JCVI: About / Bios / Andrew Allen
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Andrew Allen, Ph.D.
Associate Professor

Research Interests and Accomplishments

Andrew E. Allen is an Associate Professor in the Microbial and Environmental Genomics Department at JCVI. 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.

Select Publications

Dupont CL, McCrow JP, et al.
Genomes and Gene Expression Across Light and Productivity Gradients in Eastern Subtropical Pacific Microbial Communities.

The ISME Journal. 2015 May 01; 9: 1076-92.[more]

Morrissey J, Sutak R, et al.
A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake.

Current Biology : CB. 2015 Feb 02; 25: 364-71.[more]

Smith DR, Arrigo KR, et al.
Massive Difference in Synonymous Substitution Rates Among Mitochondrial, Plastid, and Nuclear Genes of Phaeocystis Algae.

Molecular Phylogenetics and Evolution. 2014 Feb 01; 71: 36-40.[more]

Allen AE, Allen LZ, et al.
Lineage Specific Gene Family Enrichment at the Microscale in Marine Systems.

Current Opinion in Microbiology. 2013 Oct 01; 16: 605-17.[more]

Veluchamy A, Lin X, et al.
Insights Into the Role of DNA Methylation in Diatoms by Genome-wide Profiling in Phaeodactylum Tricornutum.

Nature Communications. 2013 Sep 01; 4: 2091.[more]

Smith MW, Zeigler Allen L, et al.
Contrasting Genomic Properties of Free-living and Particle-attached Microbial Assemblages Within a Coastal Ecosystem.

Frontiers in Microbiology. 2013 Sep 01; 4: 120.[more]

Karas BJ, Molparia B, et al.
Assembly of Eukaryotic Algal Chromosomes in Yeast.

Journal of Biological Engineering. 2013 Jul 01; 7. : 30.[more]

Konotchick T, Dupont CL, et al.
Transcriptomic Analysis of Metabolic Function In the Giant Kelp, Macrocystis Pyrifera, Across Depth and Season.

The New Phytologist. 2013 Apr 01; 198: 398-407.[more]

Noble AE, Moran DM, et al.
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 Apr 01; 1: 25.[more]

Brown MV, Lauro FM, et al.
Global Biogeography of SAR11 Marine Bacteria.

Molecular Systems Biology. 2012 Sep 01; 8: 595.[more]

Shrestha RP, Tesson B, et al.
Whole Transcriptome Analysis of the Silicon Response of the Diatom Thalassiosira Pseudonana.

BMC Genomics. 2012 Sep 01; 13: 499.[more]

Bertrand EM, Allen AE
Influence of Vitamin B Auxotrophy on Nitrogen Metabolism in Eukaryotic Phytoplankton.

Frontiers in Microbiology. 2012 Sep 01; 3: 375.[more]

Zeigler Allen L, Allen EE, et al.
Influence of Nutrients and Currents on the Genomic Composition of Microbes Across an Upwelling Mosaic.

The ISME Journal. 2012 Jul 01; 6: 1403-14.[more]

Fernie AR, Obata T, et al.
Leveraging Metabolomics for Functional Investigations In Sequenced Marine Diatoms.

Trends in plant science. 2012 Jul 01; 17: 395-403.[more]

Bertrand EM, Allen AE, et al.
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 Jun 26; 109: E1762-71.[more]

Marchetti A, Schruth DM, et al.
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 Feb 07; 109: E317-25.[more]

Allen AE, Moustafa A, et al.
Evolution and Functional Diversification of Fructose Bisphosphate Aldolase Genes In Photosynthetic Marine Diatoms.

Molecular biology and evolution. 2012 Jan 01; 29: 367-79.[more]

Tachibana M, Allen AE, et al.
Localization of Putative Carbonic Anhydrases In Two Marine Diatoms, Phaeodactylum tricornutum and Thalassiosira Pseudonana.

Photosynthesis research. 2011 Sep 01; 109: 205-21.[more]

Allen, A. E., Dupont, C. L., et al.
Evolution and Metabolic Significance of the Urea Cycle In Photosynthetic Diatoms

Nature. 2011 May 12; 473(7346): 203-7.[more]

Hopkinson, B. M., Dupont, C. L., et al.
Efficiency of the CO2-concentrating Mechanism of Diatoms

Proc Natl Acad Sci U S A. 2011 Mar 08; 108(10): 3830-7.[more]

Norden-Krichmar TM, Allen AE, et al.
Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira Pseudonana.

PloS one. 2011 Jan 01; 6: e22870.[more]

Yooseph, S., Nealson, K. H., et al.
Genomic and Functional Adaptation In Surface Ocean Planktonic Prokaryotes

Nature. 2010 Nov 04; 468(7320): 60-6.[more]

Worden, A. Z., Allen, A. E.
The Voyage of the Microbial Eukaryote

Curr Opin Microbiol. 2010 Sep 08;[more]

Maheswari, U., Jabbari, K., et al.
Digital Expression Profiling of Novel Diatom Transcripts Provides Insight Into Their Biological Functions

Genome Biol. 2010 Aug 25; 11(8): R85.[more]

Cuvelier, M. L., Allen, A. E., et al.
Targeted Metagenomics and Ecology of Globally Important Uncultured Eukaryotic Phytoplankton

Proc Natl Acad Sci U S A. 2010 Jul 28; 107(33). : 14679-84.[more]

Cock, J. M., Sterck, L., et al.
The Ectocarpus Genome and the Independent Evolution of Multicellularity In Brown Algae

Nature. 2010 Jun 03; 465(7298): 617-21.[more]

Bowler, C., Verdi, A., Allen, A.E.
Oceanographic and Biogeochemical Insights from Diatom Genomes

Annual Review of Marine Sciences. 2009 Oct 07;[more]

Worden, A. Z., Lee, J. H., et al.
Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Science. 2009 Apr 10; 324(5924): 268-72.[more]

Allen, A. E., Vardi, A., et al.
An Ecological and Evolutionary Context for Integrated Nitrogen Metabolism and Related Signaling Pathways In Marine Diatoms

Curr Opin Plant Biol. 2006 Jun 01; 9(3): 264-73.[more]

Armbrust, E. V., Berges, J. A., et al.
The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism

Science. 2004 Oct 01; 306(5693): 79-86.[more]