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Items: 1 to 50 of 137

1.

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 Jr, 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.

Nat Methods. 2020 Apr 6. doi: 10.1038/s41592-020-0796-x. [Epub ahead of print]

PMID:
32251396
2.

Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9.

Moosburner MA, Gholami P, McCarthy JK, Tan M, Bielinski VA, Allen AE.

Front Microbiol. 2020 Jan 28;11:5. doi: 10.3389/fmicb.2020.00005. eCollection 2020.

3.

Modelling flexible protein-ligand binding in p38α MAP kinase using the QUBE force field.

Horton JT, Allen AEA, Cole DJ.

Chem Commun (Camb). 2020 Jan 18;56(6):932-935. doi: 10.1039/c9cc08574b. Epub 2019 Dec 18.

PMID:
31850454
4.

Evolved resistance to partial GAPDH inhibition results in loss of the Warburg effect and in a different state of glycolysis.

Liberti MV, Allen AE, Ramesh V, Dai Z, Singleton KR, Guo Z, Liu JO, Wood KC, Locasale JW.

J Biol Chem. 2020 Jan 3;295(1):111-124. doi: 10.1074/jbc.RA119.010903. Epub 2019 Nov 20.

PMID:
31748414
5.

Reduction-dependent siderophore assimilation in a model pennate diatom.

Coale TH, Moosburner M, Horák A, Oborník M, Barbeau KA, Allen AE.

Proc Natl Acad Sci U S A. 2019 Nov 19;116(47):23609-23617. doi: 10.1073/pnas.1907234116. Epub 2019 Nov 4.

6.

Appearance of Maxwell's spot in images rendered using a cyan primary.

Gardasevic M, Lucas RJ, Allen AE.

Vision Res. 2019 Dec;165:72-79. doi: 10.1016/j.visres.2019.10.004. Epub 2019 Oct 31.

7.

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.

Nat Commun. 2019 Oct 7;10(1):4552. doi: 10.1038/s41467-019-12407-y.

8.

Development and Validation of the Quantum Mechanical Bespoke Protein Force Field.

Allen AEA, Robertson MJ, Payne MC, Cole DJ.

ACS Omega. 2019 Aug 27;4(11):14537-14550. doi: 10.1021/acsomega.9b01769. eCollection 2019 Sep 10.

9.

Visual responses in the dorsal lateral geniculate nucleus at early stages of retinal degeneration in rd1 PDE6β mice.

Procyk CA, Allen AE, Martial FP, Lucas RJ.

J Neurophysiol. 2019 Oct 1;122(4):1753-1764. doi: 10.1152/jn.00231.2019. Epub 2019 Aug 28.

PMID:
31461375
10.

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.

Nat Commun. 2019 Aug 8;10(1):3582. doi: 10.1038/s41467-019-11426-z.

11.

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection.

Kolody BC, McCrow JP, Allen LZ, Aylward FO, Fontanez KM, Moustafa A, Moniruzzaman M, Chavez FP, Scholin CA, Allen EE, Worden AZ, Delong EF, Allen AE.

ISME J. 2019 Nov;13(11):2817-2833. doi: 10.1038/s41396-019-0472-2. Epub 2019 Jul 18.

12.

Silicon limitation facilitates virus infection and mortality of marine diatoms.

Kranzler CF, Krause JW, Brzezinski MA, Edwards BR, Biggs WP, Maniscalco M, McCrow JP, Van Mooy BAS, Bidle KD, Allen AE, Thamatrakoln K.

Nat Microbiol. 2019 Nov;4(11):1790-1797. doi: 10.1038/s41564-019-0502-x. Epub 2019 Jul 15.

PMID:
31308524
13.

Form vision from melanopsin in humans.

Allen AE, Martial FP, Lucas RJ.

Nat Commun. 2019 May 22;10(1):2274. doi: 10.1038/s41467-019-10113-3.

14.

Pupil responses to hidden photoreceptor-specific modulations in movies.

Spitschan M, Gardasevic M, Martial FP, Lucas RJ, Allen AE.

PLoS One. 2019 May 9;14(5):e0216307. doi: 10.1371/journal.pone.0216307. eCollection 2019.

15.

Rod Photoreceptor Activation Alone Defines the Release of Dopamine in the Retina.

Pérez-Fernández V, Milosavljevic N, Allen AE, Vessey KA, Jobling AI, Fletcher EL, Breen PP, Morley JW, Cameron MA.

Curr Biol. 2019 Mar 4;29(5):763-774.e5. doi: 10.1016/j.cub.2019.01.042. Epub 2019 Feb 21.

16.

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics.

Horton JT, Allen AEA, Dodda LS, Cole DJ.

J Chem Inf Model. 2019 Apr 22;59(4):1366-1381. doi: 10.1021/acs.jcim.8b00767. Epub 2019 Feb 22.

PMID:
30742438
17.

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.

18.

Serine synthesis through PHGDH coordinates nucleotide levels by maintaining central carbon metabolism.

Reid MA, Allen AE, Liu S, Liberti MV, Liu P, Liu X, Dai Z, Gao X, Wang Q, Liu Y, Lai L, Locasale JW.

Nat Commun. 2018 Dec 21;9(1):5442. doi: 10.1038/s41467-018-07868-6.

19.

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.

20.

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.

Science. 2018 Sep 28;361(6409):1356-1358. doi: 10.1126/science.aau0382.

21.

Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom.

Murik O, Tirichine L, Prihoda J, Thomas Y, Araújo WL, Allen AE, Fernie AR, Bowler C.

New Phytol. 2019 Feb;221(3):1303-1316. doi: 10.1111/nph.15479. Epub 2018 Nov 22.

22.

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.

23.

Exploiting metamerism to regulate the impact of a visual display on alertness and melatonin suppression independent of visual appearance.

Allen AE, Hazelhoff EM, Martial FP, Cajochen C, Lucas RJ.

Sleep. 2018 Aug 1;41(8). doi: 10.1093/sleep/zsy100.

24.

Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms.

Rastogi A, Maheswari U, Dorrell RG, Vieira FRJ, Maumus F, Kustka A, McCarthy J, Allen AE, Kersey P, Bowler C, Tirichine L.

Sci Rep. 2018 Mar 19;8(1):4834. doi: 10.1038/s41598-018-23106-x.

25.

Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms.

McQuaid JB, Kustka AB, Oborník M, Horák A, McCrow JP, Karas BJ, Zheng H, Kindeberg T, Andersson AJ, Barbeau KA, Allen AE.

Nature. 2018 Mar 22;555(7697):534-537. doi: 10.1038/nature25982. Epub 2018 Mar 14.

PMID:
29539640
26.

Glucose Metabolism in Cancer: The Saga of Pyruvate Kinase Continues.

Allen AE, Locasale JW.

Cancer Cell. 2018 Mar 12;33(3):337-339. doi: 10.1016/j.ccell.2018.02.008.

27.

Harmonic Force Constants for Molecular Mechanics Force Fields via Hessian Matrix Projection.

Allen AEA, Payne MC, Cole DJ.

J Chem Theory Comput. 2018 Jan 9;14(1):274-281. doi: 10.1021/acs.jctc.7b00785. Epub 2017 Dec 6.

PMID:
29161029
28.

Contrasting effects of copper limitation on the photosynthetic apparatus in two strains of the open ocean diatom Thalassiosira oceanica.

Hippmann AA, Schuback N, Moon KM, McCrow JP, Allen AE, Foster LJ, Green BR, Maldonado MT.

PLoS One. 2017 Aug 24;12(8):e0181753. doi: 10.1371/journal.pone.0181753. eCollection 2017.

29.

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.

30.

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.

31.

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.

32.

Melanopsin Contributions to the Representation of Images in the Early Visual System.

Allen AE, Storchi R, Martial FP, Bedford RA, Lucas RJ.

Curr Biol. 2017 Jun 5;27(11):1623-1632.e4. doi: 10.1016/j.cub.2017.04.046. Epub 2017 May 18.

33.

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.

34.

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.

35.

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.

36.

Modulation of Fast Narrowband Oscillations in the Mouse Retina and dLGN According to Background Light Intensity.

Storchi R, Bedford RA, Martial FP, Allen AE, Wynne J, Montemurro MA, Petersen RS, Lucas RJ.

Neuron. 2017 Jan 18;93(2):299-307. doi: 10.1016/j.neuron.2016.12.027.

37.

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.

38.

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.

39.

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.

Biotechnol Biofuels. 2016 Nov 25;9:258. eCollection 2016.

40.

Chemogenetic Activation of ipRGCs Drives Changes in Dark-Adapted (Scotopic) Electroretinogram.

Milosavljevic N, Allen AE, Cehajic-Kapetanovic J, Lucas RJ.

Invest Ophthalmol Vis Sci. 2016 Nov 1;57(14):6305-6312. doi: 10.1167/iovs.16-20448.

41.

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.

Nat Rev Microbiol. 2017 Jan;15(1):6-20. doi: 10.1038/nrmicro.2016.160. Epub 2016 Nov 21. Review.

PMID:
27867198
42.

Successful treatment of severe hypokalemia in a dog with acute kidney injury caused by leptospirosis.

Allen AE, Buckley GJ, Schaer M.

J Vet Emerg Crit Care (San Antonio). 2016 Nov;26(6):837-843. doi: 10.1111/vec.12416. Epub 2015 Dec 4.

PMID:
26636549
43.

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.

PLoS One. 2016 Sep 6;11(9):e0160929. doi: 10.1371/journal.pone.0160929. eCollection 2016.

44.

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.

45.

Convergence of visual and whisker responses in the primary somatosensory thalamus (ventral posterior medial region) of the mouse.

Allen AE, Procyk CA, Brown TM, Lucas RJ.

J Physiol. 2017 Feb 1;595(3):865-881. doi: 10.1113/JP272791. Epub 2016 Sep 15.

46.

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.

47.

Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms.

Diner RE, Schwenck SM, McCrow JP, Zheng H, Allen AE.

Front Microbiol. 2016 Jun 9;7:880. doi: 10.3389/fmicb.2016.00880. eCollection 2016.

48.

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.

49.

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.

50.

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.

New Phytol. 2016 May;210(3):890-904. doi: 10.1111/nph.13843. Epub 2016 Feb 4.

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