Publications

• Jallet, D., Xing, D., Hughes, A., Moosburner, M., Simmons, M. P., Allen, A. E., & Peers, G. (2020). Mitochondrial fatty acid β-oxidation is required for storage lipid catabolism in a marine diatom. New Phytologist. doi: 10.1111/nph.16744
• Schulhof, M. A., Allen, A. E., Allen, E. E., Mladenov, N., McCrow, J. P., Jones, N. T., … Shurin, J. B. (2020). Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location. Molecular Ecology. doi: 10.1111/mec.15469
• Tan, M. H., Smith, S. R., Hixson, K. K., Tan, J., McCarthy, J. K., Kustka, A. B., & Allen, A. E. (2020). The importance of protein phosphorylation for signaling and metabolism in response to diel light cycling and nutrient availability in a marine diatom. Biology, 9(7), 155. doi: 10.3390/biology9070155
• Faktorova, D., Nisbet, R. E. R., Robledo, J. A. F., Casacuberta, E., Sudek, L., Allen, A. E., … Lukes, J. (2020). Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods. doi: 10.1038/s41592-020-0796-x
• Wang, H., Guo, R. Y., Lim, W. A., Allen, A. E., & Ki, J. S. (2020). Comparative transcriptomics of toxin synthesis genes between the non-toxin producing dinoflagellate Cochlodinium polykrikoides and toxigenic Alexandrium pacificum. Harmful Algae, 93(101777). doi: 10.1016/j.hal.2020.101777
• Krause, J. W., Brzezinski, M. A., Largier, J. L., McNair, H. M., Maniscalco, M., Bidle, K. D., … Thamatrakoln, K. (2020). The interaction of physical and biological factors drives phytoplankton spatial distribution in the northern California Current. Limnology and Oceanography. doi: 10.1002/lno.11431
• Moosburner, M. A., Gholami, P., McCarthy, J. K., Tan, M., Bielinski, V. A., & Allen, A. E. (2020). Multiplexed knockouts in the model diatom phaeodactylum by episomal delivery of a selectable Cas9. Frontiers in Microbiology, 11(5). doi: 10.3389/fmicb.2020.00005

2019

• Stephens, B. M., Wankel, S. D., Beman, J. M., Rabines, A. J., Allen, A. E., & Aluwihare, L. I. (2019). Euphotic zone nitrification in the California Current Ecosystem. Limnology and Oceanography. doi: 10.1002/lno.11348
• Coale, T. H., Moosburner, M., Horak, A., Obornik, M., Barbeau, K. A., & Allen, A. E. (2019). Reduction-dependent siderophore assimilation in a model pennate diatom. Proceedings of the National Academy of Sciences of the United States of America, 116(47), 23609-23617. doi: 10.1073/pnas.1907234116
• Spackeen, J. L., Sipler, R. E., Bertrand, E. M., Xu, K., McQuaid, J. B., Walworth, N. G., … Bronk, D. A. (2019). Impact of temperature, CO2, and iron on nutrient uptake by a late-season microbial community from the Ross Sea, Antarctica. Aquatic Microbial Ecology, 82(2), 145-159. doi: 10.3354/ame01886
• Smith, S. R., Dupont, C. L., McCarthy, J. K., Broddrick, J. T., Oborník, M., Horák, A., … Allen, A. E. (2019). Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom. Nature Communications, 10(1), 4552. doi: 10.1038/s41467-019-12407-y
• Wu, M., McCain, J. S. P., Rowland, E., Middag, R., Sandgren, M., Allen, A. E., & Bertrand, E. M. (2019). Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators. Nature Communications, 10(1), 3582. doi: 10.1038/s41467-019-11426-z
• Kolody, B. C., McCrow, J. P., Allen, L. Z., Aylward, F. O., Fontanez, K. M., Moustafa, A., … Allen, A. E. (2019). Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. The ISME Journal. doi: 10.1038/s41396-019-0472-2
• Kranzler, C. F., Krause, J. W., Brzezinski, M. A., Edwards, B. R., Biggs, W. P., Maniscalco, M., … Thamatrakoln, K. (2019). Silicon limitation facilitates virus infection and mortality of marine diatoms. Nature Microbiology. doi: 10.1038/s41564-019-0502-x
• Murik, O., Tirichine, L., Prihoda, J., Thomas, Y., Araujo, W. L., Allen, A. E., … Bowler, C. (2019). Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom. New Phytologist, 221(3), 1303-1316. doi: 10.1111/nph.15479
• Broddrick, J. T., Du, N., Smith, S. R., Tsuji, Y., Jallet, D., Ware, M. A., … Allen, A. E. (2019). Cross-compartment metaoblic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum. New Phytol. doi: 10.1111/nph.15685
• Goodwin, K. D., Muller-Karger, F. E., Djurhuus, A., Zeigler Allen, L., Allen, A. E., McCrow, J. P., & Canonico Hyde, G. (2019). Chapter 32 – Molecular Approaches for an Operational Marine Biodiversity Observation Network. World Seas: an Environmental Evaluation (Second Edition) (pp. 613-631). : Academic Press. doi: 10.1016/B978-0-12-805052-1.00032-2

2018

• Hogle, S. L., Dupont, C. L., Hopkinson, B. M., King, A. L., Buck, K. N., Roe, K. L., … Barbeau, K. A. (2018). Pervasive iron limitation at subsurface chlorophyll maxima of the California Current. Proceedings of the National Academy of Sciences of the United States of America, 115(52), 13300-13305. doi: 10.1073/pnas.1813192115
• Brunson, J. K., McKinnie, S. M. K., Chekan, J. R., McCrow, J. P., Miles, Z. D., Bertrand, E. M., … Moore, B. S. (2018). Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom. Science, 361(6409), 1356-+. doi: 10.1126/science.aau0382
• Bender, S. J., Moran, D. M., McIlvin, M. R., Zheng, H., McCrow, J. P., Badger, J., … Saito, M. A. (2018). Colony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron biogeochemistry. Biogeosciences, 15(16), 4923-4942. doi: 10.5194/bg-15-4923-2018
• Spackeen, J. L., Bronk, D. A., Sipler, R. E., Bertrand, E. M., Hutchins, D. A., & Allen, A. E. (2018). Stoichiometric N:P Ratios, Temperature, and Iron Impact Carbon and Nitrogen Uptake by Ross Sea Microbial Communities. Journal of Geophysical Research: Biogeosciences. doi: 10.1029/2017JG004316
• Du, N., Gholami, P., Kline, D. I., DuPont, C. L., Dickson, A. G., Mendola, D., … Mitchell, B. G. (2018). Simultaneous quantum yield measurements of carbon uptake and oxygen evolution in microalgal cultures. Plos One, 13(6). doi: 10.1371/journal.pone.0199125
• Rastogi, A., Maheswari, U., Dorrell, R. G., Vieira, F. R. J., Maumus, F., Kustka, A., … Tirichine, L. (2018). Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms. Scientific Reports, 8(1), 4834. doi: 10.1038/s41598-018-23106-x
• McQuaid, J. B., Kustka, A. B., Oborník, M., Horák, A., McCrow, J. P., Karas, B. J., … Allen, A. E. (2018). Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms. Nature, 555, 534. doi: 10.1038/nature25982
• Berg, C., Dupont, C. L., Asplund-Samuelsson, J., Celepli, N. A., Eiler, A., Allen, A. E., … Ininbergs, K. (2018). Dissection of microbial community functions during a cyanobacterial bloom in the Baltic Sea via metatranscriptomics. Frontiers in Marine Science, 5(55). doi: 10.3389/fmars.2018.00055
• Tatters, A. O., Schnetzer, A., Xu, K., Walworth, N. G., Fu, F., Spackeen, J. L., … Hutchins, D. A. (2018). Interactive effects of temperature, CO2 and nitrogen source on a coastal California diatom assemblage. Journal of Plankton Research, 40(2), 151-164. doi: 10.1093/plankt/fbx074

2017

• Caron, D. A., Alexander, H., Allen, A. E., Archibald, J. M., Armbrust, E. V., Bachy, C., … Worden, A. Z. (2017). Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat Rev Micro, 15(1), 6-20. doi: 10.1038/nrmicro.2016.160
• Spackeen, J. L., Sipler, R. E., Xu, K., Tatters, A. O., Walworth, N. G., Bertrand, E. M., … Bronk, D. A. (2017). Interactive effects of elevated temperature and CO2 on nitrate, urea, and dissolved inorganic carbon uptake by a coastal California, USA, microbial community. Marine Ecology Progress Series, 577, 49-65. doi: 10.3354/meps12243
• McCarthy, J. K., Smith, S. R., McCrow, J. P., Tan, M., Zheng, H., Beeri, K., … Allen, A. E. (2017). Nitrate reductase knockout uncouples nitrate transport from nitrate assimilation and drives repartitioning of carbon flux in a model pennate diatom. Plant Cell, 29(8), 2047-2070. doi: 10.1105/tpc.16.00910
• Hippmann, A. A., Schuback, N., Moon, K., McCrow, J. P., Allen, A. E., Foster, L. J., … Maldonado, M. T. (2017). Contrasting effects of copper limitation on the photosynthetic apparatus in two strains of the open ocean diatom Thalassiosira oceanica. PLOS ONE, 12(8), e0181753. doi: 10.1371/journal.pone.0181753
• Diner, R. E., Noddings, C. M., Lian, N. C., Kang, A. K., McQuaid, J. B., Jablanovic, J., … Weyman, P. D. (2017). Diatom centromeres suggest a mechanism for nuclear DNA acquisition. Proceedings of the National Academy of Sciences, 114(29), E6015-E6024. doi: 10.1073/pnas.1700764114
• Lee, Z. M., Poret-Peterson, A. T., Siefert, J. L., Kaul, D., Moustafa, A., Allen, A. E., … Elser, J. J. (2017). Nutrient stoichiometry shapes microbial community structure in an evaporitic shallow pond. Frontiers in Microbiology, 8(949). doi: 10.3389/fmicb.2017.00949
• Levering, J., Dupont, C. L., Allen, A. E., Palsson, B. O., & Zengler, K. (2017). Integrated regulatory and metabolic networks of the marine diatom Phaeodactylum tricornutum predict the response to rising CO2 levels. mSystems, 2. doi: 10.1128/mSystems.00142-16
• Zeigler Allen, L., McCrow, J. P., Ininbergs, K., Dupont, C. L., Badger, J. H., Hoffman, J. M., … Venter, J. C. (2017). The Baltic Sea virome: Diversity and transcriptional activity of DNA and RNA viruses. mSystems, 2. doi: 10.1128/mSystems.00125-16
• Mock, T., Otillar, R. P., Strauss, J., McMullan, M., Paajanen, P., Schmutz, J., … Grigoriev, I. V. (2017). Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature, 1-5. doi: 10.1038/nature20803

2016

• Traller, J. C., Cokus, S. J., Lopez, D. A., Gaidarenko, O., Smith, S. R., McCrow, J. P., … Hildebrand, M. (2016). Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnology for Biofuels, 9(1), 258. doi: 10.1186/s13068-016-0670-3
• Kharbush, J. J., Allen, A. E., Moustafa, A., Dorrestein, P. C., & Aluwihare, L. I. (2016). Intact polar diacylglycerol biomarker lipids isolated from suspended particulate organic matter accumulating in an ultraoligotrophic water column. Organic Geochemistry, 100, 29-41. doi: 10.1016/j.orggeochem.2016.07.008
• Zielinski, B. L., Allen, A. E., Carpenter, E. J., Coles, V. J., Crump, B. C., Doherty, M., … Paul, J. H. (2016). Patterns of transcript abundance of eukaryotic biogeochemically-relevant genes in the Amazon River plume. PLoS One, 11(9), e0160929. doi: 10.1371/journal.pone.0160929
• Diner, R. E., Bielinski, V. A., Dupont, C. L., Allen, A. E., & Weyman, P. D. (2016). Refinement of the diatom episome maintenance sequence and improvement of conjugation-based DNA delivery methods. Frontiers in Bioengineering and Biotechnology, 4(65). doi: 10.3389/fbioe.2016.00065
• Asplund-Samuelsson, J., Sundh, J., Dupont, C. L., Allen, A. E., McCrow, J. P., Celepli, N. A., … Ekman, M. (2016). Diversity and expression of bacterial metacaspases in an aquatic ecosystem. Frontiers in Microbiology, 7(1043). doi: 10.3389/fmicb.2016.01043
• Diner, R. E., Schwenck, S. M., McCrow, J. P., Zheng, H., & Allen, A. E. (2016). Genetic manipulation of competition for nitrate between heterotrophic bacteria and diatoms. Frontiers in Microbiology, 7. doi: 10.3389/fmicb.2016.00880
• DÌez, B., Nylander, J. A. A., Ininbergs, K., Dupont, C. L., Allen, A. E., Yooseph, S., … Bergman, B. (2016). Metagenomic analysis of the Indian Ocean picocyanobacterial community: Structure, potential function and evolution. PLoS ONE, 11(5), e0155757. doi: 10.1371/journal.pone.0155757
• Levering, J., Broddrick, J., Dupont, C. L., Peers, G., Beeri, K., Mayers, J., … Zengler, K. (2016). Genome-scale model reveals metabolic basis of biomass partitioning in a model diatom. Plos One, 11(5). doi: 10.1371/journal.pone.0155038
• Smith, S. R., Glé, C., Abbriano, R. M., Traller, J. C., Davis, A., Trentacoste, E., … Hildebrand, M. (2016). Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana. New Phytologist. doi: 10.1111/nph.13843
• Smith, S. R., Gillard, J. T. F., Kustka, A. B., McCrow, J. P., Badger, J. H., Zheng, H., … Allen, A. E. (2016). Transcriptional orchestration of the global cellular response of a model pennate diatom to diel light cycling under iron limitation. PLOS Genetics, 12(12), e1006490. doi: 10.1371/journal.pgen.1006490

2015

• Dupont, C. L., McCrow, J. P., Valas, R., Moustafa, A., Walworth, N., Goodenough, U., … Allen, A. E. (2015). Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME J, 9(5), 1076-1092. doi: 10.1038/ismej.2014.198
• Weyman, P. D., Beeri, K., Lefebvre, S. C., Rivera, J., McCarthy, J. K., Heuberger, A. L., … Dupont, C. L. (2015). Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis. Plant Biotechnology Journal, 13(4), 460-470. doi: 10.1111/pbi.12254
• Bertrand, E. M., McCrow, J. P., Moustafa, A., Zheng, H., McQuaid, J. B., Delmont, T. O., … Allen, A. E. (2015). Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge. Proceedings of the National Academy of Sciences of the United States of America, 112(32), 9938-9943. doi: 10.1073/pnas.1501615112
• Llewellyn, C. A., Sommer, U., Dupont, C. L., Allen, A. E., & Viant, M. R. (2015). Using community metabolomics as a new approach to discriminate marine microbial particulate organic matter in the western English Channel. Progress in Oceanography. doi: 10.1016/j.pocean.2015.04.022
• Veluchamy, A., Rastogi, A., Lin, X., Lombard, B., Murik, O., Thomas, Y., … Tirichine, L. (2015). An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum. Genome Biol, 16(1), 102. doi: 10.1186/s13059-015-0671-8
• Karas, B. J., Diner, R. E., Lefebvre, S. C., McQuaid, J., Phillips, A. P. R., Noddings, C. M., … Weyman, P. D. (2015). Designer diatom episomes delivered by bacterial conjugation. Nat Commun, 6. doi: 10.1038/ncomms7925
• Morrissey, J., Sutak, R., Paz-Yepes, J., Tanaka, A., Moustafa, A., Veluchamy, A., … Bowler, C. (2015). A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake. Current Biology, 25(3), 364-371. doi: 10.1016/j.cub.2014.12.004
• Paerl, R. W., Bertrand, E. M., Allen, A. E., Palenik, B., & Azam, F. (2015). Vitamin B1 ecophysiology of marine picoeukaryotic algae: Strain-specific differences and a new role for bacteria in vitamin cycling. Limnology and Oceanography, 60(1), 215-228. doi: 10.1002/lno.10009

2014

• Smith, D. R., Arrigo, K. R., Alderkamp, A., & Allen, A. E. (2014). Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae. Molecular Phylogenetics and Evolution, 71, 36-40. doi: 10.1016/j.ympev.2013.10.018
• Dupont, C. L., Larsson, J., Yooseph, S., Ininbergs, K., Goll, J., Asplund-Samuelsson, J., … Bergman, B. (2014). Functional tradeoffs underpin salinity-driven divergence in microbial community composition. Plos One, 9(2). doi: 10.1371/journal.pone.0089549

2013

• Allen, A. E., Allen, L. Z., & McCrow, J. P. (2013). Lineage specific gene family enrichment at the microscale in marine systems. Current Opinion in Microbiology, 16(5), 605-617. doi: 10.1016/j.mib.2013.10.001
• Noble, A. E., Saito, M. A., Moran, D. M., & Allen, A. (2013). 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, 1. doi: 10.3389/fchem.2013.00025
• Karas, B., Molparia, B., Jablanovic, J., Hermann, W., Lin, Y., Dupont, C., … Weyman, P. (2013). Assembly of eukaryotic algal chromosomes in yeast. Journal of Biological Engineering, 7(1), 30.
• Read, B. A., Kegel, J., Klute, M. J., Kuo, A., Lefebvre, S. C., Maumus, F., … Annotation, E. H. (2013). Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature, 499(7457), 209-213. doi: 10.1038/Nature12221
• Veluchamy, A., Lin, X., Maumus, F., Rivarola, M., Bhavsar, J., Creasy, T., … Tirichine, L. (2013). Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum. Nature Communications, 4. doi: 10.1038/Ncomms3091
• Bertrand, E. M., Moran, D. M., McIlvin, M. R., Hoffman, J. M., Allen, A. E., & Saito, M. A. (2013). Methionine synthase interreplacement in diatom cultures and communities: Implications for the persistence of B-12 use by eukaryotic phytoplankton. Limnology and Oceanography, 58(4), 1431-1450. doi: 10.4319/Lo.2013.58.4.1431
• McLean, J. S., Lombardo, M., Badger, J. H., Edlund, A., Novotny, M., Yee-Greenbaum, J., … Lasken, R. S. (2013). Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proceedings of the National Academy of Sciences, 110(26), E2390-E2399. doi: 10.1073/pnas.1219809110
• Smith, M. W., Allen, L. Z., Allen, A. E., Herfort, L., & Simon, H. M. (2013). Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Frontiers in Microbiology, 4. doi: 10.3389/Fmicb.2013.00120
• Konotchick, T., Dupont, C. L., Valas, R. E., Badger, J. H., & Allen, A. E. (2013). Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season. New Phytologist, 198(2), 398-407. doi: 10.1111/Nph.12160

2012

• Bertrand, E. M., & Allen, A. E. (2012). Influence of Vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton. Frontiers in Microbiology, 3. doi: 10.3389/fmicb.2012.00375
• Shrestha, R. P., Tesson, B., Norden-Krichmar, T., Federowicz, S., Hildebrand, M., & Allen, A. E. (2012). Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana. BMC Genomics, 13.
• Allen, L. Z., Allen, E. E., Badger, J. H., McCrow, J. P., Paulsen, I. T., Elbourne, L. D. H., … Allen, A. E. (2012). Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME Journal, 6(7), 1403-1414. doi: 10.1038/ismej.2011.201
• Marchetti, A., Schruth, D. M., Durkin, C. A., Parker, M. S., Kodner, R. B., Berthiaume, C. T., … Armbrust, E. V. (2012). 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, 109(6), E317-E325. doi: 10.1073/Pnas.1118408109
• Allen, A. E., Moustafa, A., Montsant, A., Eckert, A., Kroth, P. G., & Bowler, C. (2012). Evolution and Functional Diversification of Fructose Bisphosphate Aldolase Genes in Photosynthetic Marine Diatoms. Molecular Biology and Evolution, 29(1), 367-379. doi: 10.1093/Molbev/Msr223
• Fernie, A. R., Obata, T., Allen, A. E., Araújo, W. L., & Bowler, C. (2012). Leveraging metabolomics for functional investigations in sequenced marine diatoms. Trends in Plant Science, 17(7), 395-403. doi: 10.1016/j.tplants.2012.02.005
• Bertrand, E. M., Allen, A. E., Dupont, C. L., Norden-Krichmar, T. M., Bai, J., Valas, R. E., & Saito, M. A. (2012). Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein. Proceedings of the National Academy of Sciences, 109(26), E1762–E1771. doi: 10.1073/pnas.1201731109
• Loper, J. E., Hassan, K. A., Mavrodi, D. V., Davis, E. W., Lim, C. K., Shaffer, B. T., … Paulsen, I. T. (2012). Comparative genomics of plant-associated Pseudomonas spp.: Insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet, 8(7), e1002784. doi: 10.1371/journal.pgen.1002784
• Cock, J. M., Sterck, L., Ahmed, S., Allen, A. E., Amoutzias, G., Anthouard, V., … Wincker, P. (2012). Chapter Five – The ectocarpus genome and brown algal genomics: The ectocarpus genome consortium. Advances in Botanical Research (pp. 141-184). : Academic Press.
• Brown, M. V., Lauro, F. M., DeMaere, M. Z., Muir, L., Wilkins, D., Thomas, T., … Cavicchioli, R. (2012). Global biogeography of SAR11 marine bacteria. Molecular Systems Biology, 8(1). doi: 10.1038/msb.2012.28

2011

• Tachibana, M., Allen, A. E., Kikutani, S., Endo, Y., Bowler, C., & Matsuda, Y. (2011). Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana. Photosynthesis Research, 109(1-3), 205-221. doi: 10.1007/S11120-011-9634-4
• Norden-Krichmar, T. M., Allen, A. E., Gaasterland, T., & Hildebrand, M. (2011). Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana. Plos One, 6(8). doi: 10.1371/journal.pone.0022870
• Allen, A. E., Dupont, C. L., Obornik, M., Horak, A., Nunes-Nesi, A., McCrow, J. P., … Bowler, C. (2011). Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Nature, 473(7346), 203-+. doi: 10.1038/Nature10074
• Hopkinson, B. M., Dupont, C. L., Allen, A. E., & Morel, F. M. M. (2011). Efficiency of the CO2-concentrating mechanism of diatoms. Proceedings of the National Academy of Sciences of the United States of America, 108(10), 3830-3837. doi: 10.1073/Pnas.1018062108
• Worden, A. Z., Dupont, C., & Allen, A. E. (2011). Genomes of uncultured eukaryotes: sorting FACS from fiction. Genome Biology, 12(6). doi: 10.1186/Gb-2011-12-6-117

2010

• Yooseph, S., Nealson, K. H., Rusch, D. B., McCrow, J. P., Dupont, C. L., Kim, M., … Venter, J. C. (2010). Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature, 468(7320), 60-+. doi: 10.1038/Nature09530
• Worden, A. Z., & Allen, A. E. (2010). The voyage of the microbial eukaryote. Current Opinion in Microbiology, 13(5), 652-660. doi: 10.1016/J.Mib.2010.08.001
• Cuvelier, M. L., Allen, A. E., Monier, A., McCrow, J. P., Messie, M., Tringe, S. G., … Worden, A. Z. (2010). Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences of the United States of America, 107(33), 14679-14684. doi: 10.1073/Pnas.1001665107
• Cock, J. M., Sterck, L., Rouze, P., Scornet, D., Allen, A. E., Amoutzias, G., … Wincker, P. (2010). The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature, 465(7298), 617-621. doi: 10.1038/Nature09016
• Maheswari, U., Jabbari, K., Petit, J. L., Porcel, B. M., Allen, A. E., Cadoret, J. P., … Bowler, C. (2010). Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biology, 11(8). doi: 10.1186/Gb-2010-11-8-R85
• Bowler, C., Vardi, A., & Allen, A. E. (2010). Oceanographic and Biogeochemical Insights from Diatom Genomes. Annual Review of Marine Science, 2, 333-365. doi: 10.1146/Annurev-Marine-120308-081051

2009

• Maumus, F., Allen, A. E., Mhiri, C., Hu, H. H., Jabbari, K., Vardi, A., … Bowler, C. (2009). Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. Bmc Genomics, 10. doi: 10.1186/1471-2164-10-624
• Poretsky, R. S., Hewson, I., Sun, S. L., Allen, A. E., Zehr, J. P., & Moran, M. A. (2009). Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environmental Microbiology, 11(6), 1358-1375. doi: 10.1111/J.1462-2920.2008.01863.X
• Worden, A. Z., Lee, J. H., Mock, T., Rouze, P., Simmons, M. P., Aerts, A. L., … Grigoriev, I. V. (2009). Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas. Science, 324(5924), 268-272. doi: 10.1126/Science.1167222

2008

• Bowler, C., Allen, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., … Grigoriev, I. V. (2008). The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature, 456(7219), 239-244. doi: 10.1038/Nature07410
• Allen, A. E., LaRoche, J., Maheswari, U., Lommer, M., Schauer, N., Lopez, P. J., … Bowler, C. (2008). Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proceedings of the National Academy of Sciences of the United States of America, 105(30), 10438-10443. doi: 10.1073/Pnas.0711370105

2007

• Siaut, M., Heijde, M., Mangogna, M., Montsant, A., Coesel, S., Allen, A., … Bowler, C. (2007). Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene, 406(1-2), 23-35. doi: 10.1016/j.gene.2007.05.022
• Montsant, A., Allen, A. E., Coesel, S., De Martino, A., Falciatore, A., Mangogna, M., … Bowler, C. (2007). Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana. Journal of Phycology, 43(3), 585-604. doi: 10.1111/j.1529-8817.2007.00342.x
• Kustka, A. B., Allen, A. E., & Morel, F. M. M. (2007). Sequence analysis and transcriptional regulation of iron acquisition genes in two marine diatoms1. Journal of Phycology, 43(4), 715-729. doi: 10.1111/j.1529-8817.2007.00359.x
• Bowler, C., & Allen, A. (2007). The contribution of genomics to the understanding of algal evolution. Unravelling the algae: the past, present, and future of algal systematics. London, UK: CRC Press.

2006

• Maldonado, M. T., Allen, A. E., Chong, J. S., Lin, K., Leus, D., Karpenko, N., & Harris, S. L. (2006). Copper-dependent iron transport in coastal and oceanic diatoms. Limnology and Oceanography, 51(4), 1729-1743.
• Allen, A. E., Vardi, A., & Bowler, C. (2006). An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms. Current Opinion in Plant Biology, 9(3), 264-273. doi: 10.1016/J.Pbi.2006.03.013

2005

• Allen, A. E. (2005). Defining the molecular basis for energy balance in marine diatoms under fluctuating environmental conditions. Journal of Phycology, 41(6), 1073-1076. doi: 10.1111/J.1526-8817.2005.00156.X
• Allen, A. E., Booth, M. G., Verity, P. G., & Frischer, M. E. (2005). Influence of nitrate availability on the distribution and abundance of heterotrophic bacterial nitrate assimilation genes in the Barents Sea during summer. Aquatic Microbial Ecology, 39(3), 247-255. doi: 10.3354/Ame039247
• Lopez, P. J., Descles, J., Allen, A. E., & Bowler, C. (2005). Prospects in diatom research. Current Opinion in Biotechnology, 16(2), 180-186. doi: 10.1016/J.Copbio.2005.02.002
• Allen, A. E. (2005). Beyond sequence homology: Redundant ammonium transporters in a marine diatom are not functionally equivalent. Journal of Phycology, 41(1), 4-6. doi: 10.1111/J.0022-3646.2005.41101_2.X
• Allen, A. E., Ward, B. B., & Song, B. K. (2005). Characterization of diatom (Bacillariophyceae) nitrate reductase genes and their detection in marine phytoplankton communities. Journal of Phycology, 41(1), 95-104. doi: 10.1111/J.1529-8817.2005.04090.X

2004

• Armbrust, E. V., Berges, J. A., Bowler, C., Green, B. R., Martinez, D., Putnam, N. H., … Rokhsar, D. S. (2004). The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science, 306(5693), 79-86. doi: 10.1126/science.1101156

2002

• Verity, P. G., Wassmann, P., Frischer, M. E., Howard-Jones, M. H., & Allen, A. E. (2002). Grazing of phytoplankton by microzooplankton in the Barents Sea during early summer. Journal of Marine Systems, 38(1–2), 109-123. doi: 10.1016/S0924-7963(02)00172-0
• Allen, A. E., Howard-Jones, M. H., Booth, M. G., Frischer, M. E., Verity, P. G., Bronk, D. A., & Sanderson, M. P. (2002). Importance of heterotrophic bacterial assimilation of ammonium and nitrate in the Barents Sea during summer. Journal of Marine Systems, 38(1–2), 93-108. doi: 10.1016/S0924-7963(02)00171-9
• Howard-Jones, M. H., Ballard, V. D., Allen, A. E., Frischer, M. E., & Verity, P. G. (2002). Distribution of bacterial biomass and activity in the marginal ice zone of the central Barents Sea during summer. Journal of Marine Systems, 38(1–2), 77-91. doi: 10.1016/S0924-7963(02)00170-7

2001

• Allen, A. E., Booth, M. G., Frischer, M. E., Verity, P. G., Zehr, J. P., & Zani, S. (2001). Diversity and Detection of Nitrate Assimilation Genes in Marine Bacteria. Applied and Environmental Microbiology, 67(11), 5343-5348. doi: 10.1128/AEM.67.11.5343-5348.2001