Complete publication list

Publications of Alisdair Fernie

Journal Article (49)

  1. 1.
    Braun, H.-P.; Binder, S.; Brennicke, A.; Eubel, H.; Fernie, A. R.; Finkemeier, I.; Klodmann, J.; König, A.-C.; Kühn, K.; Meyer, E. H. et al.; Obata, T.; Schwarzländer, M.; Takenaka, M.; Zehrmann, A.: The life of plant mitochondrial complex I. Mitochondrion 19, Part B (0), pp. 295 - 313 (2014)
  2. 2.
    Bolger, A. M.; Scossa, F.; Lanz, C.; Maumus, F.; Tohge, T.; Quesneville, H.; Alseekh, S.; Sorensen, I.; Lichtenstein, G.; Fich, E. A. et al.; Conte, M.; Keller, H.; Schneeberger, K.; Schwacke, R.; Ofner, I.; Vrebalov, J.; Xu, Y.; Osorio, S.; Aflitos, S. A.; Schijlen, E.; Jimenez-Gomez, J. M.; Ryngajllo, M.; Kimura, S.; Kumar, R.; Koenig, D.; Headland, L. R.; Maloof, J. N.; Sinha, N.; van Ham, R. C. H. J.; Lankhorst, R. K.; Mao, L.; Vogel, A.; Arsova, B.; Panstruga, R.; Fei, Z.; Rose, J. K. C.; Zamir, D.; Carrari, F. F.; Giovannoni, J. J.; Weigel, D.; Usadel, B.; Fernie, A. R.: The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics 46 (9), pp. 1034 - 1038 (2014)
  3. 3.
    Schwahn, K.; de Souza, L. P.; Fernie, A. R.; Tohge, T.: Metabolomics-assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade. (2014)
  4. 4.
    Tohge, T.; Alseekh, S.; Fernie, A. R.: On the regulation and function of secondary metabolism during fruit development and ripening. Journal of Experimental Botany 65 (16), pp. 4599 - 4611 (2014)
  5. 5.
    Balazadeh, S.; Schildhauer, J.; Araujo, W. L.; Munne-Bosch, S.; Fernie, A. R.; Proost, S.; Humbeck, K.; Mueller-Roeber, B.: Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences. Journal of Experimental Botany 65 (14), pp. 3975 - 3992 (2014)
  6. 6.
    Ewald, R.; Hoffmann, C.; Florian, A.; Neuhaus, E.; Fernie, A. R.; Bauwe, H.: Lipoate-Protein Ligase and Octanoyltransferase Are Essential for Protein Lipoylation in Mitochondria of Arabidopsis1[W][OPEN]. Plant Physiology 165 (3), pp. 978 - 990 (2014)
  7. 7.
    Sauvage, C.; Segura, V.; Bauchet, G.; Stevens, R.; Do, P. T.; Nikoloski, Z.; Fernie, A. R.; Causse, M.: Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits. Plant Physiology 165 (3), pp. 1120 - 1132 (2014)
  8. 8.
    Nunes-Nesi, A.; Brito, D. S.; Inostroza-Blancheteau, C.; Fernie, A. R.; Araujo, W. L.: The complex role of mitochondrial metabolism in plant aluminum resistance. Trends in Plant Science 19 (6), pp. 399 - 407 (2014)
  9. 9.
    Bellucci, E.; Bitocchi, E.; Ferrarini, A.; Benazzo, A.; Biagetti, E.; Klie, S.; Minio, A.; Rau, D.; Rodriguez, M.; Panziera, A. et al.; Venturini, L.; Attene, G.; Albertini, E.; Jackson, S. A.; Nanni, L.; Fernie, A. R.; Nikoloski, Z.; Bertorelle, G.; Delledonne, M.; Papa, R.: Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean. The Plant Cell 26 (5), pp. 1901 - 1912 (2014)
  10. 10.
    Wallstrom, S. V.; Florez-Sarasa, I.; Araujo, W. L.; Escobar, M. A.; Geisler, D. A.; Aidemark, M.; Lager, I.; Fernie, A. R.; Ribas-Carbo, M.; Rasmusson, A. G.: Suppression of NDA-Type Alternative Mitochondrial NAD(P)H Dehydrogenases in Arabidopsis thaliana Modifies Growth and Metabolism, but not High Light Stimulation of Mitochondrial Electron Transport. Plant and Cell Physiology 55 (5), pp. 881 - 896 (2014)
  11. 11.
    Martins, S. C. V.; Araújo, W. L.; Tohge, T.; Fernie, A. R.; DaMatta, F. M.: In High-Light-Acclimated Coffee Plants the Metabolic Machinery Is Adjusted to Avoid Oxidative Stress Rather than to Benefit from Extra Light Enhancement in Photosynthetic Yield. PLoS One 9 (4), e94862 (2014)
  12. 12.
    Kleessen, S.; Laitinen, R.; Fusari, C. M.; Antonio, C.; Sulpice, R.; Fernie, A. R.; Stitt, M.; Nikoloski, Z.: Metabolic efficiency underpins performance trade-offs in growth of Arabidopsis thaliana. Nature Communications (2014)
  13. 13.
    Araujo, W. L.; Nunes-Nesi, A.; Fernie, A. R.: On the role of plant mitochondrial metabolism and its impact on photosynthesis in both optimal and sub-optimal growth conditions. Photosynthesis research 119 (1-2), pp. 141 - 156 (2014)
  14. 14.
    Malinova, I.; Mahlow, S.; Alseekh, S.; Orawetz, T.; Fernie, A. R.; Baumann, O.; Steup, M.; Fettke, J.: Double Knockout Mutants of Arabidopsis Grown under Normal Conditions Reveal that the Plastidial Phosphorylase Isozyme Participates in Transitory Starch Metabolism. Plant Physiology 164 (2), pp. 907 - 921 (2014)
  15. 15.
    Araujo, W. L.; Tohge, T.; Nunes-Nesi, A.; Obata, T.; Fernie, A. R.: Analysis of Kinetic Labeling of Amino Acids and Organic Acids by GC-MS. Methods in molecular biology 1090, pp. 107 - 119 (2014)
  16. 16.
    Araujo, W. L.; Martins, A. O.; Fernie, A. R.; Tohge, T.: 2-Oxoglutarate: linking TCA cycle function with amino acid, glucosinolate, flavonoid, alkaloid, and gibberellin biosynthesis. Frontiers in Plant Science 5, p. 552 - 552 (2014)
  17. 17.
    Arrivault, S.; Guenther, M.; Florian, A.; Encke, B.; Feil, R.; Vosloh, D.; Lunn, J. E.; Sulpice, R.; Fernie, A. R.; Stitt, M. et al.; Schulze, W. X.: Dissecting the Subcellular Compartmentation of Proteins and Metabolites in Arabidopsis Leaves Using Non-aqueous Fractionation. Molecular and Cellular Proteomics 13 (9), pp. 2246 - 2259 (2014)
  18. 18.
    Avin-Wittenberg, T.; Fernie, A. R.: At Long Last: Evidence for Pexophagy in Plants. Molecular Plant 7 (8), pp. 1257 - 1260 (2014)
  19. 19.
    Bastias, A.; Yanez, M.; Osorio, S.; Arbona, V.; Gomez-Cadenas, A.; Fernie, A. R.; Casaretto, J. A.: The transcription factor AREB1 regulates primary metabolic pathways in tomato fruits. Journal of Experimental Botany 65 (9), pp. 2351 - 63 (2014)
  20. 20.
    Bermúdez, L.; de Godoy, F.; Balder, P.; Demarco, D.; Osorio, S.; Quadrana, L.; Almeida, J.; Asis, R.; Gibon, Y.; Fernie, A. R. et al.; Rossi, M.; Carrari, F.: Silencing of the tomato Sugar Partitioning Affecting protein (SPA), modifies sink strength through a shift in leaf sugar metabolism. The Plant Journal 77 (5), pp. 676 - 687 (2014)
  21. 21.
    Bolger, A.; Scossa, F.; Bolger, M. E.; Lanz, C.; Maumus, F.; Tohge, T.; Quesneville, H.; Alseekh, S.; Sorensen, I.; Lichtenstein, G. et al.; Fich, E. A.; Conte, M.; Keller, H.; Schneeberger, K.; Schwacke, R.; Ofner, I.; Vrebalov, J.; Xu, Y.; Osorio, S.; Aflitos, S. A.; Schijlen, E.; Jimenez-Gomez, J. M.; Ryngajllo, M.; Kimura, S.; Kumar, R.; Koenig, D.; Headland, L. R.; Maloof, J. N.; Sinha, N.; van Ham, R. C. H. J.; Lankhorst, R. K.; Mao, L.; Vogel, A.; Arsova, B.; Panstruga, R.; Fei, Z.; Rose, J. K. C.; Zamir, D.; Carrari, F. F.; Giovannoni, J. J.; Weigel, D.; Usadel, B.; Fernie, A. R.: The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Reviews Genetics 46 (9), pp. 1034 - 1038 (2014)
  22. 22.
    Cavalcanti, J. H. F.; Esteves-Ferreira, A. A.; Quinhones, C. G. S.; Pereira-Lima, I. A.; Nunes-Nesi, A.; Fernie, A. R.; Araujo, W. L.: Evolution and functional implications of the tricarboxylic acid cycle as revealed by phylogenetic analysis. Genome biology and evolution 6 (10), pp. 2830 - 48 (2014)
  23. 23.
    Fernandez-Calvino, L.; Osorio, S.; Hernandez, M. L.; Hamada, I. B.; Del Toro, F. J.; Donaire, L.; Yu, A.; Bustos, R.; Fernie, A. R.; Martinez-Rivas, J. M. et al.; Llave, C.: Virus-Induced Alterations in Primary Metabolism Modulate Susceptibility to Tobacco rattle virus in Arabidopsis. Plant Physiology 166 (4), pp. 1821 - 38 (2014)
  24. 24.
    Florian, A.; Nikoloski, Z.; Sulpice, R.; Timm, S.; Araujo, W. L.; Tohge, T.; Bauwe, H.; Fernie, A. R.: Analysis of Short-Term Metabolic Alterations in Arabidopsis Following Changes in the Prevailing Environmental Conditions. Molecular Plant 7 (5 Special Issue), pp. 893 - 911 (2014)
  25. 25.
    Florian, A.; Timm, S.; Nikoloski, Z.; Tohge, T.; Bauwe, H.; Araujo, W. L.; Fernie, A. R.: Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures. Journal of Integrative Plant Biology 56 (9 - SI), pp. 941 - 959 (2014)
  26. 26.
    Gago, J.; Douthe, C.; Florez-Sarasa, I. D.; Escalona, J. M.; Galmes, J.; Fernie, A. R.; Flexas, J.; Medrano, H.: Opportunities for improving leaf water use efficiency under climate change conditions. Plant Science 226, pp. 108 - 119 (2014)
  27. 27.
    Galili, G.; Avin-Wittenberg, T.; Angelovici, R.; Fernie, A. R.: The role of photosynthesis and amino acid metabolism in the energy status during seed development. Frontiers in Plant Science (2014)
  28. 28.
    Gechev, T. G.; Hille, J.; Woerdenbag, H. J.; Benina, M.; Mehterov, N.; Toneva, V.; Fernie, A. R.; Mueller-Roeber, B.: Natural products from resurrection plants: Potential for medical applications. Biotechnology Advances 32 (6), pp. 1091 - 1101 (2014)
  29. 29.
    Geigenberger, P.; Fernie, A. R.: Metabolic Control of Redox and Redox Control of Metabolism in Plants. ANTIOXIDANTS & REDOX SIGNALING 21 (9), pp. 1389 - 1421 (2014)
  30. 30.
    Heise, R.; Arrivault, S.; Szecowka, M.; Tohge, T.; Nunes-Nesi, A.; Stitt, M.; Nikoloski, Z.; Fernie, A. R.: Flux profiling of photosynthetic carbon metabolism in intact plants. Nature Protocols 9 (8), pp. 1803 - 1824 (2014)
  31. 31.
    Hu, C.; Shi, J.; Quan, S.; Cui, B.; Kleessen, S.; Nikoloski, Z.; Tohge, T.; Alexander, D.; Guo, L.; Lin, H. et al.; Wang, J.; Cui, X.; Rao, J.; Luo, Q.; Zhao, X.; Fernie, A. R.; Zhang, D.: Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomicsd. Scientific Reports (2014)
  32. 32.
    Klie, S.; Osorio, S.; Tohge, T.; Drincovich, M. F.; Fait, A.; Giovannoni, J. J.; Fernie, A. R.; Nikoloski, Z.: Conserved Changes in the Dynamics of Metabolic Processes during Fruit Development and Ripening across Species. Plant Physiology 164 (1), pp. 55 - 68 (2014)
  33. 33.
    Koenig, A. G.; Hartl, M.; Pham, P. A.; Laxa, M.; Boersema, P.; Orwat, A.; Kalitventseva, I.; Ploechinger, M.; Braun, H. P.; Leister, D. et al.; Mann , M.; Wachter, A.; Fernie, A. R.; Finkemeier, I.: The Arabidopsis class II sirtuin is a lysine deacetylase and interacts with mitochondrial energy metabolism. Plant Physiology (2014)
  34. 34.
    Lohse, M.; Nagel, A.; Herter, T.; May, P.; Schroda, M.; Zrenner, R.; Tohge, T.; Fernie, A. R.; Stitt, M.; Usadel, B.: Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environment 37 (5), pp. 1250 - 1258 (2014)
  35. 35.
    Malinova, I.; Kunz, H.-H.; Alseekh, S.; Herbst, K.; Fernie, A. R.; Gierth, M.; Fettke, J.: Reduction of the Cytosolic Phosphoglucomutase in Arabidopsis Reveals Impact on Plant Growth, Seed and Root Development, and Carbohydrate Partitioning. PLoS One 9 (11), e112468 (2014)
  36. 36.
    Nunes-Nesi, A.; Florian, A.; Howden, A.; Jahnke, K.; Timm, S.; Bauwe, H.; Sweetlove, L.; Fernie, A. R.: Is There a Metabolic Requirement for Photorespiratory Enzyme Activities in Heterotrophic Tissues? Molecular Plant 7 (1), pp. 248 - 251 (2014)
  37. 37.
    Osorio, S.; Ruan, Y.-L.; Fernie, A. R.: An update on source-to-sink carbon partitioning in tomato. FRONTIERS IN PLANT SCIENCE 5, p. 516 - 516 (2014)
  38. 38.
    Quadrana, L.; Almeida, J.; Asis, R.; Duffy, T.; Dominguez, P. G.; Bermudez, L.; Conti, G.; da Silva, J. V. C.; Peralta, I. E.; Colot, V. et al.; Asurmendi, S.; Fernie, A. R.; Rossi, M.; Carrari, F.: Natural occurring epialleles determine vitamin E accumulation in tomato fruits. Nature Communications (2014)
  39. 39.
    Ruprecht, C.; Tohge, T.; Fernie, A. R.; Mortimer, C. L.; Kozlo, A.; Fraser, P. D.; Funke, N.; Cesarino, I.; Vanholme, R.; Boerjan, W. et al.; Morreel, K.; Burgert, I.; Gierlinger, N.; Bulone, V.; Schneider, V.; Stockero, A.; Navarro, J. P.; Pudel, F.; Tambuyser, B.; Hygate, J.; Bumstead, J.; Notley, L.; Persson, S.: Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry. Journal of visualized experiments: JoVE (87), e51393 (2014)
  40. 40.
    Sade, D.; Sade, N.; Shriki, O.; Lerner, S.; Gebremedhin, A.; Karavani, A.; Brotman, Y.; Osorio, S.; Fernie, A. R.; Willmitzer, L. et al.; Czosnek, H.; Moshelion, M.: Water Balance, Hormone Homeostasis, and Sugar Signaling Are All Involved in Tomato Resistance to Tomato Yellow Leaf Curl Virus. Plant Physiology 165 (4), pp. 1684 - 1697 (2014)
  41. 41.
    Schmitz, J.; Heinrichs, L.; Scossa, F.; Fernie, A. R.; Oelze, M.-L.; Dietz, K.-J.; Rothbart, M.; Grimm, B.; Fluegge, U.-I.; Haeusler, R. E.: The essential role of sugar metabolism in the acclimation response of Arabidopsis thaliana to high light intensities. Journal of Experimental Botany 65 (6), pp. 1619 - 1636 (2014)
  42. 42.
    Schroeder, F.; Lisso, J.; Obata, T.; Erban, A.; Maximova, E.; Giavalisco, P.; Kopka, J.; Fernie, A. R.; Willmitzer, L.; Muessig, C.: Consequences of induced brassinosteroid deficiency in Arabidopsis leaves. BMC Plant Biology 14, 309 (2014)
  43. 43.
    Toepfer, N.; Scossa, F.; Fernie, A. R.; Nikoloski, Z.: Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses. PLoS Computational Biology 10 (6), e1003656 (2014)
  44. 44.
    Tohge, T.; de Souza, L. P.; Fernie, A. R.: Genome‐enabled plant metabolomics. Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences 966 (0), pp. 7 - 20 (2014)
  45. 45.
    Tohge, T.; Fernie, A. R.: Lignin, mitochondrial family, and photorespiratory transporter classification as case studies in using co-expression, co-response, and protein locations to aid in identifying transport functions. Frontiers in Plant Science (2014)
  46. 46.
    Tohge, T.; Obata, T.; Fernie, A. R.: Biosynthesis of the Essential Respiratory Cofactor Ubiquinone from Phenylalanine in Plants. Molecular Plant 7 (9), pp. 1403 - 1405 (2014)
  47. 47.
    Wallström, S. V.; Florez-Sarasa, I.; Araujo, W. L.; Aidemark, M.; Fernández-Fernández, M.; Fernie, A. R.; Ribas-Carbó, M.; Rasmusson, A. G.: Suppression of the External Mitochondrial NADPH Dehydrogenase, NDB1, in Arabidopsis thaliana Affects Central Metabolism and Vegetative Growth. Molecular Plant 7 (2), pp. 356 - 368 (2014)
  48. 48.
    Wang, L.; Czedik-Eysenberg, A.; Mertz, R. A.; Si, Y.; Tohge, T.; Nunes-Nesi, A.; Arrivault, S.; Dedow, L. K.; Bryant, D. W.; Zhou, W. et al.; Xu, J.; Weissmann, S.; Studer, A.; Li, P.; Zhang, C.; LaRue, T.; Shao, Y.; Ding, Z.; Sun, Q.; Patel, R. V.; Turgeon, R.; Zhu, X.; Provart, N. J.; Mockler, T. C.; Fernie, A. R.; Stitt, M.; Liu, P.; Brutnell, T. P.: Comparative analyses of C-4 and C-3 photosynthesis in developing leaves of maize and rice. Nature biotechnology 32 (11), pp. 1158 - 1165 (2014)
  49. 49.
    Zhang, Y.; Sun, F.; Fettke, J.; Schöttler, M. A.; Ramsden, L.; Fernie, A. R.; Lim, B. L.: Heterologous expression of AtPAP2 in transgenic potato influences carbon metabolism and tuber development. FEBS Letters 588 (20), pp. 3726 - 3731 (2014)

Meeting Abstract (1)

  1. 50.
    Hincha, D. K.; Schulz, E.; Thalhammer, A.; Tohge, T.; Sulpice, R.; Fernie, A. R.; Zuther, E.: The Role of Secondary Metabolites and COR Proteins in Plant Freezing Tolerance. In: In Vitro Cellular & Developmental Biology-Animal, Vol. 50, p. S13 - S13. Tissue Culture Association, Columbia, MD (2014)
 
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