Publications of the institute

Journal Article (177)

1.
Journal Article
Duan, G. Y.; Walther, D.; Schulze, W. X.: Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. Frontiers in Plant Science 4, 540 (2013)
2.
Journal Article
Benina, M.; Obata, T.; Mehterov, N.; Ivanov, I.; Petrov, V.; Toneva, V.; Fernie, A. R.; Gechev, T. S.: Comparative metabolic profiling of Haberlea rhodopensis, Thellungiella halophyla, and Arabidopsis thaliana exposed to low temperature. Frontiers in Plant Science 4, 499 (2013)
3.
Journal Article
Crumpton-Taylor, M.; Pike, M.; Lu, K. J.; Hylton, C. M.; Feil, R.; Eicke, S.; Lunn, J. E.; Zeeman, S. C.; Smith, A. M.: Starch synthase 4 is essential for coordination of starch granule formation with chloroplast division during Arabidopsis leaf expansion. New Phytologist 200 (4), pp. 1064 - 1075 (2013)
4.
Journal Article
Ischebeck, T.; Werner , S.; Krishnamoorthy, P.; Lerche, J.; Meijón, M.; Stenzel, I.; Löfke, C.; Wiessner, T.; Im , Y. J.; Perera, I. Y. et al.; Iven , T.; Feussner, I.; Busch, W.; Boss, W. F.; Teichmann, T.; Hause, B.; Persson, S.; Heilmann, I.: Phosphatidylinositol 4,5-Bisphosphate Influences PIN Polarization by Controlling Clathrin-Mediated Membrane Trafficking in Arabidopsis. The Plant Cell (2013)
5.
Journal Article
Malinova, I.; Mahlow, S.; Alseekh, S.; Orawetz, T.; Fernie, A. R.; Baumann, O.; Steup, M.; Fettke, J.: Double knock-out mutants of Arabidopsis thaliana grown under normal conditions reveal that the plastidial phosphorylase isozyme (PHS1) participates in transitory starch metabolism. Plant Physiology 164 (2), pp. 907 - 921 (2013)
6.
Journal Article
Mueller-Roeber, B.; Balazadeh, S.: Auxin and Its Role in Plant Senescence. Journal of Plant Growth Regulation 33 (1), pp. 21 - 33 (2013)
7.
Journal Article
Muñoz-Bertomeu , J.; Anoman, A.; Flores-Tornero, M.; Toujani, W.; Rosa-Téllez, S.; Fernie, A. R.; Roje, S.; Segura , J.; Ros, R.: The essential role of the phosphorylated pathway of serine biosynthesis in Arabidopsis. Plant Signaling & Behavior 8 (11), e27104 (2013)
8.
Journal Article
Omidbakhshfard, M. A.; Wink, F. V.; Arvidsson, S.; Riaño-Pachón, D. M.; Mueller-Roeber, B.: A Step-by-Step Protocol for Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) from Arabidopsis thaliana. Journal of Integrative Plant Biology 56 (1) (2013)
9.
Journal Article
Rauf, M.; Arif, M.; Fisahn, J.; Xue, G. P.; Balazadeh, S.; Mueller-Roeber, B.: NAC Transcription Factor SPEEDY HYPONASTIC GROWTH Regulates Flooding-Induced Leaf Movement in Arabidopsis. The Plant Cell 25 (12), pp. 4941 - 4955 (2013)
10.
Journal Article
Sajitz-Hermstein, M.; Nikoloski, Z.: Structural control of metabolic flux. PLoS Computational Biology 9 (12), e1003368 (2013)
11.
Journal Article
Sulpice, R.; Ishihara, H.; Schlereth, A.; Cawthray, G. R.; Encke, B.; Giavalisco, P.; Ivakov, A.; Arrivault, S.; Jost, R.; Krohn, N. et al.; Kuo, J.; Laliberte, E.; Pearse, S. J.; Raven, J. A.; Scheible, W.-R.; Teste, F.; Veneklaas, E. J.; Stitt, M.; Lambers, H.: Low levels of ribosomal RNA partly account for the very high photosynthetic phosphorus-use efficiency of Proteaceae species. Plant, Cell and Environment 36 (6), pp. 1276 - 1298 (2013)
12.
Journal Article
Trost, G.; Vi, S. L.; Czesnick, H.; Lange, P.; Holton, N.; Giavalisco, P.; Zipfel, C.; Kappel, C.; Lenhard, M.: Arabidopsis poly(A) polymerase PAPS1 limits founder-cell recruitment to organ primordia and suppresses the salicylic acid-independent immune response downstream of EDS1/PAD4. The Plant Journal 77 (5), pp. 688 - 699 (2013)
13.
Journal Article
Ivakov, A.; Persson, S.: Plant cell shape: modulators and measurements. Frontiers in Plant Science 4, 439 (2013)
14.
Journal Article
Lee, Y. P.; Giorgi, F. M.; Lohse, M.; Kvederaviciute, K.; Klages, S.; Usadel, B.; Meskiene, I.; Reinhardt, R.; Hincha, D. K.: Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum). BMC Genomics 14, p. 793 - 793 (2013)
15.
Journal Article
Blaby, I. K.; Glaesener, A. G.; Mettler, T.; Fitz-Gibbon, S. T.; Gallaher, S. D.; Liu, B.; Boyle, N. R.; Kropat, J.; Stitt, M.; Johnson, S. et al.; Benning, C.; Pellegrini, M.; Casero, D.; Merchant, S. S.: Systems-Level Analysis of Nitrogen Starvation-Induced Modifications of Carbon Metabolism in a Chlamydomonas reinhardtii Starchless Mutant. The Plant Cell 5 (11), pp. 4305- - 4323 (2013)
16.
Journal Article
Hochberg, U.; Degu, A.; Toubiana, D.; Gendler, T.; Nikoloski, Z.; Rachmilevitch, S.; Fait, A.: Metabolic profiling and network analysis reveal coordinated changes in grapevine water stress response. BMC Plant Biology 13 (184) (2013)
17.
Journal Article
Nardozza, S.; Boldingh, H. L.; Osorio, S.; Höhne, M.; Wohlers, M.; Gleave, A. P.; MacRae, E. A.; Richardson, A. C.; Atkinson, R. G.; Sulpice, R. et al.; Fernie, A. R.; Clearwater, M. J.: Metabolic analysis of kiwifruit (Actinidia deliciosa) berries from extreme genotypes reveals hallmarks for fruit starch metabolism. Journal of Experimental Botany 64 (16), pp. 5049 - 5063 (2013)
18.
Journal Article
Rhee, S. Y.; Mutwil, M.: Towards revealing the functions of all genes in plants. Trends in Plant Science 19 (4), pp. 212 - 221 (2013)
19.
Journal Article
Toujani, W.; Munoz-Bertomeu, J.; Flores-Tornero, M.; Rosa-Tellez, S.; Anoman, A. D.; Alseekh, S.; Fernie, A. R.; Ros, R.: Functional Characterization of the Plastidial 3-Phosphoglycerate Dehydrogenase Family in Arabidopsis. Plant Physiology 163 (3), pp. 1164 - 1178 (2013)
20.
Journal Article
Alseekh, S.; Ofner, I.; Pleban, T.; Tripodi, P.; Di Dato, F.; Cammareri, M.; Mohammad, A.; Grandillo, S.; Fernie, A. R.; Zamir, D.: Resolution by recombination: breaking up Solanum pennellii introgressions. Trends in Plant Science 18 (10), pp. 536 - 538 (2013)
21.
Journal Article
Armbruster, U.; Ruehle, T.; Kreller, R.; Strotbek, C.; Zuehlke, J.; Tadini, L.; Blunder, T.; Hertle, A. P.; Qi, Y.; Rengstl, B. et al.; Nickelsen, J.; Frank, W.; Leister, D.: The PHOTOSYNTHESIS AFFECTED MUTANT68-LIKE Protein Evolved from a PSII Assembly Factor to Mediate Assembly of the Chloroplast NAD(P)H Dehydrogenase Complex in Arabidopsis. The Plant Cell 25 (10), pp. 3926 - 3943 (2013)
22.
Journal Article
Scarpeci, T. E.; Zanor, M. I.; Mueller-Roeber, B.; Valle, E. M.: Overexpression of AtWRKY30 enhances abiotic stress tolerance during early growth stages in Arabidopsis thaliana. Plant Molecular Biology 83 (3), pp. 265 - 277 (2013)
23.
Journal Article
Schmidt, R.; Schippers, J. H. M.; Mieulet, D.; Obata, T.; Fernie, A. R.; Guiderdoni, E.; Mueller-Roeber, B.: MULTIPASS, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways. Plant Journal 76 (2), pp. 258 - 273 (2013)
24.
Journal Article
Shao, N.; Duan, G. Y.; Bock, R.: A Mediator of Singlet Oxygen Responses in Chlamydomonas reinhardtii and Arabidopsis Identified by a Luciferase-Based Genetic Screen in Algal Cells. The Plant Cell 25 (10), pp. 4209 - 4226 (2013)
25.
Journal Article
Sweetlove, L. J.; Obata, T.; Fernie, A. R.: Systems analysis of metabolic phenotypes – what have we learnt? Trends in Plant Science 19 (4), pp. 222 - 230 (2013)
26.
Journal Article
Wydro, M. M.; Sharma, P.; Foster, J. M.; Bych, K.; Meyer, E. H.; Balk, J.: The Evolutionarily Conserved Iron-Sulfur Protein INDH Is Required for Complex I Assembly and Mitochondrial Translation in Arabidopsis. The Plant Cell 25 (10), pp. 4014 - 4027 (2013)
27.
Journal Article
Barlow, P. W.; Fisahn, J.: Swarms, swarming and entanglements of fungal hyphae and of plant roots. Communicative & Integrative Biology 6 (5), e25299 (2013)
28.
Journal Article
Krech, K.; Fu, H.-Y.; Thiele, W.; Ruf, S.; Schöttler, M. A.; Bock, R.: Reverse genetics in complex multigene operons by co-transformation of the plastid genome and its application to the open reading frame previously designated psbN. The Plant Journal 75 (6), pp. 1062 - 1074 (2013)
29.
Journal Article
Lauxmann, M.; Borsani, J.; Osorio, S.; Lombardo, V. A.; Budde, C. O.; Bustamante, C. A.; Monti, L. L.; Andreo, C. S.; Fernie, A. R.; Drincovich, M. F. et al.; Lara, M. V.: Deciphering the metabolic pathways influencing heat and cold responses during post-harvest physiology of peach fruit. Plant, Cell and Environment 37 (3), pp. 601 - 616 (2013)
30.
Journal Article
Li, J.-W.; Bolser, D.; Manske, M.; Giorgi, F.; Vyahhi, N.; Usadel, B.; Clavijo, B. J.; Chan, T.-F.; Wong, N.; Zerbino, D. et al.; Schneider, M. V.: The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. Briefings in Bioinformatics 14 (5), pp. 548 - 555 (2013)
31.
Journal Article
Long, S.; Stitt, M.: Special issue on plant computational biology. Plant, Cell and Environment 36 (9), pp. 1573 - 1574 (2013)
32.
Journal Article
Ragel, P.; Streb, S.; Feil, R.; Sahrawy, M.; Annunziata, M. G.; Lunn, J. E.; Zeeman, S.; Merida, A.: Loss of Starch Granule Initiation Has a Deleterious Effect on the Growth of Arabidopsis Plants Due to an Accumulation of ADP-Glucose. PLANT PHYSIOLOGY 163 (1), pp. 75 - 85 (2013)
33.
Journal Article
Schippers, J. H. M.; Lai, A. G.; Mueller-Roeber, B.; Dijkwel, P. P.: Could ROS signals drive tissue-specific clocks? Landes Bioscience 4 (5), pp. 206 - 208 (2013)
34.
Journal Article
Toepfer, N.; Nikoloski, Z.: Large-scale modeling provides insights into Arabidopsis's acclimation to changing light and temperature conditions. Plant Signaling & Behavior 8 (9), e25480 (2013)
35.
Journal Article
Toepel, J.; Illmer-Kephalides, M.; Jaenicke, S.; Straube, J.; May, P.; Goesmann, A.; Kruse, O.: New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. PLANT BIOTECHNOLOGY JOURNAL 11 (6), pp. 717 - 733 (2013)
36.
Journal Article
Armbruster, U.; Labs, M.; Pribil, M.; Viola, S.; Xu, W.; Scharfenberg, M.; Hertle, A. P.; Rojahn, U.; Jensen, P. E.; Rappaport, F. et al.; Joliot, P.; Doermann, P.; Wanner, G.; Leister, D.: Arabidopsis CURVATURE THYLAKOID1 Proteins Modify Thylakoid Architecture by Inducing Membrane Curvature. The Plant Cell 25 (7), pp. 2661 - 2678 (2013)
37.
Journal Article
Carillo, P.; Feil, R.; Gibon, Y.; Satoh-Nagasawa, N.; Jackson, D.; Bläsing, O. E.; Stitt, M.; Lunn, J. E.: A fluorometric assay for trehalose in the picomole range. Plant Methods 9, p. 21 - 21 (2013)
38.
Journal Article
Osorio, S.; Scossa, F.; Fernie, A. R.: Molecular regulation of fruit ripening. Frontiers in Plant Science 4, 198 (2013)
39.
Journal Article
Cascales-Minana, B.; Munoz-Bertomeu, J.; Flores-Tornero, M.; Anoman, A. D.; Pertusa, J.; Alaiz, M.; Osorio, S.; Fernie, A. R.; Segura, J.; Ros, R.: The Phosphorylated Pathway of Serine Biosynthesis Is Essential Both for Male Gametophyte and Embryo Development and for Root Growth in Arabidopsis. The Plant Cell 25 (6), pp. 2084 - 2101 (2013)
40.
Journal Article
Chen, L.; Lee, J. H.; Weber, H.; Tohge, T.; Witt, S.; Roje, S.; Fernie, A. R.; Hellmann, H.: Arabidopsis BPM Proteins Function as Substrate Adaptors to a CULLIN3-Based E3 Ligase to Affect Fatty Acid Metabolism in Plants. The Plant Cell 25 (6), pp. 2253 - 2264 (2013)
41.
Journal Article
Hill, N.; Leow, A.; Bleidorn, C.; Groth, D.; Tiedemann, R.; Selbig, J.; Hartmann, S.: Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information. THEORY IN BIOSCIENCES 132 (2), pp. 93 - 104 (2013)
42.
Journal Article
Kleessen, S.; Klie, S.; Nikoloski, Z.: Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales. The Plant Cell 25 (6), pp. 1917 - 1927 (2013)
43.
Journal Article
Matsuba, Y.; Nguyen, T. T. H.; Wiegert, K.; Falar, V.; Gonzales-Vigil, E.; Leong, B.; Schaefer, P.; Kudrna, D.; Wing, R. A.; Bolger, A. M. et al.; Usadel, B.; Tissier, A.; Fernie, A. R.; Barry, C. S.; Pichersky, E.: Evolution of a Complex Locus for Terpene Biosynthesis in Solanum. The Plant Cell 25 (6), pp. 2022 - 2036 (2013)
44.
Journal Article
Schmidt, R.; Mieulet, D.; Hubberten, H. M.; Obata, T.; Hoefgen, R.; Fernie, A. R.; Fisahn, J.; Segundo, B. S.; Guiderdoni, E.; Schippers, J. H. M. et al.; Mueller-Roeber, B.: SALT-RESPONSIVE ERF1 Regulates Reactive Oxygen Species-Dependent Signaling during the Initial Response to Salt Stress in Rice. The Plant Cell 25 (6), pp. 2115 - 2131 (2013)
45.
Journal Article
Stitt, M.: Systems-integration of plant metabolism: means, motive and opportunity. CURRENT OPINION IN PLANT BIOLOGY 16 (3), pp. 381 - 388 (2013)
46.
Journal Article
Finkemeier, I.; König, A.-C.; Heard, W.; Nunes-Nesi, A.; Pham, P. A.; Leister, D.; Fernie, A. R.; Sweetlove, L. J.: Transcriptomic Analysis of the Role of Carboxylic Acids in Metabolite Signaling in Arabidopsis Leaves. Plant Physiology 162 (1), pp. 239 - 253 (2013)
47.
Journal Article
Strenkert, D.; Schmollinger, S.; Schroda, M.: Heat shock factor 1 counteracts epigenetic silencing of nuclear transgenes in Chlamydomonas reinhardtii. Nucleic Acids Research 41 (10), pp. 5273 - 5289 (2013)
48.
Journal Article
Zelcbuch, L.; Antonovsky, N.; Bar-Even, A.; Levin-Karp, A.; Barenholz, U.; Dayagi, M.; Liebermeister, W.; Flamholz, A.; Noor, E.; Amram, S. et al.; Brandis, A.; Bareia, T.; Yofe, I.; Jubran, H.; Milo, R.: Spanning high-dimensional expression space using ribosome-binding site combinatorics. Nucleic Acids Research 41 (9), e98 (2013)
49.
Journal Article
Bar-Even, A.; Tawfik, D. S.: Engineering specialized metabolic pathways-is there a room for enzyme improvements? Current Opinion in Biotechnology 24 (2), pp. 310 - 319 (2013)
50.
Journal Article
Toepfer, N.; Caldana, C.; Grimbs, S.; Willmitzer, L.; Fernie, A. R.; Nikoloski, Z.: Integration of Genome-Scale Modeling and Transcript Profiling Reveals Metabolic Pathways Underlying Light and Temperature Acclimation in Arabidopsis. The Plant Cell 25 (4), pp. 1197 - 1211 (2013)
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