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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.

New Phytol. 2019 May;222(3):1364-1379. doi: 10.1111/nph.15685. Epub 2019 Feb 14.


Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea.

Jaffe AL, Castelle CJ, Dupont CL, Banfield JF.

Mol Biol Evol. 2019 Mar 1;36(3):435-446. doi: 10.1093/molbev/msy234.


Pervasive iron limitation at subsurface chlorophyll maxima of the California Current.

Hogle SL, Dupont CL, Hopkinson BM, King AL, Buck KN, Roe KL, Stuart RK, Allen AE, Mann EL, Johnson ZI, Barbeau KA.

Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):13300-13305. doi: 10.1073/pnas.1813192115. Epub 2018 Dec 10.


Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.

Espinoza JL, Harkins DM, Torralba M, Gomez A, Highlander SK, Jones MB, Leong P, Saffery R, Bockmann M, Kuelbs C, Inman JM, Hughes T, Craig JM, Nelson KE, Dupont CL.

MBio. 2018 Nov 27;9(6). pii: e01631-18. doi: 10.1128/mBio.01631-18.


Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea.

Zhu Q, Dupont CL, Jones MB, Pham KM, Jiang ZD, DuPont HL, Highlander SK.

Microbiome. 2018 Nov 8;6(1):201. doi: 10.1186/s40168-018-0579-0.


Planktonic Marine Archaea.

Santoro AE, Richter RA, Dupont CL.

Ann Rev Mar Sci. 2019 Jan 3;11:131-158. doi: 10.1146/annurev-marine-121916-063141. Epub 2018 Sep 13.


Simultaneous quantum yield measurements of carbon uptake and oxygen evolution in microalgal cultures.

Du N, Gholami P, Kline DI, DuPont CL, Dickson AG, Mendola D, Martz T, Allen AE, Mitchell BG.

PLoS One. 2018 Jun 19;13(6):e0199125. doi: 10.1371/journal.pone.0199125. eCollection 2018.


Tracking the rise of eukaryotes to ecological dominance with zinc isotopes.

Isson TT, Love GD, Dupont CL, Reinhard CT, Zumberge AJ, Asael D, Gueguen B, McCrow J, Gill BC, Owens J, Rainbird RH, Rooney AD, Zhao MY, Stueeken EE, Konhauser KO, John SG, Lyons TW, Planavsky NJ.

Geobiology. 2018 Jul;16(4):341-352. doi: 10.1111/gbi.12289. Epub 2018 Jun 5.


Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm.

Michaud JM, Thompson LR, Kaul D, Espinoza JL, Richter RA, Xu ZZ, Lee C, Pham KM, Beall CM, Malfatti F, Azam F, Knight R, Burkart MD, Dupont CL, Prather KA.

Nat Commun. 2018 May 22;9(1):2017. doi: 10.1038/s41467-018-04409-z.


Patterns of thaumarchaeal gene expression in culture and diverse marine environments.

Carini P, Dupont CL, Santoro AE.

Environ Microbiol. 2018 Jun;20(6):2112-2124. doi: 10.1111/1462-2920.14107. Epub 2018 Apr 30.


Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont.

Warshan D, Liaimer A, Pederson E, Kim SY, Shapiro N, Woyke T, Altermark B, Pawlowski K, Weyman PD, Dupont CL, Rasmussen U.

Mol Biol Evol. 2018 May 1;35(5):1160-1175. doi: 10.1093/molbev/msy029.


Host Genetic Control of the Oral Microbiome in Health and Disease.

Gomez A, Espinoza JL, Harkins DM, Leong P, Saffery R, Bockmann M, Torralba M, Kuelbs C, Kodukula R, Inman J, Hughes T, Craig JM, Highlander SK, Jones MB, Dupont CL, Nelson KE.

Cell Host Microbe. 2017 Sep 13;22(3):269-278.e3. doi: 10.1016/j.chom.2017.08.013.


Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant-cyanobacteria symbiosis.

Warshan D, Espinoza JL, Stuart RK, Richter RA, Kim SY, Shapiro N, Woyke T, C Kyrpides N, Barry K, Singan V, Lindquist E, Ansong C, Purvine SO, M Brewer H, Weyman PD, Dupont CL, Rasmussen U.

ISME J. 2017 Dec;11(12):2821-2833. doi: 10.1038/ismej.2017.134. Epub 2017 Aug 11.


A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells.

Fridman S, Flores-Uribe J, Larom S, Alalouf O, Liran O, Yacoby I, Salama F, Bailleul B, Rappaport F, Ziv T, Sharon I, Cornejo-Castillo FM, Philosof A, Dupont CL, Sánchez P, Acinas SG, Rohwer FL, Lindell D, Béjà O.

Nat Microbiol. 2017 Oct;2(10):1350-1357. doi: 10.1038/s41564-017-0002-9. Epub 2017 Aug 7.


Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom.

McCarthy JK, Smith SR, McCrow JP, Tan M, Zheng H, Beeri K, Roth R, Lichtle C, Goodenough U, Bowler CP, Dupont CL, Allen AE.

Plant Cell. 2017 Aug;29(8):2047-2070. doi: 10.1105/tpc.16.00910. Epub 2017 Aug 1.


Mechanisms of carbon dioxide acquisition and CO2 sensing in marine diatoms: a gateway to carbon metabolism.

Matsuda Y, Hopkinson BM, Nakajima K, Dupont CL, Tsuji Y.

Philos Trans R Soc Lond B Biol Sci. 2017 Sep 5;372(1728). pii: 20160403. doi: 10.1098/rstb.2016.0403. Review.


Diatom centromeres suggest a mechanism for nuclear DNA acquisition.

Diner RE, Noddings CM, Lian NC, Kang AK, McQuaid JB, Jablanovic J, Espinoza JL, Nguyen NA, Anzelmatti MA Jr, Jansson J, Bielinski VA, Karas BJ, Dupont CL, Allen AE, Weyman PD.

Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E6015-E6024. doi: 10.1073/pnas.1700764114. Epub 2017 Jul 3.


Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond.

Lee ZM, Poret-Peterson AT, Siefert JL, Kaul D, Moustafa A, Allen AE, Dupont CL, Eguiarte LE, Souza V, Elser JJ.

Front Microbiol. 2017 May 30;8:949. doi: 10.3389/fmicb.2017.00949. eCollection 2017.


The diversity of CO2-concentrating mechanisms in marine diatoms as inferred from their genetic content.

Shen C, Dupont CL, Hopkinson BM.

J Exp Bot. 2017 Jun 1;68(14):3937-3948. doi: 10.1093/jxb/erx163.


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.

PLoS Genet. 2017 Mar 29;13(3):e1006688. doi: 10.1371/journal.pgen.1006688. eCollection 2017 Mar.


Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels.

Levering J, Dupont CL, Allen AE, Palsson BO, Zengler K.

mSystems. 2017 Feb 14;2(1). pii: e00142-16. doi: 10.1128/mSystems.00142-16. eCollection 2017 Jan-Feb.


The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses.

Zeigler Allen L, McCrow JP, Ininbergs K, Dupont CL, Badger JH, Hoffman JM, Ekman M, Allen AE, Bergman B, Venter JC.

mSystems. 2017 Feb 14;2(1). pii: e00125-16. doi: 10.1128/mSystems.00125-16. eCollection 2017 Jan-Feb.


Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, van Oosterhout C, Grigoriev IV.

Nature. 2017 Jan 26;541(7638):536-540. doi: 10.1038/nature20803. Epub 2017 Jan 16.


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.

PLoS Genet. 2016 Dec 14;12(12):e1006490. doi: 10.1371/journal.pgen.1006490. eCollection 2016 Dec. Erratum in: PLoS Genet. 2017 Mar 29;13(3):e1006688.


Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.

Celepli N, Sundh J, Ekman M, Dupont CL, Yooseph S, Bergman B, Ininbergs K.

Environ Microbiol. 2017 Feb;19(2):673-686. doi: 10.1111/1462-2920.13592. Epub 2017 Jan 27.


Refinement of the Diatom Episome Maintenance Sequence and Improvement of Conjugation-Based DNA Delivery Methods.

Diner RE, Bielinski VA, Dupont CL, Allen AE, Weyman PD.

Front Bioeng Biotechnol. 2016 Aug 8;4:65. doi: 10.3389/fbioe.2016.00065. eCollection 2016.


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.

Front Microbiol. 2016 Jul 6;7:1043. doi: 10.3389/fmicb.2016.01043. eCollection 2016.


Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly.

Llorens-Marès T, Liu Z, Allen LZ, Rusch DB, Craig MT, Dupont CL, Bryant DA, Casamayor EO.

ISME J. 2017 Jan;11(1):201-211. doi: 10.1038/ismej.2016.93. Epub 2016 Jul 8.


Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.

Brindefalk B, Ekman M, Ininbergs K, Dupont CL, Yooseph S, Pinhassi J, Bergman B.

Environ Microbiol. 2016 Dec;18(12):4442-4455. doi: 10.1111/1462-2920.13407. Epub 2016 Jul 14.


Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.

Díez B, Nylander JA, Ininbergs K, Dupont CL, Allen AE, Yooseph S, Rusch DB, Bergman B.

PLoS One. 2016 May 19;11(5):e0155757. doi: 10.1371/journal.pone.0155757. eCollection 2016.


Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.

Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K.

PLoS One. 2016 May 6;11(5):e0155038. doi: 10.1371/journal.pone.0155038. eCollection 2016.


The physiology and genetics of CO2 concentrating mechanisms in model diatoms.

Hopkinson BM, Dupont CL, Matsuda Y.

Curr Opin Plant Biol. 2016 Jun;31:51-7. doi: 10.1016/j.pbi.2016.03.013. Epub 2016 Apr 4. Review.


Global biogeography of Prochlorococcus genome diversity in the surface ocean.

Kent AG, Dupont CL, Yooseph S, Martiny AC.

ISME J. 2016 Aug;10(8):1856-65. doi: 10.1038/ismej.2015.265. Epub 2016 Feb 2.


Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies.

Hogle SL, Thrash JC, Dupont CL, Barbeau KA.

Appl Environ Microbiol. 2016 Jan 4;82(5):1613-1624. doi: 10.1128/AEM.03128-15.


High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling.

Llorens-Marès T, Triadó-Margarit X, Borrego CM, Dupont CL, Casamayor EO.

Microb Ecol. 2016 Apr;71(3):566-74. doi: 10.1007/s00248-015-0696-2. Epub 2015 Nov 9.


Closing the gaps on the viral photosystem-I psaDCAB gene organization.

Roitman S, Flores-Uribe J, Philosof A, Knowles B, Rohwer F, Ignacio-Espinoza JC, Sullivan MB, Cornejo-Castillo FM, Sánchez P, Acinas SG, Dupont CL, Béjà O.

Environ Microbiol. 2015 Dec;17(12):5100-8. doi: 10.1111/1462-2920.13036. Epub 2015 Oct 14.


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 3rd, Smith HO, Venter JC, Allen AE, Dupont CL, Weyman PD.

Nat Commun. 2015 Apr 21;6:6925. doi: 10.1038/ncomms7925.


Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": an ammonia-oxidizing archaeon from the open ocean.

Santoro AE, Dupont CL, Richter RA, Craig MT, Carini P, McIlvin MR, Yang Y, Orsi WD, Moran DM, Saito MA.

Proc Natl Acad Sci U S A. 2015 Jan 27;112(4):1173-8. doi: 10.1073/pnas.1416223112. Epub 2015 Jan 13.


Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.

Llorens-Marès T, Yooseph S, Goll J, Hoffman J, Vila-Costa M, Borrego CM, Dupont CL, Casamayor EO.

ISME J. 2015 Jul;9(7):1648-61. doi: 10.1038/ismej.2014.254. Epub 2015 Jan 9.


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.

ISME J. 2015 May;9(5):1076-92. doi: 10.1038/ismej.2014.198. Epub 2014 Oct 21.


Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis.

Weyman PD, Beeri K, Lefebvre SC, Rivera J, McCarthy JK, Heuberger AL, Peers G, Allen AE, Dupont CL.

Plant Biotechnol J. 2015 May;13(4):460-70. doi: 10.1111/pbi.12254. Epub 2014 Oct 10.


Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.

Larsson J, Celepli N, Ininbergs K, Dupont CL, Yooseph S, Bergman B, Ekman M.

ISME J. 2014 Sep;8(9):1892-903. doi: 10.1038/ismej.2014.35. Epub 2014 Mar 13.


Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagström Å, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B.

PLoS One. 2014 Feb 27;9(2):e89549. doi: 10.1371/journal.pone.0089549. eCollection 2014.


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 3rd, Smith HO, Venter JC, Weyman PD.

J Biol Eng. 2013 Dec 10;7(1):30. doi: 10.1186/1754-1611-7-30.


Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species.

Tetu SG, Johnson DA, Varkey D, Phillippy K, Stuart RK, Dupont CL, Hassan KA, Palenik B, Paulsen IT.

Front Microbiol. 2013 Aug 16;4:232. doi: 10.3389/fmicb.2013.00232. eCollection 2013.


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.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):E2390-9. doi: 10.1073/pnas.1219809110. Epub 2013 Jun 10.


Authigenic iron oxide proxies for marine zinc over geological time and implications for eukaryotic metallome evolution.

Robbins LJ, Lalonde SV, Saito MA, Planavsky NJ, Mloszewska AM, Pecoits E, Scott C, Dupont CL, Kappler A, Konhauser KO.

Geobiology. 2013 Jul;11(4):295-306. doi: 10.1111/gbi.12036. Epub 2013 Apr 22.


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.

New Phytol. 2013 Apr;198(2):398-407. doi: 10.1111/nph.12160. Epub 2013 Mar 13.


Draft Genome Sequence of a Single Cell of SAR86 Clade Subgroup IIIa.

Rusch DB, Lombardo MJ, Yee-Greenbaum J, Novotny M, Brinkac LM, Lasken RS, Dupont CL.

Genome Announc. 2013 Jan;1(1). pii: e00030-12. doi: 10.1128/genomeA.00030-12. Epub 2013 Jan 15.


Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast.

Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY, Benders GA, Ramon A, Novotny M, Montague MG, Venepally P, Brami D, Schwartz A, Andrews-Pfannkoch C, Gibson DG, Glass JI, Smith HO, Venter JC, Hutchison CA 3rd.

Nucleic Acids Res. 2012 Nov 1;40(20):10375-83. doi: 10.1093/nar/gks823. Epub 2012 Aug 31.

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