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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.
Publications
Proceedings of the National Academy of Sciences of the United States of America. 2024-10-01; 121.40: e2319177121.
Molecular forecasting of domoic acid during a pervasive toxic diatom bloom
Brunson JK, Thukral M, Ryan JP, Anderson CR, Kolody BC, James CC, Chavez FP, Leaw CP, Rabines AJ, Venepally P, Fussy Z, Zheng H, Kudela RM, Smith GJ, Moore BS, Allen AE
PMID: 39298472
Scientific reports. 2024-09-28; 14.1: 22408.
Endemic, cosmopolitan, and generalist taxa and their habitat affinities within a coastal marine microbiome
James CC, Allen AE, Lampe RH, Rabines A, Barton AD
PMID: 39333653
Applied and environmental microbiology. 2024-08-21; 90.8: e0108324.
Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant
Peña-Montenegro TD, Kleindienst S, Allen AE, Eren AM, McCrow JP, Arnold J, Joye SB
PMID: 39041797
Annual review of microbiology. 2024-07-17;
Molecular Mechanisms for Iron Uptake and Homeostasis in Marine Eukaryotic Phytoplankton
Lampe RH, Coale TH, McQuaid JB, Allen AE
PMID: 39018471
Plant physiology. 2024-05-26;
Delta-5 elongase knockout reduces docosahexaenoic acid and lipid synthesis and increases heat sensitivity in a diatom
Zhu J, Li S, Chen W, Xu X, Wang X, Wang X, Han J, Jouhet J, Amato A, Maréchal E, Hu H, Allen AE, Gong Y, Jiang H
PMID: 38796833
Proceedings of the National Academy of Sciences of the United States of America. 2024-02-06; 121.6: e2204075121.
Flexible B12 ecophysiology of Phaeocystis antarctica due to a fusion B12-independent methionine synthase with widespread homologues
Rao D, Füssy Z, Brisbin MM, McIlvin MR, Moran DM, Allen AE, Follows MJ, Saito MA
PMID: 38306482
The New phytologist. 2024-02-01; 241.4: 1543-1558.
Two plastidial lysophosphatidic acid acyltransferases differentially mediate the biosynthesis of membrane lipids and triacylglycerols in Phaeodactylum tricornutum
You L, Połońska A, Jasieniecka-Gazarkiewicz K, Richard F, Jouhet J, Maréchal E, Banaś A, Hu H, Pan Y, Hao X, Jin H, Allen AE, Amato A, Gong Y
PMID: 38031462
The ISME journal. 2024-01-08; 18.1:
Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron
Manck LE, Coale TH, Stephens BM, Forsch KO, Aluwihare LI, Dupont CL, Allen AE, Barbeau KA
PMID: 38624181
The ISME journal. 2023-12-01; 17.12: 2147-2159.
Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics
Thukral M, Allen AE, Petras D
PMID: 37857709
The ISME journal. 2023-12-01; 17.12: 2459.
Publisher Correction: Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics
Thukral M, Allen AE, Petras D
PMID: 37993599
Nature communications. 2023-11-08; 14.1: 7215.
Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton
Lampe RH, Coale TH, Forsch KO, Jabre LJ, Kekuewa S, Bertrand EM, Horák A, Oborník M, Rabines AJ, Rowland E, Zheng H, Andersson AJ, Barbeau KA, Allen AE
PMID: 37940668
ISME communications. 2023-09-22; 3.1: 99.
Species-specific responses of marine bacteria to environmental perturbation
Peña-Montenegro TD, Kleindienst S, Allen AE, Eren AM, McCrow JP, Sánchez-Calderón JD, Arnold J, Joye SB
PMID: 37736763
Applied and environmental microbiology. 2023-07-26; 89.7: e0031823.
Host and Water Microbiota Are Differentially Linked to Potential Human Pathogen Accumulation in Oysters
Diner RE, Zimmer-Faust A, Cooksey E, Allard S, Kodera SM, Kunselman E, Garodia Y, Verhougstraete MP, Allen AE, Griffith J, Gilbert JA
PMID: 37318344
Plant direct. 2022-12-26; 6.12: e472.
In vivo localization of iron starvation induced proteins under variable iron supplementation regimes in Phaeodactylum tricornutum
Kazamia E, Mach J, McQuaid JB, Gao X, Coale TH, Malych R, Camadro JM, Lesuisse E, Allen AE, Bowler C, Sutak R
PMID: 36582220
Environmental microbiology. 2022-11-01; 24.11: 5408-5424.
Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations
Koester I, Quinlan ZA, Nothias LF, White ME, Rabines A, Petras D, Brunson JK, Dührkop K, Ludwig M, Böcker S, Azam F, Allen AE, Dorrestein PC, Aluwihare LI
PMID: 36222155
Nature communications. 2022-05-04; 13.1: 2448.
Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region
James CC, Barton AD, Allen LZ, Lampe RH, Rabines A, Schulberg A, Zheng H, Goericke R, Goodwin KD, Allen AE
PMID: 35508497
Nature communications. 2022-04-14; 13.1: 1995.
Adaptive responses of marine diatoms to zinc scarcity and ecological implications
Kellogg RM, Moosburner MA, Cohen NR, Hawco NJ, McIlvin MR, Moran DM, Ditullio GR, Subhas AV, Allen AE, Saito MA
PMID: 35422102
Proceedings of the National Academy of Sciences of the United States of America. 2022-02-08; 119.6:
Domoic acid biosynthesis in the red alga Chondria armata suggests a complex evolutionary history for toxin production
Steele TS, Brunson JK, Maeno Y, Terada R, Allen AE, Yotsu-Yamashita M, Chekan JR, Moore BS
PMID: 35110408
Nature methods. 2022-02-01; 19.2: 134-136.
GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser
Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M
PMID: 34862502
The ISME journal. 2022-02-01; 16.2: 569-579.
Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom
McCain JSP, Allen AE, Bertrand EM
PMID: 34482372
Journal of phycology. 2022-02-01; 58.1: 36-54.
Blowin' in the wind: Dispersal, structure, and metacommunity dynamics of aeolian diatoms in the McMurdo Sound region, Antarctica
Schulte NO, Khan AL, Smith EW, Zoumplis A, Kaul D, Allen AE, Adams BJ, McKnight DM
PMID: 34817069
The New phytologist. 2022-02-01; 233.4: 1797-1812.
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
Hao X, Chen W, Amato A, Jouhet J, Maréchal E, Moog D, Hu H, Jin H, You L, Huang F, Moosburner M, Allen AE, Gong Y
PMID: 34882804
Plant direct. 2022-01-20; 6.1: e376.
Proteomic analysis of metabolic pathways supports chloroplast-mitochondria cross-talk in a Cu-limited diatom
Hippmann AA, Schuback N, Moon KM, McCrow JP, Allen AE, Foster LF, Green BR, Maldonado MT
PMID: 35079683
Environmental microbiology. 2021-11-01; 23.11: 6734-6748.
Relating sinking and suspended microbial communities in the California Current Ecosystem: digestion resistance and the contributions of phytoplankton taxa to export
Valencia B, Stukel MR, Allen AE, McCrow JP, Rabines A, Palenik B, Landry MR
PMID: 34431195
mSystems. 2021-08-31; 6.4: e0057121.
Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
Diner RE, Kaul D, Rabines A, Zheng H, Steele JA, Griffith JF, Allen AE
PMID: 34227831
Science advances. 2021-08-06; 7.32:
Cellular costs underpin micronutrient limitation in phytoplankton
McCain JSP, Tagliabue A, Susko E, Achterberg EP, Allen AE, Bertrand EM
PMID: 34362734
Scientific reports. 2021-08-02; 11.1: 15592.
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
Oliver A, Podell S, Pinowska A, Traller JC, Smith SR, McClure R, Beliaev A, Bohutskyi P, Hill EA, Rabines A, Zheng H, Allen LZ, Kuo A, Grigoriev IV, Allen AE, Hazlebeck D, Allen EE
PMID: 34341414
Proceedings of the National Academy of Sciences of the United States of America. 2021-07-27; 118.30:
Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean
Jabre LJ, Allen AE, McCain JSP, McCrow JP, Tenenbaum N, Spackeen JL, Sipler RE, Green BR, Bronk DA, Hutchins DA, Bertrand EM
PMID: 34301906
eLife. 2021-02-16; 10.
Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway
Turnšek J, Brunson JK, Viedma MDPM, Deerinck TJ, Horák A, Oborník M, Bielinski VA, Allen AE
PMID: 33591270
Nature microbiology. 2021-02-01; 6.2: 173-186.
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean
Cohen NR, McIlvin MR, Moran DM, Held NA, Saunders JK, Hawco NJ, Brosnahan M, Ditullio GR, Lamborg C, McCrow JP, Dupont CL, Allen AE, Saito MA
PMID: 33398100
Science robotics. 2020-11-25; 5.48:
Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle
Breier JA, Jakuba MV, Saito MA, Dick GJ, Grim SL, Chan EW, McIlvin MR, Moran DM, Alanis BA, Allen AE, Dupont CL, Johnson R
PMID: 33239321
The New phytologist. 2020-11-01; 228.3: 946-958.
Mitochondrial fatty acid β-oxidation is required for storage-lipid catabolism in a marine diatom
Jallet D, Xing D, Hughes A, Moosburner M, Simmons MP, Allen AE, Peers G
PMID: 32535932
Scientific reports. 2020-10-07; 10.1: 16687.
Common origin of ornithine-urea cycle in opisthokonts and stramenopiles
Horák A, Allen AE, Oborník M
PMID: 33028894
Biology. 2020-07-06; 9.7:
The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom
Tan MH, Smith SR, Hixson KK, Tan J, McCarthy JK, Kustka AB, Allen AE
PMID: 32640597
Molecular ecology. 2020-06-24; 29.11: 2080-2093.
Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location
Schulhof MA, Allen AE, Allen EE, Mladenov N, McCrow JP, Jones NT, Blanton J, Cavalheri HB, Kaul D, Symons CC, Shurin JB
PMID: 32578266
Nature methods. 2020-05-01; 17.5: 551.
Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology
Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J
PMID: 32296171
Nature methods. 2020-05-01; 17.5: 481-494.
Genetic tool development in marine protists: emerging model organisms for experimental cell biology
Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J
PMID: 32251396
Harmful algae. 2020-03-10; 93.101777.
Comparative transcriptomics of toxin synthesis genes between the non-toxin producing dinoflagellate Cochlodinium polykrikoides and toxigenic Alexandrium pacificum
Wang H, Guo R, Lim WA, Allen AE, Ki JS
PMID: 32307068
Proceedings of the National Academy of Sciences of the United States of America. 2019-11-19; 116.47: 23609-23617.
Reduction-dependent siderophore assimilation in a model pennate diatom
Coale TH, Moosburner M, Horák A, Oborník M, Barbeau KA, Allen AE
PMID: 31685631
Nature communications. 2019-10-07; 10.1: 4552.
Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom
Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlář J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, Nikoloski Z, Palsson BO, Allen AE
PMID: 31591397
Nature communications. 2019-08-08; 10.1: 3582.
Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators
Wu M, McCain JSP, Rowland E, Middag R, Sandgren M, Allen AE, Bertrand EM
PMID: 31395884
The New phytologist. 2019-05-01; 222.3: 1364-1379.
Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum
Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, Dupont CL, Mitchell BG, Palsson BO, Allen AE
PMID: 30636322
Science (New York, N.Y.). 2018-09-28; 361.6409: 1356-1358.
Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom
Brunson JK, McKinnie SMK, Chekan JR, McCrow JP, Miles ZD, Bertrand EM, Bielinski VA, Luhavaya H, Oborník M, Smith GJ, Hutchins DA, Allen AE, Moore BS
PMID: 30262498
The Plant cell. 2017-08-01; 29.8: 2047-2070.
Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom
McCarthy JK, McCarthy JK, Smith SR, McCrow JP, Tan M, Zheng H, Beeri K, Roth RA, Roth R, Lichtle C, Lichtle C, Goodenough U, Bowler C, Bowler CP, Dupont CL, Dupont CL, Allen AE
PMID: 28765511
PLoS genetics. 2017-03-29; 13.3: e1006688.
Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
Smith SR, Gillard JT, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE
PMID: 28355217
Nature reviews. Microbiology. 2017-01-01; 15.1: 6-20.
Probing the evolution, ecology and physiology of marine protists using transcriptomics
Caron DA, Alexander H, Allen AE, Archibald JM, Armbrust EV, Bachy C, Bell CJ, Bharti A, Dyhrman ST, Guida SM, Heidelberg KB, Kaye JZ, Metzner J, Smith SR, Worden AZ
PMID: 27867198
PLoS genetics. 2016-12-01; 12.12: e1006490.
Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
Smith SR, Gillard JT, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE
PMID: 27973599
Frontiers in microbiology. 2016-07-06; 7.1043.
Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem
Asplund-Samuelsson J, Sundh J, Dupont CL, Allen AE, McCrow JP, Celepli NA, Bergman B, Ininbergs K, Ekman M
PMID: 27458440
Frontiers in microbiology. 2016-06-09; 7.880.
Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms
Diner RE, Schwenck SM, McCrow JP, Zheng H, Allen AE
PMID: 27375600
The New phytologist. 2016-05-01; 210.3: 890-904.
Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana
Smith SR, Glé C, Abbriano RM, Traller JC, Davis A, Trentacoste E, Vernet M, Allen AE, Hildebrand M
PMID: 26844818
Biotechnology for biofuels. 2016-01-01; 9.258.
Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype
Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M
PMID: 27933100
PloS one. 2016-01-01; 11.3: e0160929.
Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume
Zielinski BL, Allen AE, Carpenter EJ, Coles VJ, Crump BC, Doherty M, Foster RA, Goes JI, Gomes HR, Hood RR, McCrow JP, Montoya JP, Moustafa A, Satinsky BM, Sharma S, Smith CB, Yager PL, Paul JH
PMID: 27598790
The ISME journal. 2015-05-01; 9.5: 1076-92.
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities
Dupont CL, McCrow JP, Valas R, Moustafa A, Walworth N, Goodenough U, Roth R, Hogle SL, Bai J, Johnson ZI, Mann E, Palenik B, Barbeau KA, Venter JC, Allen AE
PMID: 25333462
Nature communications. 2015-04-21; 6.6925.
Designer diatom episomes delivered by bacterial conjugation
Karas BJ, Diner RE, Lefebvre SC, McQuaid J, Phillips AP, Noddings CM, Brunson JK, Valas RE, Deerinck TJ, Jablanovic J, Gillard JT, Beeri K, Ellisman MH, Glass JI, Hutchison CA, Smith HO, Venter JC, Allen AE, Dupont CL, Weyman PD
PMID: 25897682
Current biology : CB. 2015-02-02; 25.3: 364-71.
A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake
Morrissey J, Sutak R, Paz-Yepes J, Tanaka A, Moustafa A, Veluchamy A, Thomas Y, Botebol H, Bouget FY, McQuaid JB, Tirichine L, Allen AE, Lesuisse E, Bowler C
PMID: 25557662
Molecular phylogenetics and evolution. 2014-02-01; 71.36-40.
Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae
Smith DR, Arrigo KR, Alderkamp AC, Allen AE
PMID: 24216019
Journal of biological engineering. 2013-12-10; 7.1: 30.
Assembly of eukaryotic algal chromosomes in yeast
Karas BJ, Molparia B, Jablanovic J, Hermann WJ, Lin YC, Dupont CL, Tagwerker C, Yonemoto IT, Noskov VN, Chuang RY, Allen AE, Glass JI, Hutchison CA, Smith HO, Venter JC, Weyman PD
PMID: 24325901
Frontiers in chemistry. 2013-10-30; 1.25.
Dissolved and particulate trace metal micronutrients under the McMurdo Sound seasonal sea ice: basal sea ice communities as a capacitor for iron
Noble AE, Moran DM, Allen AE, Saito MA
PMID: 24790953
Current opinion in microbiology. 2013-10-01; 16.5: 605-17.
Lineage specific gene family enrichment at the microscale in marine systems
Allen AE, Allen LZ, McCrow JP
PMID: 24377115
Proceedings of the National Academy of Sciences of the United States of America. 2013-06-25; 110.26: E2390-9.
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken RS
PMID: 23754396
Frontiers in microbiology. 2013-05-30; 4.120.
Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem
Smith MW, Zeigler Allen L, Allen AE, Herfort L, Simon HM
PMID: 23750156
The New phytologist. 2013-04-01; 198.2: 398-407.
Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
Konotchick T, Dupont CL, Valas RE, Badger JH, Allen AE
PMID: 23488966
Nature communications. 2013-01-01; 4.2091.
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum
Veluchamy A, Lin X, Maumus F, Rivarola M, Bhavsar J, Creasy T, O'Brien K, Sengamalay NA, Tallon LJ, Smith AD, Rayko E, Ahmed I, Le Crom S, Farrant GK, Sgro JY, Olson SA, Bondurant SS, Allen AE, Allen A, Rabinowicz PD, Sussman MR, Bowler C, Tirichine L
PMID: 23820484
BMC genomics. 2012-09-20; 13.499.
Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana
Shrestha RP, Tesson B, Norden-Krichmar T, Federowicz S, Hildebrand M, Allen AE
PMID: 22994549
Molecular systems biology. 2012-07-17; 8.595.
Global biogeography of SAR11 marine bacteria
Brown MV, Lauro FM, DeMaere MZ, Muir L, Wilkins D, Thomas T, Riddle MJ, Fuhrman JA, Andrews-Pfannkoch C, Hoffman JM, McQuaid JB, Allen A, Rintoul SR, Cavicchioli R
PMID: 22806143
Trends in plant science. 2012-07-01; 17.7: 395-403.
Leveraging metabolomics for functional investigations in sequenced marine diatoms
Fernie AR, Obata T, Allen AE, Araújo WL, Bowler C
PMID: 22465020
The ISME journal. 2012-07-01; 6.7: 1403-14.
Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic
Zeigler Allen L, Allen EE, Badger JH, McCrow JP, Paulsen IT, Elbourne LD, Thiagarajan M, Rusch DB, Nealson KH, Williamson SJ, Venter JC, Allen AE
PMID: 22278668
Proceedings of the National Academy of Sciences of the United States of America. 2012-06-26; 109.26: E1762-71.
Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein
Bertrand EM, Allen AE, Dupont CL, Norden-Krichmar TM, Bai J, Valas RE, Saito MA
PMID: 22652568
Proceedings of the National Academy of Sciences of the United States of America. 2012-02-07; 109.6: E317-25.
Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability
Marchetti A, Schruth DM, Durkin CA, Parker MS, Kodner RB, Berthiaume CT, Morales R, Allen AE, Armbrust EV
PMID: 22308424
Molecular biology and evolution. 2012-01-01; 29.1: 367-79.
Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms
Allen AE, Moustafa A, Montsant A, Eckert A, Kroth PG, Bowler C
PMID: 21903677
Frontiers in microbiology. 2012-01-01; 3.375.
Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton
Bertrand EM, Allen AE
PMID: 23091473
Photosynthesis research. 2011-09-01; 109.1-3: 205-21.
Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana
Tachibana M, Allen AE, Kikutani S, Endo Y, Bowler C, Matsuda Y
PMID: 21365259
PloS one. 2011-08-12; 6.8: e22870.
Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana
Norden-Krichmar TM, Allen AE, Gaasterland T, Hildebrand M
PMID: 21857960
Nature. 2011-05-12; 473.7346: 203-7.
Evolution and metabolic significance of the urea cycle in photosynthetic diatoms
Allen AE, Dupont CL, Oborník M, Horák A, Nunes-Nesi A, McCrow JP, Zheng H, Johnson DA, Hu H, Fernie AR, Bowler C
PMID: 21562560
Proceedings of the National Academy of Sciences of the United States of America. 2011-03-08; 108.10: 3830-7.
Efficiency of the CO2-concentrating mechanism of diatoms
Hopkinson BM, Dupont CL, Allen AE, Morel FM
PMID: 21321195
Nature. 2010-11-04; 468.7320: 60-6.
Genomic and functional adaptation in surface ocean planktonic prokaryotes
Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, Johnson J, Montgomery R, Ferriera S, Beeson K, Williamson SJ, Tovchigrechko A, Allen AE, Zeigler LA, Sutton G, Eisenstadt E, Rogers YH, Friedman R, Frazier M, Venter JC
PMID: 21048761
Current opinion in microbiology. 2010-10-01; 13.5: 652-60.
The voyage of the microbial eukaryote
Worden AZ, Allen AE
PMID: 20832353
Genome biology. 2010-08-25; 11.8: R85.
Digital expression profiling of novel diatom transcripts provides insight into their biological functions
Maheswari U, Jabbari K, Petit JL, Porcel BM, Allen AE, Cadoret JP, De Martino A, Heijde M, Kaas R, La Roche J, Lopez PJ, Martin-Jézéquel V, Meichenin A, Mock T, Schnitzler Parker M, Vardi A, Armbrust EV, Weissenbach J, Katinka M, Bowler C
PMID: 20738856
Proceedings of the National Academy of Sciences of the United States of America. 2010-08-17; 107.33: 14679-84.
Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton
Cuvelier ML, Allen AE, Monier A, McCrow JP, Messié M, Tringe SG, Woyke T, Welsh RM, Ishoey T, Lee JH, Binder BJ, Dupont CL, Latasa M, Guigand C, Buck KR, Hilton J, Thiagarajan M, Caler E, Read B, Lasken RS, Chavez FP, Worden AZ
PMID: 20668244
Nature. 2010-06-03; 465.7298: 617-21.
The Ectocarpus genome and the independent evolution of multicellularity in brown algae
Cock JM, Sterck L, Rouzé P, Scornet D, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Aury JM, Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JH, Bowler C, Boyen C, Brownlee C, Carrano CJ, Charrier B, Cho GY, Coelho SM, Collén J, Corre E, Da Silva C, Delage L, Delaroque N, Dittami SM, Doulbeau S, Elias M, Farnham G, Gachon CM, Gschloessl B, Heesch S, Jabbari K, Jubin C, Kawai H, Kimura K, Kloareg B, Küpper FC, Lang D, Le Bail A, Leblanc C, Lerouge P, Lohr M, Lopez PJ, Martens C, Maumus F, Michel G, Miranda-Saavedra D, Morales J, Moreau H, Motomura T, Nagasato C, Napoli CA, Nelson DR, Nyvall-Collén P, Peters AF, Pommier C, Potin P, Poulain J, Quesneville H, Read B, Rensing SA, Ritter A, Rousvoal S, Samanta M, Samson G, Schroeder DC, Ségurens B, Strittmatter M, Tonon T, Tregear JW, Valentin K, von Dassow P, Yamagishi T, Van de Peer Y, Wincker P
PMID: 20520714
Science (New York, N.Y.). 2009-04-10; 324.5924: 268-72.
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas
Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV
PMID: 19359590
Current opinion in plant biology. 2006-06-01; 9.3: 264-73.
An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms
Allen AE, Vardi A, Bowler C
PMID: 16603409
Science (New York, N.Y.). 2004-10-01; 306.5693: 79-86.
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism
Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kröger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS
PMID: 15459382
METAREP
Metagenomics Reports (METAREP) is an open source tool for high-performance comparative metagenomics.
Ariel Rabines
Research Associate III
Anne Schulberg
Laboratory Assistant
Hong Zheng, MS
Research Associate IV
19-Sep-2024
Press Release
Scientists discover molecular predictors of toxic algal blooms that pose health risk, ecological and economic harm
Genes in the algae Pseudo-nitzschia genus have been identified that act as a warning beacon for a dangerous neurotoxin
21-May-2024
Collaborator Release
Phytoplankton Genetically Sequenced at Sea for the First Time
Viking’s Initiative with UC San Diego’s Scripps Institution of Oceanography and J. Craig Venter Institute Aims to Provide Better Understanding of the “World’s Lungs”
10-Nov-2023
Press Release
Coastal upwelling regions threatened by increased ocean acidification
Increased acidification shown to limit iron availability, a critical element for the survival of phytoplankton, the foundation of the oceanic food web
04-May-2022
Collaborator Release
Scientists announce comprehensive regional diagnostic of microbial ocean life using DNA testing
Large-scale ‘metabarcoding’ methods could revolutionize how society understands forces that drive seafood supply, planet’s ability to remove greenhouse gases
26-Jul-2021
Press Release
Climate change and iron availability may drastically alter algae blooms in the Southern Ocean, trapping vast nutrients
Shifts in diatom population may have profound effects on global nutrient distribution and carbon cycling
18-Mar-2021
Press Release
Scientists map how iron, a critical mineral for survival, is processed by algae, a cornerstone of the ocean food web
Nearly forty proteins identified in the intracellular process, helping to build a conceptual overview of how iron is allocated within diatom cells
10-Apr-2020
Blog
JCVI Researchers Help Advance Our Understanding of Ocean Microbes, Developing New Tools and Protocols Through Large-Scale Study
21-Nov-2019
Blog
Diatoms Have Found a Way to Pirate Bacterial Iron Sources, JCVI Scientists use CRISPR Technology to Discover How
27-Sep-2018
Press Release
Domoic Acid Decoded: Scientists Discover Genetic Basis for How Harmful Algal Blooms Become Toxic
Research into gene function in microalgae helps determine how toxins are made in oceanic harmful algal blooms
27-Sep-2018
Blog
Scientists Discover Genetic Basis for Toxic Algal Blooms
16-Jul-2018
Media Advisory