A.E Allen on Google Scholar

A.E. Allen on ResearchGate (PDFs for all publications)

A.E Allen on Scripps Scholar

Lampe, R. H., Coale, T. H., McQuaid, J. B., & Allen, A. E. (2024). Molecular Mechanisms for Iron Uptake and Homeostasis in Marine Eukaryotic Phytoplankton. Annual Review of Microbiology, 78(1), 213–232. https://doi.org/10.1146/annurev-micro-041222-023252
Brunson, J. K., Thukral, M., Ryan, J. P., Anderson, C. R., Kolody, B. C., James, C. C., Chavez, F. P., Leaw, C. P., Rabines, A. J., Venepally, P., Fussy, Z., Zheng, H., Kudela, R. M., Smith, G. J., Moore, B. S., & Allen, A. E. (2024). Molecular forecasting of domoic acid during a pervasive toxic diatom bloom. Proceedings of the National Academy of Sciences, 121(40). https://doi.org/10.1073/pnas.2319177121
James, C. C., Allen, A. E., Lampe, R. H., Rabines, A., & Barton, A. D. (2024). Endemic, cosmopolitan, and generalist taxa and their habitat affinities within a coastal marine microbiome. Scientific Reports, 14(1), 22408. https://doi.org/10.1038/s41598-024-69991-3
Peña-Montenegro, T. D., Kleindienst, S., Allen, A. E., Eren, A. M., McCrow, J. P., Arnold, J., & Joye, S. B. (2024). Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant. Applied and Environmental Microbiology, 90(8), e01083-24. https://doi.org/10.1128/aem.01083-24
Zhu, J., Li, S., Chen, W., Xu, X., Wang, X., Wang, X., Han, J., Jouhet, J., Amato, A., Maréchal, E., Hu, H., Allen, A. E., Gong, Y., & Jiang, H. (2024). Delta-5 elongase knockout reduces docosahexaenoic acid and lipid synthesis and increases heat sensitivity in a diatom. Plant Physiology, kiae297. https://doi.org/10.1093/plphys/kiae297
Landry, M., Freibott, A., Rabines, A., & Allen, A. (2024). Determining growth rates of heterotrophic bacteria from 16S rRNA gene sequence-based analyses of dilution experiments. Aquatic Microbial Ecology, 90, 23–39. https://doi.org/10.3354/ame02006
Rao, D., Füssy, Z., Brisbin, M. M., McIlvin, M. R., Moran, D. M., Allen, A. E., Follows, M. J., & Saito, M. A. (2024). Flexible B 12 ecophysiology of Phaeocystis antarctica due to a fusion B 12 –independent methionine synthase with widespread homologues. Proceedings of the National Academy of Sciences, 121(6), e2204075121. https://doi.org/10.1073/pnas.2204075121
Juéry, C., Auladell, A., Füssy, Z., Chevalier, F., Yee, D. P., Pelletier, E., Corre, E., Allen, A. E., Richter, D. J., & Decelle, J. (2024). Transportome remodeling of a symbiotic microalga inside a planktonic host. The ISME Journal, 18(1), wrae239. https://doi.org/10.1093/ismejo/wrae239
Manck, L. E., Coale, T. H., Stephens, B. M., Forsch, K. O., Aluwihare, L. I., Dupont, C. L., Allen, A. E., & Barbeau, K. A. (2024). Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron. The ISME Journal, 18(1), wrae061. https://doi.org/10.1093/ismejo/wrae061
Landry, M. R., Freibott, A. L., Stukel, M. R., Selph, K. E., Allen, A. E., & Rabines, A. (2024). Phytoplankton growth and grazing dynamics during anomalous heat wave and suppressed upwelling conditions in the southern California Current. Deep Sea Research Part I: Oceanographic Research Papers, 210, 104353. https://doi.org/10.1016/j.dsr.2024.104353
Ternon, E., Carter, M. L., Cancelada, L., Lampe, R. H., Allen, A. E., Anderson, C. R., Prather, K. A., & Gerwick, W. H. (2023). Yessotoxin production and aerosolization during the unprecedented red tide of 2020 in southern California. Elem Sci Anth, 11(1), 00021. https://doi.org/10.1525/elementa.2023.00021
Peña-Montenegro, T. D., Kleindienst, S., Allen, A. E., Eren, A. M., McCrow, J. P., Sánchez-Calderón, J. D., Arnold, J., & Joye, S. B. (2023). Species-specific responses of marine bacteria to environmental perturbation. ISME Communications, 3(1), 99. https://doi.org/10.1038/s43705-023-00310-z
You, L., Połońska, A., Jasieniecka‐Gazarkiewicz, K., Richard, F., Jouhet, J., Maréchal, E., Banaś, A., Hu, H., Pan, Y., Hao, X., Jin, H., Allen, A. E., Amato, A., & Gong, Y. (2023). Two plastidial lysophosphatidic acid acyltransferases differentially mediate the biosynthesis of membrane lipids and triacylglycerols in Phaeodactylum tricornutum. New Phytologist, nph.19434. https://doi.org/10.1111/nph.19434
Lampe, R. H., Coale, T. H., Forsch, K. O., Jabre, L. J., Kekuewa, S., Bertrand, E. M., Horák, A., Oborník, M., Rabines, A. J., Rowland, E., Zheng, H., Andersson, A. J., Barbeau, K. A., & Allen, A. E. (2023). Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton. Nature Communications, 14(1), 7215. https://doi.org/10.1038/s41467-023-42949-1
Diner, R. E., Zimmer-Faust, A., Cooksey, E., Allard, S., Kodera, S. M., Kunselman, E., Garodia, Y., Verhougstraete, M. P., Allen, A. E., Griffith, J., & Gilbert, J. A. (2023). Host and Water Microbiota Are Differentially Linked to Potential Human Pathogen Accumulation in Oysters. Applied and Environmental Microbiology, e00318-23. https://doi.org/10.1128/aem.00318-23
Zoumplis, A., Kolody, B., Kaul, D., Zheng, H., Venepally, P., McKnight, D. M., Takacs-Vesbach, C., DeVries, A., & Allen, A. E. (2023). Impact of meltwater flow intensity on the spatiotemporal heterogeneity of microbial mats in the McMurdo Dry Valleys, Antarctica. ISME Communications, 3(1), 3. https://doi.org/10.1038/s43705-022-00202-8
Thukral, M., Allen, A. E., & Petras, D. (2023). Progress and chAllenges in exploring aquatic microbial communities using non-targeted metabolomics. The ISME Journal, 17(12), 2147–2159. https://doi.org/10.1038/s41396-023-01532-8
Kolody, B. C., Smith, S. R., Zeigler Allen, L., McCrow, J. P., Moustafa, A., Shi, D., Hopkinson, B. M., Morel, F. M. M., Ward, B. B., & Allen, A. E. (2022). Nitrogen and Iron Availability Drive Metabolic Remodeling and Natural Selection of Diverse Phytoplankton during Experimental Upwelling. MSystems, e00729-22. https://doi.org/10.1128/msystems.00729-22
de Vargas, C., Le Bescot, N., Pollina, T., Henry, N., Romac, S., Colin, S., Haëntjens, N., Carmichael, M., Berger, C., Le Guen, D., Decelle, J., Mahé, F., Poulain, J., Malpot, E., Beaumont, C., Hardy, M., Guiffant, D., Probert, I., Gruber, D. F., … the Plankton Planet core team. (2022). Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale. Frontiers in Marine Science, 9, 936972. https://doi.org/10.3389/fmars.2022.936972
James, C. C., Barton, A. D., Allen, L. Z., Lampe, R. H., Rabines, A., Schulberg, A., Zheng, H., Goericke, R., Goodwin, K. D., & Allen, A. E. (2022). Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region. Nature Communications, 13(1), 2448. https://doi.org/10.1038/s41467-022-30139-4
Kellogg, R. M., Moosburner, M. A., Cohen, N. R., Hawco, N. J., McIlvin, M. R., Moran, D. M., DiTullio, G. R., Subhas, A. V., Allen, A. E., & Saito, M. A. (2022). Adaptive responses of marine diatoms to zinc scarcity and ecological implications. Nature Communications, 13(1), 13. https://doi.org/10.1038/s41467-022-29603-y
Steele, T. S., Brunson, J. K., Maeno, Y., Terada, R., Allen, A. E., Yotsu-Yamashita, M., Chekan, J. R., & Moore, B. S. (2022). 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, 119(6). https://doi.org/10.1073/pnas.2117407119
Kolody, B. C., Harke, M. J., Hook, S. E., & Allen, A. E. (2022). Chapter 13 - Transcriptomic and metatranscriptomic approaches in phytoplankton: insights and advances. In L. A. Clementson, R. S. Eriksen, & A. Willis (Eds.), Advances in Phytoplankton Ecology (pp. 435–485). Elsevier. https://doi.org/10.1016/B978-0-12-822861-6.00022-4
Valencia, B., Stukel, M. R., Allen, A. E., McCrow, J. P., Rabines, A., & Landry, M. R. (2022). Microbial communities associated with sinking particles across an environmental gradient from coastal upwelling to the oligotrophic ocean. Deep-Sea Research Part I-Oceanographic Research Papers, 179, 13. https://doi.org/10.1016/j.dsr.2021.103668
Petras, D., Phelan, V. V., Acharya, D., Allen, A. E., Aron, A. T., Bandeira, N., Bowen, B. P., Belle-Oudry, D., Boecker, S., Cummings, D. A., Deutsch, J. M., Fahy, E., Garg, N., Gregor, R., Handelsman, J., Navarro-Hoyos, M., Jarmusch, A. K., Jarmusch, S. A., Louie, K., … Wang, M. X. (2022). GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nature Methods, 3. https://doi.org/10.1038/s41592-021-01339-5
Hippmann, A. A., Schuback, N., Moon, K. M., McCrow, J. P., Allen, A. E., Foster, L. F., Green, B. R., & Maldonado, M. T. (2022). Proteomic analysis of metabolic pathways supports chloroplast-mitochondria cross-talk in a Cu-limited diatom. Plant Direct, 6(1), 16. https://doi.org/10.1002/pld3.376
Kazamia, E., Mach, J., McQuaid, J. B., Gao, X., Coale, T. H., Malych, R., Camadro, J., Lesuisse, E., Allen, A. E., Bowler, C., & Sutak, R. (2022). In vivo localization of iron starvation induced proteins under variable iron supplementation regimes in Phaeodactylum tricornutum. Plant Direct, 6(12). https://doi.org/10.1002/pld3.472
Kellogg, R. M., Moran, D. M., McIlvin, M. R., Subhas, A. V., Allen, A. E., & Saito, M. A. (2022). Lack of a Zn/Co substitution ability in the polar diatom Chaetoceros neogracile RS19. Limnology and Oceanography, n/a(n/a). https://doi.org/https://doi.org/10.1002/lno.12201
Moosburner, M., Allen, A. E. (corresponding author), & Daboussi, F. (2022). Genetic Engineering in Marine Diatoms: Current Practices and Emerging Technologies. In A. Falciatore & T. Mock (Eds.), The Molecular Life of Diatoms (pp. 743–773). Springer International Publishing. https://doi.org/10.1007/978-3-030-92499-7_25
Smith, S. R., & Allen, A. E. (2022). Comparative and Functional Genomics of Macronutrient Utilization in Marine Diatoms. In A. Falciatore & T. Mock (Eds.), The Molecular Life of Diatoms (pp. 529–566). Springer International Publishing. https://doi.org/10.1007/978-3-030-92499-7_19
Kumar, M., Zuniga, C., Tibocha-Bonilla, J. D., Smith, S. R., Coker, J., Allen, A. E., & Zengler, K. (2022). Constraint-Based Modeling of Diatoms Metabolism and Quantitative Biology Approaches. In A. Falciatore & T. Mock (Eds.), The Molecular Life of Diatoms (pp. 775–808). Springer International Publishing. https://doi.org/10.1007/978-3-030-92499-7_26
Coale, T. H., Bertrand, E. M., Lampe, R. H., & Allen, A. E. (2022). Molecular Mechanisms Underlying Micronutrient Utilization in Marine Diatoms. In A. Falciatore & T. Mock (Eds.), The Molecular Life of Diatoms (pp. 567–604). Springer International Publishing. https://doi.org/10.1007/978-3-030-92499-7_20
Hao, X. H., Chen, W. C., Amato, A., Jouhet, J., Marechal, E., Moog, D., Hu, H. H., Jin, H., You, L. J., Huang, F. H., Moosburner, M., Allen, A. E., & Gong, Y. M. (2021). 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. New Phytologist, 16. https://doi.org/10.1111/nph.17911
Schulte, N. O., Khan, A. L., Smith, E. W., Zoumplis, A., Kaul, D., Allen, A. E., Adams, B. J., & McKnight, D. M. (2021). Blowin’ in the wind: Dispersal, structure, and metacommunity dynamics of aeolian diatoms in the McMurdo Sound region, Antarctica. Journal of Phycology, 19. https://doi.org/10.1111/jpy.13223
Valencia, B., Stukel, M. R., Allen, A. E., McCrow, J. P., Rabines, A., Palenik, B., & Landry, M. R. (2021). Relating sinking and suspended microbial communities in the California Current Ecosystem: digestion resistance and the contributions of phytoplankton taxa to export. Environmental Microbiology, 15. https://doi.org/10.1111/1462-2920.15736
McCain, J. S. P., Allen, A. E., & Bertrand, E. M. (2021). Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom. Isme Journal, 11. https://doi.org/10.1038/s41396-021-01084-9
Oliver, A., Podell, S., Pinowska, A., Traller, J. C., Smith, S. R., McClure, R., Beliaev, A., Bohutskyi, P., Hill, E. A., Rabines, A., Zheng, H., Allen, L. Z., Kuo, A., Grigoriev, I. V., Allen, A. E., Hazlebeck, D., & Allen, E. E. (2021). Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. Scientific Reports, 11(1), 14. https://doi.org/10.1038/s41598-021-95106-3
McCain, J. S. P., Tagliabue, A., Susko, E., Achterberg, E. P., Allen, A. E., & Bertrand, E. M. (2021). Cellular costs underpin micronutrient limitation in phytoplankton. Science Advances, 7(32), 17. https://doi.org/10.1126/sciadv.abg6501
Jabre, L. J., Allen, A. E., McCain, J. S. P., McCrow, J. P., Tenenbaum, N., Spackeen, J. L., Sipler, R. E., Green, B. R., Bronk, D. A., Hutchins, D. A., & Bertrand, E. M. (2021). Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a Southern Ocean. Proceedings of the National Academy of Sciences of the United States of America, 118(30), 9. https://doi.org/10.1073/pnas.2107238118
Turnšek, J., Brunson, J. K., Viedma, M. del P. M., Deerinck, T. J., Horák, A., Oborník, M., Bielinski, V. A., & Allen, A. E. (2021). Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. Elife, 10, e52770. https://doi.org/10.7554/eLife.52770
Cohen, N. R., McIlvin, M. R., Moran, D. M., Held, N. A., Saunders, J. K., Hawco, N. J., Brosnahan, M., DiTullio, G. R., Lamborg, C., McCrow, J. P., Dupont, C. L., Allen, A. E., & Saito, M. A. (2020). Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. Nature Microbiology. https://doi.org/10.1038/s41564-020-00814-7
Breier, J. A., Jakuba, M. V., Saito, M. A., Dick, G. J., Grim, S. L., Chan, E. W., McIlvin, M. R., Moran, D. M., Alanis, B. A., Allen, A. E., Dupont, C. L., & Johnson, R. (2020). Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle. Science Robotics, 5(48). https://doi.org/10.1126/scirobotics.abc7104
Horak, A., Allen, A. E., & Obornik, M. (2020). Common origin of ornithine-urea cycle in opisthokonts and stramenopiles. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-73715-8
Jallet, D., Xing, D. H., Hughes, A., Moosburner, M., Simmons, M. P., Allen, A. E., & Peers, G. (2020). Mitochondrial fatty acid beta-oxidation is required for storage-lipid catabolism in a marine diatom. New Phytologist. https://doi.org/10.1111/nph.16744
Schulhof, M. A., Allen, A. E., Allen, E. E., Mladenov, N., McCrow, J. P., Jones, N. T., Blanton, J., Cavalheri, H. B., Kaul, D., Symons, C. C., & Shurin, J. B. (2020). Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location. Molecular Ecology. https://doi.org/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. https://doi.org/10.3390/biology9070155
Faktorova, D., Nisbet, R. E. R., Robledo, J. A. F., Casacuberta, E., Sudek, L., Allen, A. E., Ares, M., Areste, C., Balestreri, C., Barbrook, A. C., Beardslee, P., Bender, S., Booth, D. S., Bouget, F. Y., Bowler, C., Breglia, S. A., Brownlee, C., Burger, G., Cerutti, H., … Lukes, J. (2020). Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods. https://doi.org/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. https://doi.org/10.1016/j.hal.2020.101777
Krause, J. W., Brzezinski, M. A., Largier, J. L., McNair, H. M., Maniscalco, M., Bidle, K. D., Allen, A. E., & Thamatrakoln, K. (2020). The interaction of physical and biological factors drives phytoplankton spatial distribution in the northern California Current. Limnology and Oceanography. https://doi.org/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. https://doi.org/10.3389/fmicb.2020.00005