental microbiology. 2022-10-12;
PMID: 36222155
Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region.
Nature communications. 2022-05-04; 13.1: 2448.
PMID: 35508497
Adaptive responses of marine diatoms to zinc scarcity and ecological implications.
Nature communications. 2022-04-14; 13.1: 1995.
PMID: 35422102
Domoic acid biosynthesis in the red alga Chondria armata suggests a complex evolutionary history for toxin production.
Proceedings of the National Academy of Sciences of the United States of America. 2022-02-08; 119.6:
PMID: 35110408
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.
The New phytologist. 2022-02-01; 233.4: 1797-1812.
PMID: 34882804
Blowin' in the wind: Dispersal, structure, and metacommunity dynamics of aeolian diatoms in the McMurdo Sound region, Antarctica.
Journal of phycology. 2022-02-01; 58.1: 36-54.
PMID: 34817069
Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom.
The ISME journal. 2022-02-01; 16.2: 569-579.
PMID: 34482372
Proteomic analysis of metabolic pathways supports chloroplast-mitochondria cross-talk in a Cu-limited diatom.
Plant direct. 2022-01-20; 6.1: e376.
PMID: 35079683
Relating sinking and suspended microbial communities in the California Current Ecosystem: digestion resistance and the contributions of phytoplankton taxa to export.
Environmental microbiology. 2021-11-01; 23.11: 6734-6748.
PMID: 34431195
Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes.
mSystems. 2021-08-31; 6.4: e0057121.
PMID: 34227831
Cellular costs underpin micronutrient limitation in phytoplankton.
Science advances. 2021-08-06; 7.32:
PMID: 34362734
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom.
Scientific reports. 2021-08-02; 11.1: 15592.
PMID: 34341414
Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean.
Proceedings of the National Academy of Sciences of the United States of America. 2021-07-27; 118.30:
PMID: 34301906
Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway.
eLife. 2021-02-16; 10.
PMID: 33591270
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean.
Nature microbiology. 2021-02-01; 6.2: 173-186.
PMID: 33398100
Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle.
Science robotics. 2020-11-25; 5.48:
PMID: 33239321
Mitochondrial fatty acid β-oxidation is required for storage-lipid catabolism in a marine diatom.
The New phytologist. 2020-11-01; 228.3: 946-958.
PMID: 32535932
Common origin of ornithine-urea cycle in opisthokonts and stramenopiles.
Scientific reports. 2020-10-07; 10.1: 16687.
PMID: 33028894
The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom.
Biology. 2020-07-06; 9.7:
PMID: 32640597
Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location.
Molecular ecology. 2020-06-24; 29.11: 2080-2093.
PMID: 32578266
Comparative transcriptomics of toxin synthesis genes between the non-toxin producing dinoflagellate Cochlodinium polykrikoides and toxigenic Alexandrium pacificum.
Harmful algae. 2020-03-10; 93.101777.
PMID: 32307068
Reduction-dependent siderophore assimilation in a model pennate diatom.
Proceedings of the National Academy of Sciences of the United States of America. 2019-11-19; 116.47: 23609-23617.
PMID: 31685631
Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.
Nature communications. 2019-10-07; 10.1: 4552.
PMID: 31591397
Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators.
Nature communications. 2019-08-08; 10.1: 3582.
PMID: 31395884
Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum.
The New phytologist. 2019-05-01; 222.3: 1364-1379.
PMID: 30636322
Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom.
Science (New York, N.Y.). 2018-09-28; 361.6409: 1356-1358.
PMID: 30262498
Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom.
The Plant cell. 2017-08-01; 29.8: 2047-2070.
PMID: 28765511
Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation.
PLoS genetics. 2017-03-29; 13.3: e1006688.
PMID: 28355217
Probing the evolution, ecology and physiology of marine protists using transcriptomics.
Nature reviews. Microbiology. 2017-01-01; 15.1: 6-20.
PMID: 27867198
Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation.
PLoS genetics. 2016-12-01; 12.12: e1006490.
PMID: 27973599
Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana.
The New phytologist. 2016-05-01; 210.3: 890-904.
PMID: 26844818
Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype.
Biotechnology for biofuels. 2016-01-01; 9.258.
PMID: 27933100
Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume.
PloS one. 2016-01-01; 11.3: e0160929.
PMID: 27598790
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities.
The ISME journal. 2015-05-01; 9.5: 1076-92.
PMID: 25333462
A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake.
Current biology : CB. 2015-02-02; 25.3: 364-71.
PMID: 25557662
Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae.
Molecular phylogenetics and evolution. 2014-02-01; 71.36-40.
PMID: 24216019
Assembly of eukaryotic algal chromosomes in yeast.
Journal of biological engineering. 2013-12-10; 7.1: 30.
PMID: 24325901
Dissolved and particulate trace metal micronutrients under the McMurdo Sound seasonal sea ice: basal sea ice communities as a capacitor for iron.
Frontiers in chemistry. 2013-10-30; 1.25.
PMID: 24790953
Lineage specific gene family enrichment at the microscale in marine systems.
Current opinion in microbiology. 2013-10-01; 16.5: 605-17.
PMID: 24377115
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.
Proceedings of the National Academy of Sciences of the United States of America. 2013-06-25; 110.26: E2390-9.
PMID: 23754396
Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season.
The New phytologist. 2013-04-01; 198.2: 398-407.
PMID: 23488966
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum.
Nature communications. 2013-01-01; 4.2091.
PMID: 23820484
Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem.
Frontiers in microbiology. 2013-01-01; 4.120.
PMID: 23750156
Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana.
BMC genomics. 2012-09-20; 13.499.
PMID: 22994549
Global biogeography of SAR11 marine bacteria.
Molecular systems biology. 2012-07-17; 8.595.
PMID: 22806143
Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic.
The ISME journal. 2012-07-01; 6.7: 1403-14.
PMID: 22278668
Leveraging metabolomics for functional investigations in sequenced marine diatoms.
Trends in plant science. 2012-07-01; 17.7: 395-403.
PMID: 22465020
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. 2012-06-26; 109.26: E1762-71.
PMID: 22652568
Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability.
Proceedings of the National Academy of Sciences of the United States of America. 2012-02-07; 109.6: E317-25.
PMID: 22308424
Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms.
Molecular biology and evolution. 2012-01-01; 29.1: 367-79.
PMID: 21903677
Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton.
Frontiers in microbiology. 2012-01-01; 3.375.
PMID: 23091473
Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana.
Photosynthesis research. 2011-09-01; 109.1-3: 205-21.
PMID: 21365259
Evolution and metabolic significance of the urea cycle in photosynthetic diatoms.
Nature. 2011-05-12; 473.7346: 203-7.
PMID: 21562560
Efficiency of the CO2-concentrating mechanism of diatoms.
Proceedings of the National Academy of Sciences of the United States of America. 2011-03-08; 108.10: 3830-7.
PMID: 21321195
Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana.
PloS one. 2011-01-01; 6.12: e22870.
PMID: 21857960
The voyage of the microbial eukaryote.
Current opinion in microbiology. 2010-10-01; 13.5: 652-60.
PMID: 20832353
Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton.
Proceedings of the National Academy of Sciences of the United States of America. 2010-08-17; 107.33: 14679-84.
PMID: 20668244
Digital expression profiling of novel diatom transcripts provides insight into their biological functions.
Genome biology. 2010-01-01; 11.11: R85.
PMID: 20738856
An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms.
Current opinion in plant biology. 2006-06-01; 9.3: 264-73.
PMID: 16603409
Diatoms Have Found a Way to Pirate Bacterial Iron Sources
Domoic Acid Decoded: Scientists Discover Genetic Basis for How Harmful Algal Blooms Become Toxic
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Domoic Acid Decoded: Scientists Discover Genetic Basis for How Harmful Algal Blooms Become Toxic

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