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.


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
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
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
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
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
Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton.
Frontiers in microbiology. 2012-01-01; 3.375.
PMID: 23091473
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
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

Improving Algal Genetics for Biofuels and Biological Chemical Production

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Metagenomics Reports (METAREP) is an open source tool for high-performance comparative metagenomics.

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Engineering Diatoms to Optimize Production of Desired Products

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Assembly-Enabled Genome-Resolved Examinations of Microbiomes

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Diatoms Have Found a Way to Pirate Bacterial Iron Sources
Domoic Acid Decoded: Scientists Discover Genetic Basis for How Harmful Algal Blooms Become Toxic